diff --git a/Makefile b/Makefile index d1701459e0..08ee2c0647 100644 --- a/Makefile +++ b/Makefile @@ -1,7 +1,7 @@ SHELL := /bin/bash MONOREPO_URI := https://github.com/Opentrons/opentrons.git -OT2_VERSION_TAG := v4.3.0 +OT2_VERSION_TAG := v6.1.0 OT2_MONOREPO_DIR := ot2monorepoClone # Parsers output to here diff --git a/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json b/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json index d6f858e137..9fd86cd7c5 100644 --- a/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json +++ b/protoBuilds/007992/rna_isolation.ot2.apiv2.py.json @@ -4449,5 +4449,18 @@ "protocolName": "Viral RNA Isolation (Magnetic Beads)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw isolation plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw elution plate on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json b/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json index cdc3f84f73..34cb2a72ca 100644 --- a/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json +++ b/protoBuilds/00f7b1_part2/00f7b1_part2.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "# flake8: noqa\n\n\"\"\"OPENTRONS.\"\"\"\nfrom opentrons import protocol_api\nimport math\nimport threading\nfrom time import sleep\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Part 2: RNA Isolation',\n 'author': 'John C. Lynch ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n# Definitions for deck light flashing\n\n\nclass CancellationToken:\n \"\"\"FLASH SETUP.\"\"\"\n\n def __init__(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n def set_true(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = True\n\n def set_false(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n\ndef turn_on_blinking_notification(hardware, pause):\n \"\"\"FLASH SETUP.\"\"\"\n while pause.is_continued:\n hardware.set_lights(rails=True)\n sleep(1)\n hardware.set_lights(rails=False)\n sleep(1)\n\n\ndef create_thread(ctx, cancel_token):\n \"\"\"FLASH SETUP.\"\"\"\n t1 = threading.Thread(target=turn_on_blinking_notification,\n args=(ctx._hw_manager.hardware, cancel_token))\n t1.start()\n return t1\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n \"\"\"PROTOCOLS.\"\"\"\n [\n num_samples,\n m300_mount, flash\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m300_mount\", \"flash\")\n\n 'Global variables'\n TEST_MODE = True\n bead_delay_time = 7\n wash_delay_time = 7\n supernatant_headspeed_modulator = 10\n mag_height = 8\n ctx.max_speeds['Z'] = 125\n ctx.max_speeds['A'] = 125\n # Setup for flashing lights notification to empty trash\n cancellationToken = CancellationToken()\n\n # define all custom variables above here with descriptions:\n num_columns = math.ceil(num_samples/8)\n if m300_mount == 'right':\n m20_mount = 'left'\n else:\n m20_mount = 'right'\n # load modules\n mag_deck = ctx.load_module('magnetic module gen2', '1')\n mag_deck.disengage()\n temp_deck = ctx.load_module('temperature module gen2', '3')\n print(num_columns)\n\n # load labware\n mag_plate = mag_deck.load_labware('thermofisher_96_wellplate_200ul') # changed from thermofisher_96_wellplate_200ul\n temp_plate = temp_deck.load_labware('opentrons_96_aluminumblock_generic_'\n 'pcr_strip_200ul')\n dwp = ctx.load_labware('nest_96_wellplate_2ml_deep', '4')\n final_plate = ctx.load_labware('thermofisher_96_wellplate_200ul', '2') # changed from thermofisher_96_wellplate_200ul\n trash = ctx.load_labware('nest_1_reservoir_195ml', '9').wells()[0].top()\n # load tipracks\n\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['7', '10']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['11']]\n # load instrument\n\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE REPLACE TIPRACKS~~~~~~~~~~~~~~~\\n') # noqa: E501\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n pip.reset_tipracks()\n pick_up(pip)\n\n tips_dropped = 0\n\n def drop_tip(pip, home=True):\n nonlocal tips_dropped\n pip.drop_tip(home_after=home)\n if pip == m300:\n tips_dropped += 8\n else:\n tips_dropped += 1\n if tips_dropped == 288:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE EMPTY TRASH~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n tips_dropped = 0\n\n def bead_mixing(well, pip, mvol, side_disp=0, mix_reps=10):\n \"\"\"bead_mixing.\"\"\"\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the middle of the well & dispensing from the bottom to\n mix the beads with the other liquids as much as possible. Aspiration &\n dispensing will also be reversed to ensure proper mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n\n ctx.comment('MIXING\\n')\n vol = mvol * .8\n\n pip.move_to(well.center())\n for _ in range(mix_reps):\n pip.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=3)), rate=2)\n pip.dispense(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=5)), rate=2)\n\n def remove_supernatant(vol):\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol-20, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m300.move_to(dest.top())\n m300.aspirate(10, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, trash)\n m300.blow_out()\n m300.air_gap(50)\n drop_tip(m300)\n\n pick_up(m20)\n m20.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m20.aspirate(19, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m20.move_to(dest.top())\n m20.aspirate(1, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m20.dispense(m20.current_volume, trash)\n m20.blow_out()\n m20.aspirate(10, trash)\n drop_tip(m20)\n ctx.comment('\\n')\n\n def wash_beads(vol, source, dest, side_disp, mix_reps=15):\n pick_up(m300)\n m300.aspirate(vol, source)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n # bead_mixing(dest, m300, vol, reps=6)\n for _ in range(mix_reps):\n m300.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=3)), rate=2)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n drop_tip(m300)\n\n # reagents\n\n samples = mag_plate.rows()[0][:num_columns]\n beads = temp_plate.rows()[0][:math.ceil(num_columns/2)]*12\n wash_1 = dwp.rows()[0][0]\n wash_2 = dwp.rows()[0][2]\n tris = dwp.rows()[0][6]\n wash_3 = dwp.rows()[0][4]\n strand_primer_mix = temp_plate.rows()[0][-1]\n rna_wash = temp_plate.rows()[0][6:6+math.ceil(num_columns/3)]*12\n final_dest = final_plate.rows()[0][:num_columns]\n\n # protocol\n ctx.comment('\\n~~~~~~~~~~~~~~ADDING BEADS~~~~~~~~~~~~~~\\n')\n for i, (dest, bead_col) in enumerate(zip(samples, beads)):\n pick_up(m300)\n if i < math.ceil(num_columns/2):\n m300.mix(5, 65, bead_col)\n m300.aspirate(50, bead_col, rate=0.5)\n ctx.delay(seconds=1.5)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.move_to(bead_col.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, dest, rate=0.5)\n m300.mix(5, 80, dest)\n # bead_mixing(dest, m300, 100, reps=5)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\n MOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.12 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\n \"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~~MIXING~~~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.mix(6, 80, dest)\n # bead_mixing(dest, m300, 100, reps=6)\n drop_tip(m300)\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~~ENGAGING MAGNET~~~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(95)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS TWICE WITH BUFFER~~~~~~~~~~~~\\n')\n for wash in [wash_1, wash_2]:\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING TRIS BUFFER~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.aspirate(50, tris)\n m300.dispense(50, dest)\n m300.mix(6, 40, dest)\n # bead_mixing(dest, m300, 50, reps=6)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.24 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING BINDING BUFFER~~~~~~~~~~~~\\n')\n for i, (source, dest) in enumerate(zip(rna_wash, samples)):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(50, source)\n m300.dispense(50, dest)\n # m300.mix(6, 80, dest)\n bead_mixing(dest, m300, 100, side, mix_reps=15)\n drop_tip(m300)\n\n ctx.comment('\\n~~~~~~~~~~~~~INCUBATING 5 MINUTES~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~ENGAGING MAGNETIC MODULE~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(150)\n mag_deck.disengage()\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS WITH BUFFER~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash_3, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING MASTER MIX ELUTION~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m20)\n m20.aspirate(11.5, strand_primer_mix)\n m20.dispense(11.5, dest.bottom().move(types.Point(x=-side, y=0, z=3)))\n bead_mixing(dest, m20, 11, side)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.37 FOR SPECIFIC HEATING/COOLING CYCLE\n SPIN PLATE DOWN BEFORE RETURNING TO DECK\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~SEPARATING RNA SOLUTION~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~MOVING RNA TO NEW PLATE~~~~~~~~~~~~\\n')\n for s, d in zip(samples, final_dest):\n pick_up(m20)\n m20.aspirate(10, s)\n m20.dispense(10, d)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PROTOCOL COMPLETE~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n for c in ctx.commands():\n print(c)\n", + "content": "# flake8: noqa\n\n\"\"\"OPENTRONS.\"\"\"\nfrom opentrons import protocol_api\nimport math\nimport threading\nfrom time import sleep\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Part 2: RNA Isolation',\n 'author': 'John C. Lynch ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n# Definitions for deck light flashing\n\n\nclass CancellationToken:\n \"\"\"FLASH SETUP.\"\"\"\n\n def __init__(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n def set_true(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = True\n\n def set_false(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n\ndef turn_on_blinking_notification(hardware, pause):\n \"\"\"FLASH SETUP.\"\"\"\n while pause.is_continued:\n hardware.set_lights(rails=True)\n sleep(1)\n hardware.set_lights(rails=False)\n sleep(1)\n\n\ndef create_thread(ctx, cancel_token):\n \"\"\"FLASH SETUP.\"\"\"\n t1 = threading.Thread(target=turn_on_blinking_notification,\n args=(ctx._hw_manager.hardware, cancel_token))\n t1.start()\n return t1\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n \"\"\"PROTOCOLS.\"\"\"\n [\n num_samples,\n m300_mount, flash\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m300_mount\", \"flash\")\n\n 'Global variables'\n TEST_MODE = False\n bead_delay_time = 7\n wash_delay_time = 7\n supernatant_headspeed_modulator = 10\n mag_height = 8\n ctx.max_speeds['Z'] = 125\n ctx.max_speeds['A'] = 125\n # Setup for flashing lights notification to empty trash\n cancellationToken = CancellationToken()\n\n # define all custom variables above here with descriptions:\n num_columns = math.ceil(num_samples/8)\n if m300_mount == 'right':\n m20_mount = 'left'\n else:\n m20_mount = 'right'\n # load modules\n mag_deck = ctx.load_module('magnetic module gen2', '1')\n mag_deck.disengage()\n temp_deck = ctx.load_module('temperature module gen2', '3')\n print(num_columns)\n\n # load labware\n mag_plate = mag_deck.load_labware('thermofisher_96_wellplate_200ul') # changed from thermofisher_96_wellplate_200ul\n temp_plate = temp_deck.load_labware('opentrons_96_aluminumblock_generic_'\n 'pcr_strip_200ul')\n dwp = ctx.load_labware('nest_96_wellplate_2ml_deep', '4')\n final_plate = ctx.load_labware('thermofisher_96_wellplate_200ul', '2') # changed from thermofisher_96_wellplate_200ul\n trash = ctx.load_labware('nest_1_reservoir_195ml', '9').wells()[0].top()\n # load tipracks\n\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['7', '10']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['11']]\n # load instrument\n\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE REPLACE TIPRACKS~~~~~~~~~~~~~~~\\n') # noqa: E501\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n pip.reset_tipracks()\n pick_up(pip)\n\n tips_dropped = 0\n\n def drop_tip(pip, home=True):\n nonlocal tips_dropped\n pip.drop_tip(home_after=home)\n if pip == m300:\n tips_dropped += 8\n else:\n tips_dropped += 1\n if tips_dropped == 288:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE EMPTY TRASH~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n tips_dropped = 0\n\n def bead_mixing(well, pip, mvol, side_disp=0, mix_reps=10):\n \"\"\"bead_mixing.\"\"\"\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the middle of the well & dispensing from the bottom to\n mix the beads with the other liquids as much as possible. Aspiration &\n dispensing will also be reversed to ensure proper mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n\n ctx.comment('MIXING\\n')\n vol = mvol * .8\n\n pip.move_to(well.center())\n for _ in range(mix_reps):\n pip.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=3)), rate=2)\n pip.dispense(vol, dest.bottom().move(types.Point(x=-side_disp,\n y=0, z=5)), rate=2)\n\n def remove_supernatant(vol):\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol-20, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m300.move_to(dest.top())\n m300.aspirate(10, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, trash)\n m300.blow_out()\n m300.air_gap(50)\n drop_tip(m300)\n\n pick_up(m20)\n m20.move_to(dest.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m20.aspirate(19, dest.bottom().move(types.Point(x=side, y=0, z=1)),\n rate=0.1)\n ctx.delay(seconds=1)\n m20.move_to(dest.top())\n m20.aspirate(1, dest.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m20.dispense(m20.current_volume, trash)\n m20.blow_out()\n m20.aspirate(10, trash)\n drop_tip(m20)\n ctx.comment('\\n')\n\n def wash_beads(vol, source, dest, side_disp, mix_reps=15):\n pick_up(m300)\n m300.aspirate(vol, source)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n # bead_mixing(dest, m300, vol, reps=6)\n for _ in range(mix_reps):\n m300.aspirate(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=3)), rate=2)\n m300.dispense(vol, dest.bottom().move(types.Point(x=-side_disp, y=0, z=5)), rate=2)\n drop_tip(m300)\n\n # reagents\n\n samples = mag_plate.rows()[0][:num_columns]\n beads = temp_plate.rows()[0][:math.ceil(num_columns/2)]*12\n wash_1 = dwp.rows()[0][0]\n wash_2 = dwp.rows()[0][2]\n tris = dwp.rows()[0][6]\n wash_3 = dwp.rows()[0][4]\n strand_primer_mix = temp_plate.rows()[0][-1]\n rna_wash = temp_plate.rows()[0][6:6+math.ceil(num_columns/3)]*12\n final_dest = final_plate.rows()[0][:num_columns]\n\n # protocol\n ctx.comment('\\n~~~~~~~~~~~~~~ADDING BEADS~~~~~~~~~~~~~~\\n')\n for i, (dest, bead_col) in enumerate(zip(samples, beads)):\n pick_up(m300)\n if i < math.ceil(num_columns/2):\n m300.mix(5, 65, bead_col)\n m300.aspirate(50, bead_col, rate=0.5)\n ctx.delay(seconds=1.5)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.move_to(bead_col.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, dest, rate=0.5)\n m300.mix(5, 80, dest)\n # bead_mixing(dest, m300, 100, reps=5)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\n MOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.12 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\n \"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~~MIXING~~~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.mix(6, 80, dest)\n # bead_mixing(dest, m300, 100, reps=6)\n drop_tip(m300)\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~~ENGAGING MAGNET~~~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(95)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS TWICE WITH BUFFER~~~~~~~~~~~~\\n')\n for wash in [wash_1, wash_2]:\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING TRIS BUFFER~~~~~~~~~~~~\\n')\n for dest in samples:\n pick_up(m300)\n m300.aspirate(50, tris)\n m300.dispense(50, dest)\n m300.mix(6, 40, dest)\n # bead_mixing(dest, m300, 50, reps=6)\n drop_tip(m300)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.24 FOR SPECIFIC HEATING/COOLING CYCLE\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING BINDING BUFFER~~~~~~~~~~~~\\n')\n for i, (source, dest) in enumerate(zip(rna_wash, samples)):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(50, source)\n m300.dispense(50, dest)\n # m300.mix(6, 80, dest)\n bead_mixing(dest, m300, 100, side, mix_reps=15)\n drop_tip(m300)\n\n ctx.comment('\\n~~~~~~~~~~~~~INCUBATING 5 MINUTES~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=5)\n else:\n ctx.delay(minutes=5)\n\n ctx.comment('\\n~~~~~~~~~~~~~ENGAGING MAGNETIC MODULE~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(150)\n mag_deck.disengage()\n ctx.comment('\\n~~~~~~~~~~~~~WASHING BEADS WITH BUFFER~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n wash_beads(180, wash_3, dest, side)\n\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=wash_delay_time)\n else:\n ctx.delay(minutes=wash_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~\\n')\n remove_supernatant(190)\n mag_deck.disengage()\n\n ctx.comment('\\n~~~~~~~~~~~~~ADDING MASTER MIX ELUTION~~~~~~~~~~~~\\n')\n for i, dest in enumerate(samples):\n side = -1 if i % 2 == 0 else 1\n pick_up(m20)\n m20.aspirate(11.5, strand_primer_mix)\n m20.dispense(11.5, dest.bottom().move(types.Point(x=-side, y=0, z=3)))\n bead_mixing(dest, m20, 11, side)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause(\"\"\"\\n\\nMOVE PLATE IN SLOT 1 TO OFF-DECK THERMOCYCLER\n REFER TO 1.2.37 FOR SPECIFIC HEATING/COOLING CYCLE\n SPIN PLATE DOWN BEFORE RETURNING TO DECK\n RETURN PLATE TO SLOT 1 WHEN FINISHED. ENSURE SAMPLE PLATE IS\n FLAT AND SECURE WHEN RETURNING TO MAGNETIC MODULE!\"\"\")\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n ctx.comment('\\n~~~~~~~~~~~~~SEPARATING RNA SOLUTION~~~~~~~~~~~~\\n')\n mag_deck.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(minutes=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n ctx.comment('\\n~~~~~~~~~~~~~MOVING RNA TO NEW PLATE~~~~~~~~~~~~\\n')\n for s, d in zip(samples, final_dest):\n pick_up(m20)\n m20.aspirate(10, s)\n m20.dispense(10, d)\n drop_tip(m20)\n\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n m300.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PROTOCOL COMPLETE~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n\n for c in ctx.commands():\n print(c)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/010526/010526.ot2.apiv2.py.json b/protoBuilds/010526/010526.ot2.apiv2.py.json index b1544c4c53..9552b92dba 100644 --- a/protoBuilds/010526/010526.ot2.apiv2.py.json +++ b/protoBuilds/010526/010526.ot2.apiv2.py.json @@ -859,5 +859,18 @@ "description": "Custom Protocol Request", "protocolName": "Restriction Digests" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 24 Well Aluminum Block with Variant Tubes on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json index 2cd45e381b..887f95e5c3 100644 --- a/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-2/04eeb1-part-2.ot2.apiv2.py.json @@ -105,5 +105,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Synthesize First Strand cDNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json index 756fea7fdb..584f617a00 100644 --- a/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-3/04eeb1-part-3.ot2.apiv2.py.json @@ -190,5 +190,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Amplify cDNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json index f1e47d16e6..365fb74ec6 100644 --- a/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-4/04eeb1-part-4.ot2.apiv2.py.json @@ -135,5 +135,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Tagment PCR Amplicons" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json index 42b70c96b4..7c892ab668 100644 --- a/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-5/04eeb1-part-5.ot2.apiv2.py.json @@ -123,5 +123,18 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Post Tagmentation Clean Up" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json index da598773d7..9354612ea5 100644 --- a/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-6/04eeb1-part-6.ot2.apiv2.py.json @@ -123,5 +123,18 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Amplify Tagmented Amplicons" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json b/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json index 5b4b72c9d9..c9c4626d59 100644 --- a/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1-part-7/04eeb1-part-7.ot2.apiv2.py.json @@ -87,5 +87,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Pool and Clean Up Libraries" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json b/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json index 0ccaacd37f..3681ac236c 100644 --- a/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json +++ b/protoBuilds/04eeb1/04eeb1.ot2.apiv2.py.json @@ -99,5 +99,12 @@ "description": "Custom Protocol Request", "protocolName": "Illumina COVIDSeq Test: Anneal RNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Master Mix Reservoir on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json b/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json index 4e0fb060d6..7bbbc054da 100644 --- a/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json +++ b/protoBuilds/0556be-covid-mm-qc-v3/0556be-covid-mm-qc-v3.ot2.apiv2.py.json @@ -74,5 +74,12 @@ "description": "Custom Protocol Request", "protocolName": "COVID MM-QC-v3 Protocol" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json b/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json index de15d3b853..8991828e8e 100644 --- a/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json +++ b/protoBuilds/0556be-covid-mm-qc/0556be-covid-mm-qc.ot2.apiv2.py.json @@ -147,5 +147,12 @@ "description": "Custom Protocol Request", "protocolName": "COVID MM-QC Protocol" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json b/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json index eee21ce4df..5e8c6a91bd 100644 --- a/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json +++ b/protoBuilds/060c4f/060c4f.ot2.apiv2.py.json @@ -4773,5 +4773,12 @@ "protocolName": "96-well to 384-well transfer", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/08878b/08878b.ot2.apiv2.py.json b/protoBuilds/08878b/08878b.ot2.apiv2.py.json index be76922075..18cd77c9cb 100644 --- a/protoBuilds/08878b/08878b.ot2.apiv2.py.json +++ b/protoBuilds/08878b/08878b.ot2.apiv2.py.json @@ -51,7 +51,7 @@ ], "labware": [ { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module GEN1 on 4", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -99,5 +99,12 @@ "protocolName": "Transfer with Temperature Module", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json b/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json index 5dfd7e4cae..3694a329ad 100644 --- a/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/0944e4/ngs_cleanup.ot2.apiv2.py.json @@ -1297,5 +1297,12 @@ "protocolName": "NGS Library Cleanup with Ampure XP Beads", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw magnetic plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json b/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json index 846574120f..0b66fbb77c 100644 --- a/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json +++ b/protoBuilds/0a23c6/0a23c6.ot2.apiv2.py.json @@ -81,5 +81,12 @@ "protocolName": "", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 9 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json b/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json index 21d79a3e20..d9f76e474d 100644 --- a/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json +++ b/protoBuilds/0bf4f4-pt2/0bf4f4-pt2.ot2.apiv2.py.json @@ -1328,5 +1328,12 @@ "protocolName": "Ilumina DNA Prep Part 2 - Post Tagmentation Cleanup", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json b/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json index aa24eb9813..2882591523 100644 --- a/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json +++ b/protoBuilds/0bf4f4-pt3/0bf4f4-pt3.ot2.apiv2.py.json @@ -214,5 +214,12 @@ "protocolName": "Ilumina DNA Prep Part 3 - Clean up Libraries", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json b/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json index 5a625e0394..256e7499f6 100644 --- a/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json +++ b/protoBuilds/0e8e3/0e8e3.ot2.apiv2.py.json @@ -2457,5 +2457,12 @@ "protocolName": "PCR Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Plate B (DNAse Dilution Plate) on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/0f4405/extraction.ot2.apiv2.py.json b/protoBuilds/0f4405/extraction.ot2.apiv2.py.json deleted file mode 100644 index f2a4ee89d1..0000000000 --- a/protoBuilds/0f4405/extraction.ot2.apiv2.py.json +++ /dev/null @@ -1,2406 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'NEB NExt Ultra II Illumina Library Prep',\n 'author': 'Opentrons ',\n 'apiLevel': '2.11'\n}\n\n\n# Start protocol\ndef run(ctx):\n\n [num_samples, _ratio_beads_dna, time_mag_incubation,\n mount_m300, mount_m20] = get_values( # noqa: F821\n 'num_samples', '_ratio_beads_dna', 'time_mag_incubation', 'mount_m300',\n 'mount_m20')\n park_tips = True\n tip_track = False\n mag_height = 11\n x_offset = 2.0\n z_offset_beads = 2.0\n z_offset_supernatant = 1.0\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n magdeck = ctx.load_module('magnetic module gen2', '1')\n magdeck.disengage()\n mag_plate = magdeck.load_labware('eppendorftwin.tec_96_wellplate_150ul')\n tips20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['2', '4', '5']]\n tempdeck = ctx.load_module('Temperature Module Gen2', '3')\n tempdeck.set_temperature(4)\n elution_plate = tempdeck.load_labware(\n 'eppendorftwin.tec_96_aluminumblock_150ul')\n tc = ctx.load_module('thermocycler')\n tc.open_lid()\n tc.set_block_temperature(20)\n tc.set_lid_temperature(105)\n tc_plate = tc.load_labware('eppendorftwin.tec_96_wellplate_150ul',\n 'DNA plate')\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['6']]\n reservoir = ctx.load_labware('nest_96_wellplate_2ml_deep', '9',\n 'reagent reservoir')\n\n num_cols = math.ceil(num_samples/8)\n if park_tips:\n parking_spots300 = tips300[0].rows()[0][:num_cols]\n parking_spots20 = tips20[0].rows()[0][:num_cols]\n else:\n parking_spots300 = [None for none in range(12)]\n parking_spots20 = [None for none in range(12)]\n\n # load pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', mount_m300, tip_racks=tips300)\n m20 = ctx.load_instrument(\n 'p20_multi_gen2', mount_m20, tip_racks=tips20)\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n mastermix = reservoir.rows()[0][0]\n adaptor = reservoir.rows()[0][1]\n mastermix2 = reservoir.rows()[0][2]\n user = reservoir.rows()[0][3]\n etoh = reservoir.rows()[0][4]\n elution_buffer = reservoir.rows()[0][5]\n waste = reservoir.rows()[0][-1]\n\n mag_samples_m = mag_plate.rows()[0][:num_cols]\n elution_samples_m = elution_plate.rows()[0][:num_cols]\n tc_samples_m = tc_plate.rows()[0][:num_cols]\n\n magdeck.disengage() # just in case\n tempdeck.set_temperature(4)\n\n m300.flow_rate.aspirate = 50\n m300.flow_rate.dispense = 150\n m300.flow_rate.blow_out = 300\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip, loc=None):\n nonlocal switch\n nonlocal drop_count\n if loc:\n pip.drop_tip(loc)\n else:\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n ctx.pause('Please empty tips from waste before \\\n resuming.')\n drop_count = 0\n\n def remove_supernatant(vol, pip=m300, park=False):\n pip.flow_rate.aspirate /= 5\n parking_spots = parking_spots300 if pip == m300 else parking_spots20\n for i, (m, p) in enumerate(zip(mag_samples_m, parking_spots)):\n if park:\n _pick_up(pip, p)\n else:\n _pick_up(pip)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side, z=z_offset_supernatant))\n pip.move_to(m.center())\n pip.transfer(vol, loc, waste, new_tip='never',\n air_gap=pip.min_volume)\n pip.blow_out(waste)\n pip.air_gap(pip.min_volume)\n _drop(pip)\n pip.flow_rate.aspirate *= 5\n\n \"\"\" 1. NEBNext End Prep \"\"\"\n for t in tc_samples_m:\n _pick_up(m20)\n m20.transfer(10, mastermix, t, mix_after=(10, 20), new_tip='never')\n _drop(m20)\n\n profile = [\n {'temperature': 20, 'hold_time_minutes': 30},\n {'temperature': 65, 'hold_time_minutes': 30}]\n tc.close_lid()\n tc.execute_profile(steps=profile, repetitions=1, block_max_volume=60)\n tc.set_block_temperature(4)\n tc.open_lid()\n\n \"\"\" 2. Adapter Ligation \"\"\"\n for t in tc_samples_m:\n _pick_up(m20)\n m20.transfer(2.5, adaptor, t, mix_after=(10, 20), new_tip='never')\n _drop(m20)\n\n for t in tc_samples_m:\n _pick_up(m300)\n m300.transfer(31, mastermix2, t, mix_after=(10, 50), new_tip='never')\n _drop(m300)\n\n tc.close_lid()\n tc.set_block_temperature(20, hold_time_minutes=15)\n tc.open_lid()\n\n for t in tc_samples_m:\n _pick_up(m20)\n m20.transfer(3, user, t, mix_after=(10, 20), new_tip='never')\n _drop(m20)\n\n tc.close_lid()\n tc.set_block_temperature(37, hold_time_minutes=15)\n tc.set_block_temperature(4)\n tc.open_lid()\n\n \"\"\" 3. Clean Up \"\"\"\n dna_vol_total = 96.5\n elution_vol_total = 17\n num_washes = math.ceil(_ratio_beads_dna/0.9)\n dna_vol_wash = dna_vol_total/num_washes\n elution_vol_wash = elution_vol_total/num_washes\n elution_vol_final = 15/num_washes\n\n for wash_ind in range(num_washes):\n # add sample\n for t, m, p in zip(tc_samples_m, mag_samples_m, parking_spots300):\n if wash_ind == 0:\n _pick_up(m300)\n else:\n _pick_up(m300, p)\n m300.transfer(dna_vol_wash, t, m, mix_after=(10, 50),\n new_tip='never')\n _drop(m300, p)\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating off magnet for \\\n{time_mag_incubation} minutes.')\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating on magnet for \\\n{time_mag_incubation} minutes.')\n remove_supernatant(200, pip=m300, park=True)\n\n # wash 2x\n for _ in range(2):\n _pick_up(m300)\n for i, m in enumerate(mag_samples_m):\n m300.aspirate(200, etoh)\n m300.dispense(200, m.top())\n ctx.delay(seconds=30, msg='Incubating on magnet for 30 seconds.')\n m300.drop_tip()\n remove_supernatant(200, pip=m300, park=True)\n\n # remove residual\n remove_supernatant(20, pip=m20, park=False)\n\n # air dry\n ctx.delay(minutes=5, msg='Air drying for 5 minutes.')\n magdeck.disengage()\n\n # elute\n for i, m in enumerate(mag_samples_m):\n _pick_up(m20)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=x_offset*side, z=z_offset_beads))\n m20.aspirate(elution_vol_wash, elution_buffer)\n m20.move_to(m.center())\n m20.dispense(elution_vol_wash, loc)\n for _ in range(10): # custom mix\n m20.aspirate(20, m.bottom(1))\n m20.dispense(20, loc)\n _drop(m20)\n\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating off magnet for \\\n{time_mag_incubation} minutes.')\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=time_mag_incubation, msg=f'Incubating on magnet for \\\n{time_mag_incubation} minutes.')\n\n # elute\n for m, e in zip(mag_samples_m, elution_samples_m):\n _pick_up(m20)\n m20.flow_rate.aspirate /= 5\n m20.transfer(elution_vol_final, m.bottom(0.5), e, new_tip='never')\n m20.flow_rate.aspirate *= 5\n m20.mix(10, 20, e)\n _drop(m20)\n\n magdeck.disengage()\n tc.deactivate_lid()\n tc.deactivate_block()\n\n # track final used tip\n if not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Eppendorf twin.tec", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 21.2 - }, - "groups": [ - { - "metadata": { - "displayCategory": "wellPlate", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Eppendorf Twin.tec 96 Aluminum Block 150 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - 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{ - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "eppendorftwin.tec_96_wellplate_150ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 2", - "share": false, - "slot": "2", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Eppendorf Twin.tec 96 Aluminum Block 150 \u00b5L on Temperature Module GEN2 on 3", - "share": false, - "slot": "3", - "type": "eppendorftwin.tec_96_aluminumblock_150ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "DNA plate on Thermocycler Module on 7", - "share": false, - "slot": "7", - "type": "eppendorftwin.tec_96_wellplate_150ul" - }, - { - "name": "reagent reservoir on 9", - "share": false, - "slot": "9", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "NEB NExt Ultra II Illumina Library Prep" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json b/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json index 6bddc035bd..02395cf66b 100644 --- a/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json +++ b/protoBuilds/10bf60-station-B/extraction.ot2.apiv2.py.json @@ -196,5 +196,18 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution strips on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json b/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json index 3ead026558..68fb43b7ef 100644 --- a/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json +++ b/protoBuilds/10bf60-station-C/generic_station_C.ot2.apiv2.py.json @@ -1234,5 +1234,12 @@ "protocolName": "Covid-19 qPCR Setup Protocol", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 7 lw mastermix (tube A1) on Temperature Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json b/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json index a9e805098f..712d08f5df 100644 --- a/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-10/111210-part-10.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Cleanup of Universal PCR with QIAseq Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json b/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json index 0be049afb8..84b5901c6d 100644 --- a/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-2/111210-part-2.ot2.apiv2.py.json @@ -68,5 +68,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Reverse Transcription" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json b/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json index 372fe92cc5..1792ac0986 100644 --- a/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-3/111210-part-3.ot2.apiv2.py.json @@ -68,5 +68,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Second strand synthesis" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json b/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json index 2a2419f028..21907a76ec 100644 --- a/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-4/111210-part-4.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n End repair / dA tailing" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json b/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json index 3098026bf7..4016db8990 100644 --- a/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-5/111210-part-5.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Adaptor ligation" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw None", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json b/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json index 58b7ecd717..77d440e3c8 100644 --- a/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-6/111210-part-6.ot2.apiv2.py.json @@ -117,5 +117,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Cleanup of Adapter-ligated DNA with QIAseq Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json b/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json index cc9e9950ec..08ae49f215 100644 --- a/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-7/111210-part-7.ot2.apiv2.py.json @@ -68,5 +68,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Target Enrichment PCR" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json b/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json index 4c35cdd097..d98e67f167 100644 --- a/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-8/111210-part-8.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Cleanup of Target Enrichment PCR with QIAseq Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json b/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json index 2a175ba374..829f5cc012 100644 --- a/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json +++ b/protoBuilds/111210-part-9/111210-part-9.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n Universal PCR Amplification" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/111210/111210.ot2.apiv2.py.json b/protoBuilds/111210/111210.ot2.apiv2.py.json index 029625ddb2..4c85baa34c 100644 --- a/protoBuilds/111210/111210.ot2.apiv2.py.json +++ b/protoBuilds/111210/111210.ot2.apiv2.py.json @@ -89,5 +89,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung RNA Fusion UMI Panel Kit:\n First strand cDNA synthesis" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json b/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json index fecb1a8abf..aac7e7a661 100644 --- a/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json +++ b/protoBuilds/1185d3/1185d3.ot2.apiv2.py.json @@ -88,5 +88,12 @@ "protocolName": "MagMAX Viral/Pathogen Nucleic Acid Isolation Kit wash", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json b/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json index 073e447b9a..190b19e12b 100644 --- a/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json +++ b/protoBuilds/118e8c/118e8c.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons.protocol_api.labware import Well\nfrom opentrons import types\nimport math\nimport csv\nimport os\n\nmetadata = {\n 'protocolName': 'FluoGene HLA NX 96-Well or 384-Well Setup',\n 'author': 'Steve ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n [use_384, p20_blowout_height, disposal_volume, p300_transfer_height,\n dispense_volume, p300_mixing_height,\n p20_tube_height, relative_height, tracking_reset,\n p20_reservoir_height, tip_max, water_volume, fluomix_volume,\n dna_volume, reservoir_fill_volume] = get_values( # noqa: F821\n \"use_384\", \"p20_blowout_height\", \"disposal_volume\",\n \"p300_transfer_height\", \"dispense_volume\", \"p300_mixing_height\",\n \"p20_tube_height\", \"relative_height\", \"tracking_reset\",\n \"p20_reservoir_height\", \"tip_max\", \"water_volume\", \"fluomix_volume\",\n \"dna_volume\", \"reservoir_fill_volume\")\n\n ctx.set_rail_lights(True)\n ctx.delay(seconds=10)\n\n # constant values\n reduced_pick_up_current = 0.15\n touch_radius = 0.75\n touch_v_offset = -3\n touch_speed = 10\n\n # constrain reduced_pick_up_current value to acceptable range\n if reduced_pick_up_current < 0.1 or reduced_pick_up_current > 0.15:\n raise Exception('''Invalid value for reduced_pick_up_current parameter\n (must be between 0.1 and 0.15).''')\n\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # for reservoir column tracking between protocol runs\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n file_path = '/data/temporary/columnandtiptracking.csv'\n file_dir = os.path.dirname(file_path)\n # check for file directory\n if not os.path.exists(file_dir):\n os.makedirs(file_dir)\n # check for file; if not there, create initial csv\n if (not os.path.isfile(file_path) or tracking_reset):\n with open(file_path, 'w') as outfile:\n outfile.write(\",\".join([\n \"0\", \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\", \"\\n\"]))\n\n current_data_list = []\n # if not ctx.is_simulating(): # logic reversed for simulation\n if ctx.is_simulating():\n current_data_list = [0,\n \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"]\n else:\n with open(file_path) as csv_file:\n csv_reader = csv.reader(csv_file, delimiter=',')\n current_data_list = next(csv_reader)\n\n current_col_index = int(current_data_list[0])\n [current_starting_tip_20, current_starting_tip_300] = [\n current_data_list[i] for i in range(1, 3)]\n\n if current_col_index == 0:\n ctx.pause(\"Please place an unused, clean source plate in deck slot 7.\")\n\n # reservoir with column tracking between protocol runs\n reservoir = ctx.load_labware('nunc_96_wellplate_500ul', '7')\n\n # increment column index for future protocol run\n if current_col_index < len(reservoir.columns()) - 1:\n new_col_index = current_col_index + 1\n else:\n new_col_index = 0\n \"\"\"\n protocol steps using tracked reservoir column\n \"\"\"\n # reagent mix in reservoir column tracked across protocol runs\n reservoir_col = reservoir.columns()[current_col_index]\n ctx.set_rail_lights(True)\n\n # tips and p300 multi\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '11')]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '10')]\n p300s = ctx.load_instrument('p300_single_gen2', 'left', tip_racks=tips300)\n p20m = ctx.load_instrument('p20_multi_gen2', 'right', tip_racks=tips20)\n\n # trays\n if not use_384:\n trays = [\n ctx.load_labware(labware, slot) for labware, slot in zip(\n ['innotrainot2pcrplate_96_wellplate_200ul',\n 'innotrainot22pcrplate_96_wellplate_200ul'], ['5', '6'])]\n else:\n trays = [ctx.load_labware('custom_384_well_tray', '5')]\n\n # tube rack rxn components: water in A1, pcr mix in A2, DNA dilution in A3\n tube_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')\n [w, p, d] = [\n tube_rack.wells_by_name()[well] for well in ['A1', 'A2', 'A3']]\n\n class WellH(Well):\n def __init__(self, well, min_height=5, comp_coeff=1.15,\n current_volume=0):\n super().__init__(well._impl)\n self.well = well\n self.min_height = min_height\n self.comp_coeff = comp_coeff\n self.current_volume = current_volume\n if self.diameter is not None:\n self.radius = self.diameter/2\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n self.height = current_volume/cse\n if self.height < min_height:\n self.height = min_height\n elif self.height > well.parent.highest_z:\n raise Exception(\"\"\"Specified liquid volume\n can not exceed the height of the labware.\"\"\")\n\n def height_dec(self, vol):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n dh = (vol/cse)*self.comp_coeff\n if self.height - dh > self.min_height:\n self.height = self.height - dh\n else:\n self.height = self.min_height\n if self.current_volume - vol > 0:\n self.current_volume = self.current_volume - vol\n else:\n self.current_volume = 0\n return(self.well.bottom(self.height))\n\n def height_inc(self, vol, top=False):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n ih = (vol/cse)*self.comp_coeff\n if self.height < self.min_height:\n self.height = self.min_height\n if self.height + ih < self.depth:\n self.height = self.height + ih\n else:\n self.height = self.depth\n self.current_volume += vol\n if top is False:\n return(self.well.bottom(self.height))\n else:\n return(self.well.top())\n\n # to track liquid height\n water = WellH(w, min_height=1, current_volume=water_volume)\n pcr_mix = WellH(p, min_height=1, current_volume=0.9*fluomix_volume)\n dna_dilution = WellH(d, min_height=1, current_volume=dna_volume)\n\n \"\"\"\n pick_up() function to use only the rear-most channel of the p20 multi\n \"\"\"\n num_channels_per_pickup = 1 # (only pickup tips on rear-most channel)\n tips_ordered = [\n tip for rack in tips20\n for row in rack.rows(\n )[len(rack.rows())-num_channels_per_pickup::-1*num_channels_per_pickup]\n for tip in row]\n\n tip_count = tips_ordered.index(\n tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0].replace('A', 'H')])\n\n def pick_up(pip):\n nonlocal tip_count\n pip.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # one-tip transfer water, fluomix to 1st col last well\n p20m.flow_rate.aspirate = 3.8\n p20m.flow_rate.dispense = 3.8\n\n # capture and report original value for p20m pick_up_current\n default_current = ctx._implementation._hw_manager.hardware.\\\n _attached_instruments[p20m._implementation.get_mount()].\\\n config.pick_up_current\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n initially configured to {} mAmp.\"\"\".format(str(default_current)))\n\n # temporarily reduce p20m pick_up_current for one-channel tip pickup\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', reduced_pick_up_current)\n ctx.comment(\"\"\"Tip pick-up current configuration for the p20 multi-channel\n pipette temporarily reduced to {} mAmp for one-tip pickup.\"\"\".format(\n str(reduced_pick_up_current)))\n\n # one-tip pickup with p20m\n pick_up(p20m)\n\n # reset p20m pick_up_current to original value\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', default_current)\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n restored to initial value of {} mAmp for standard 8-tip pickup.\"\"\".format(\n str(ctx._implementation._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].config.pick_up_current)))\n\n # water then fluomix to last well of 1st col each tray\n for reagent in [water, pcr_mix]:\n for tray in trays:\n p20m.aspirate(4, reagent.height_dec(4))\n p20m.dispense(4, reagent.height_inc(4))\n p20m.aspirate(4, reagent.height_dec(4))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(\n 4, tray.columns()[0][-1].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][-1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n # helper function for repeat large vol transfers\n def repeat_max_transfer(current_pipette, remaining, source, dest,\n flowrate, touch=False):\n while remaining > tip_max:\n current_pipette.aspirate(\n tip_max, source.height_dec(tip_max), rate=flowrate)\n current_pipette.dispense(\n tip_max, dest.height_inc(tip_max), rate=flowrate)\n remaining -= tip_max\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n current_pipette.aspirate(\n remaining, source.height_dec(remaining), rate=flowrate)\n current_pipette.dispense(\n remaining, dest.height_inc(remaining), rate=flowrate)\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n\n # combine DNA dilution with pcr mix\n p300s.starting_tip = tips300[0].wells_by_name()[\n current_starting_tip_300.split()[0]]\n p300s.pick_up_tip()\n for rep in range(10):\n p300s.aspirate(200, dna_dilution.height_dec(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n p300s.dispense(200, dna_dilution.height_inc(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n repeat_max_transfer(p300s, dna_volume, dna_dilution, pcr_mix, 0.5)\n for rep in range(20):\n p300s.aspirate(200, pcr_mix.height_dec(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n p300s.dispense(200, pcr_mix.height_inc(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n\n # reservoir filling\n reservoir_mix = [WellH(well, min_height=3) for well in reservoir_col]\n for well in reservoir_mix:\n for rep in range(2):\n repeat_max_transfer(\n p300s, reservoir_fill_volume / 16, pcr_mix,\n well, 0.5, touch=True)\n p300s.drop_tip()\n if tips300[0].next_tip(1, p300s.starting_tip) is not None:\n future_tip_300 = tips300[0].next_tip(1, p300s.starting_tip)\n else:\n future_tip_300 = \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"\n\n # 7-tip transfer 8 ul to wells A1-G1 if 96-well tray\n # 7-tip transfer 8 ul to wells B1, D1, F1, H1, J1, L1, N1 if 384\n p20m.flow_rate.dispense = 22\n p20m.reset_tipracks()\n p20m.starting_tip = tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0]]\n p20m.pick_up_tip()\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n d_well = 1 if use_384 else 0\n p20m.dispense(dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n p20m.pick_up_tip()\n # 8-tip transfer 8 ul to wells A1, C1, E1, G1, I1, K1, M1, O1 if 384\n if use_384:\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3\n d_well = 0\n p20m.dispense(\n dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n\n # 8-tip transfer 8 ul to columns 2-12 of each tray\n for tray in trays:\n for index, column in enumerate(tray.columns()[1:12]):\n if use_384:\n p20m.aspirate(2*dispense_volume + disposal_volume,\n reservoir_mix[0].bottom(p20_reservoir_height))\n else:\n if not index % 2:\n if index < len(tray.columns()[1:]) - 1:\n p20m.aspirate(\n 2*dispense_volume + disposal_volume, reservoir_mix[\n 0].bottom(p20_reservoir_height))\n else:\n p20m.aspirate(\n dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(dispense_volume, column[0].top(d_height))\n p20m.touch_tip(\n column[0], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n if use_384:\n p20m.dispense(dispense_volume, column[1].top(d_height))\n p20m.touch_tip(\n column[1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.dispense(\n disposal_volume, reservoir_mix[0].bottom(p20_blowout_height))\n else:\n if index % 2:\n p20m.dispense(disposal_volume, reservoir_mix[0].bottom(\n p20_blowout_height))\n\n p20m.drop_tip()\n if tips20[0].next_tip(8, p20m.starting_tip) is not None:\n future_tip_20 = tips20[0].next_tip(8, p20m.starting_tip)\n else:\n future_tip_20 = \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\"\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # write future column and starting tips to csv for next protocol run\n new_data = \",\".join([\n str(new_col_index), str(future_tip_20), str(future_tip_300), '\\n'])\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n with open(file_path, 'w') as outfile:\n outfile.write(new_data)\n", + "content": "from opentrons.protocol_api.labware import Well\nfrom opentrons import types\nimport math\nimport csv\nimport os\n\nmetadata = {\n 'protocolName': 'FluoGene HLA NX 96-Well or 384-Well Setup',\n 'author': 'Steve ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n [use_384, p20_blowout_height, disposal_volume, p300_transfer_height,\n dispense_volume, p300_mixing_height,\n p20_tube_height, relative_height, tracking_reset,\n p20_reservoir_height, tip_max, water_volume, fluomix_volume,\n dna_volume, reservoir_fill_volume] = get_values( # noqa: F821\n \"use_384\", \"p20_blowout_height\", \"disposal_volume\",\n \"p300_transfer_height\", \"dispense_volume\", \"p300_mixing_height\",\n \"p20_tube_height\", \"relative_height\", \"tracking_reset\",\n \"p20_reservoir_height\", \"tip_max\", \"water_volume\", \"fluomix_volume\",\n \"dna_volume\", \"reservoir_fill_volume\")\n\n ctx.set_rail_lights(True)\n ctx.delay(seconds=10)\n\n # constant values\n reduced_pick_up_current = 0.15\n touch_radius = 0.75\n touch_v_offset = -3\n touch_speed = 10\n\n # constrain reduced_pick_up_current value to acceptable range\n if reduced_pick_up_current < 0.1 or reduced_pick_up_current > 0.15:\n raise Exception('''Invalid value for reduced_pick_up_current parameter\n (must be between 0.1 and 0.15).''')\n\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # for reservoir column tracking between protocol runs\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n file_path = '/data/temporary/columnandtiptracking.csv'\n file_dir = os.path.dirname(file_path)\n # check for file directory\n if not os.path.exists(file_dir):\n os.makedirs(file_dir)\n # check for file; if not there, create initial csv\n if (not os.path.isfile(file_path) or tracking_reset):\n with open(file_path, 'w') as outfile:\n outfile.write(\",\".join([\n \"0\", \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\", \"\\n\"]))\n\n current_data_list = []\n # if not ctx.is_simulating(): # logic reversed for simulation\n if ctx.is_simulating():\n current_data_list = [0,\n \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\",\n \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"]\n else:\n with open(file_path) as csv_file:\n csv_reader = csv.reader(csv_file, delimiter=',')\n current_data_list = next(csv_reader)\n\n current_col_index = int(current_data_list[0])\n [current_starting_tip_20, current_starting_tip_300] = [\n current_data_list[i] for i in range(1, 3)]\n\n if current_col_index == 0:\n ctx.pause(\"Please place an unused, clean source plate in deck slot 7.\")\n\n # reservoir with column tracking between protocol runs\n reservoir = ctx.load_labware('nunc_96_wellplate_500ul', '7')\n\n # increment column index for future protocol run\n if current_col_index < len(reservoir.columns()) - 1:\n new_col_index = current_col_index + 1\n else:\n new_col_index = 0\n \"\"\"\n protocol steps using tracked reservoir column\n \"\"\"\n # reagent mix in reservoir column tracked across protocol runs\n reservoir_col = reservoir.columns()[current_col_index]\n ctx.set_rail_lights(True)\n\n # tips and p300 multi\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '11')]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '10')]\n p300s = ctx.load_instrument('p300_single_gen2', 'left', tip_racks=tips300)\n p20m = ctx.load_instrument('p20_multi_gen2', 'right', tip_racks=tips20)\n\n # trays\n if not use_384:\n trays = [\n ctx.load_labware(labware, slot) for labware, slot in zip(\n ['innotrainot2pcrplate_96_wellplate_200ul',\n 'innotrainot22pcrplate_96_wellplate_200ul'], ['5', '6'])]\n else:\n trays = [ctx.load_labware('custom_384_well_tray', '5')]\n\n # tube rack rxn components: water in A1, pcr mix in A2, DNA dilution in A3\n tube_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')\n [w, p, d] = [\n tube_rack.wells_by_name()[well] for well in ['A1', 'A2', 'A3']]\n\n class WellH(Well):\n def __init__(self, well, min_height=5, comp_coeff=1.15,\n current_volume=0):\n super().__init__(well._impl)\n self.well = well\n self.min_height = min_height\n self.comp_coeff = comp_coeff\n self.current_volume = current_volume\n if self.diameter is not None:\n self.radius = self.diameter/2\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n self.height = current_volume/cse\n if self.height < min_height:\n self.height = min_height\n elif self.height > well.parent.highest_z:\n raise Exception(\"\"\"Specified liquid volume\n can not exceed the height of the labware.\"\"\")\n\n def height_dec(self, vol):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n dh = (vol/cse)*self.comp_coeff\n if self.height - dh > self.min_height:\n self.height = self.height - dh\n else:\n self.height = self.min_height\n if self.current_volume - vol > 0:\n self.current_volume = self.current_volume - vol\n else:\n self.current_volume = 0\n return (self.well.bottom(self.height))\n\n def height_inc(self, vol, top=False):\n if self.diameter is not None:\n cse = math.pi*(self.radius**2)\n elif self.length is not None:\n cse = self.length*self.width\n ih = (vol/cse)*self.comp_coeff\n if self.height < self.min_height:\n self.height = self.min_height\n if self.height + ih < self.depth:\n self.height = self.height + ih\n else:\n self.height = self.depth\n self.current_volume += vol\n if top is False:\n return (self.well.bottom(self.height))\n else:\n return (self.well.top())\n\n # to track liquid height\n water = WellH(w, min_height=1, current_volume=water_volume)\n pcr_mix = WellH(p, min_height=1, current_volume=0.9*fluomix_volume)\n dna_dilution = WellH(d, min_height=1, current_volume=dna_volume)\n\n \"\"\"\n pick_up() function to use only the rear-most channel of the p20 multi\n \"\"\"\n num_channels_per_pickup = 1 # (only pickup tips on rear-most channel)\n tips_ordered = [\n tip for rack in tips20\n for row in rack.rows(\n )[len(rack.rows())-num_channels_per_pickup::-1*num_channels_per_pickup]\n for tip in row]\n\n tip_count = tips_ordered.index(\n tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0].replace('A', 'H')])\n\n def pick_up(pip):\n nonlocal tip_count\n pip.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # one-tip transfer water, fluomix to 1st col last well\n p20m.flow_rate.aspirate = 3.8\n p20m.flow_rate.dispense = 3.8\n\n # capture and report original value for p20m pick_up_current\n default_current = ctx._hw_manager.hardware.\\\n _attached_instruments[p20m._implementation.get_mount()].\\\n config.pick_up_current\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n initially configured to {} mAmp.\"\"\".format(str(default_current)))\n\n # temporarily reduce p20m pick_up_current for one-channel tip pickup\n ctx._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', reduced_pick_up_current)\n ctx.comment(\"\"\"Tip pick-up current configuration for the p20 multi-channel\n pipette temporarily reduced to {} mAmp for one-tip pickup.\"\"\".format(\n str(reduced_pick_up_current)))\n\n # one-tip pickup with p20m\n pick_up(p20m)\n\n # reset p20m pick_up_current to original value\n ctx._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].update_config_item(\n 'pick_up_current', default_current)\n ctx.comment(\"\"\"Tip pick-up current for the p20 multi-channel pipette\n restored to initial value of {} mAmp for standard 8-tip pickup.\"\"\".format(\n str(ctx._hw_manager.hardware._attached_instruments[\n p20m._implementation.get_mount()].config.pick_up_current)))\n\n # water then fluomix to last well of 1st col each tray\n for reagent in [water, pcr_mix]:\n for tray in trays:\n p20m.aspirate(4, reagent.height_dec(4))\n p20m.dispense(4, reagent.height_inc(4))\n p20m.aspirate(4, reagent.height_dec(4))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(\n 4, tray.columns()[0][-1].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][-1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n # helper function for repeat large vol transfers\n def repeat_max_transfer(current_pipette, remaining, source, dest,\n flowrate, touch=False):\n while remaining > tip_max:\n current_pipette.aspirate(\n tip_max, source.height_dec(tip_max), rate=flowrate)\n current_pipette.dispense(\n tip_max, dest.height_inc(tip_max), rate=flowrate)\n remaining -= tip_max\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n current_pipette.aspirate(\n remaining, source.height_dec(remaining), rate=flowrate)\n current_pipette.dispense(\n remaining, dest.height_inc(remaining), rate=flowrate)\n if touch:\n ctx.delay(seconds=0.5)\n current_pipette.blow_out()\n current_pipette.touch_tip(radius=0.75, v_offset=-2, speed=10)\n\n # combine DNA dilution with pcr mix\n p300s.starting_tip = tips300[0].wells_by_name()[\n current_starting_tip_300.split()[0]]\n p300s.pick_up_tip()\n for rep in range(10):\n p300s.aspirate(200, dna_dilution.height_dec(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n p300s.dispense(200, dna_dilution.height_inc(200).move(\n types.Point(x=0, y=0, z=-dna_dilution.height*(relative_height))),\n rate=3.2)\n repeat_max_transfer(p300s, dna_volume, dna_dilution, pcr_mix, 0.5)\n for rep in range(20):\n p300s.aspirate(200, pcr_mix.height_dec(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n p300s.dispense(200, pcr_mix.height_inc(200).move(\n types.Point(x=0, y=0, z=-pcr_mix.height*(relative_height))), rate=3.2)\n\n # reservoir filling\n reservoir_mix = [WellH(well, min_height=3) for well in reservoir_col]\n for well in reservoir_mix:\n for rep in range(2):\n repeat_max_transfer(\n p300s, reservoir_fill_volume / 16, pcr_mix,\n well, 0.5, touch=True)\n p300s.drop_tip()\n if tips300[0].next_tip(1, p300s.starting_tip) is not None:\n future_tip_300 = tips300[0].next_tip(1, p300s.starting_tip)\n else:\n future_tip_300 = \"A1 of Opentrons 96 Filter Tip Rack 200 \u00b5L on 11\"\n\n # 7-tip transfer 8 ul to wells A1-G1 if 96-well tray\n # 7-tip transfer 8 ul to wells B1, D1, F1, H1, J1, L1, N1 if 384\n p20m.flow_rate.dispense = 22\n p20m.reset_tipracks()\n p20m.starting_tip = tips20[0].wells_by_name()[\n current_starting_tip_20.split()[0]]\n p20m.pick_up_tip()\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n d_well = 1 if use_384 else 0\n p20m.dispense(dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.drop_tip()\n\n p20m.pick_up_tip()\n # 8-tip transfer 8 ul to wells A1, C1, E1, G1, I1, K1, M1, O1 if 384\n if use_384:\n for tray in trays:\n p20m.aspirate(dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3\n d_well = 0\n p20m.dispense(\n dispense_volume, tray.columns()[0][d_well].top(d_height))\n p20m.touch_tip(\n tray.columns()[0][d_well], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n\n # 8-tip transfer 8 ul to columns 2-12 of each tray\n for tray in trays:\n for index, column in enumerate(tray.columns()[1:12]):\n if use_384:\n p20m.aspirate(2*dispense_volume + disposal_volume,\n reservoir_mix[0].bottom(p20_reservoir_height))\n else:\n if not index % 2:\n if index < len(tray.columns()[1:]) - 1:\n p20m.aspirate(\n 2*dispense_volume + disposal_volume, reservoir_mix[\n 0].bottom(p20_reservoir_height))\n else:\n p20m.aspirate(\n dispense_volume, reservoir_mix[0].bottom(\n p20_reservoir_height))\n d_height = -3 if use_384 else -11.2\n p20m.dispense(dispense_volume, column[0].top(d_height))\n p20m.touch_tip(\n column[0], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n if use_384:\n p20m.dispense(dispense_volume, column[1].top(d_height))\n p20m.touch_tip(\n column[1], radius=touch_radius,\n v_offset=touch_v_offset, speed=touch_speed)\n p20m.dispense(\n disposal_volume, reservoir_mix[0].bottom(p20_blowout_height))\n else:\n if index % 2:\n p20m.dispense(disposal_volume, reservoir_mix[0].bottom(\n p20_blowout_height))\n\n p20m.drop_tip()\n if tips20[0].next_tip(8, p20m.starting_tip) is not None:\n future_tip_20 = tips20[0].next_tip(8, p20m.starting_tip)\n else:\n future_tip_20 = \"A1 of Opentrons 96 Filter Tip Rack 20 \u00b5L on 10\"\n \"\"\"\n for reservoir column tracking between protocol runs\n \"\"\"\n # write future column and starting tips to csv for next protocol run\n new_data = \",\".join([\n str(new_col_index), str(future_tip_20), str(future_tip_300), '\\n'])\n # if ctx.is_simulating(): # logic reversed for simulation\n if not ctx.is_simulating():\n with open(file_path, 'w') as outfile:\n outfile.write(new_data)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json b/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json index f9bd398a12..51c31c8022 100644 --- a/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json +++ b/protoBuilds/11beaa/11beaa.ot2.apiv2.py.json @@ -6779,5 +6779,12 @@ "protocolName": "qPCR Prep with 384 Well Plate", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Biorad 96 Aluminum Block 200 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/121d15-2-96/README.json b/protoBuilds/121d15-2-96/README.json deleted file mode 100644 index 0354380117..0000000000 --- a/protoBuilds/121d15-2-96/README.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Sample Prep": [ - "Cherrypicking" - ] - }, - "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (96)\n\n\n* Redo Replacement Picking (384)\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", - "internal": "121d15", - "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Sample Prep\n\t* Cherrypicking\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/121d15/deck2-96.png)\n\n---\n\n", - "description": "\nLinks:\n* [Manual Cleave](./121d15)\n
\n
\n* [Manual Cleave Elution (Off-deck Vacuum)](./121d15-4)\n
\n
\n* [Manual Cleave, ACN + Elution (Off-deck Vacuum)](./121d15-5)\n
\n
\n* [Manual Cleave, ACN + Elution (On-deck Vacuum)](./121d15-6)\n
\n
\n* [HPLC Picking](./121d15-3)\n
\n
\n* [Redo Replacement Picking (96)](./121d15-2-96)\n
\n
\n* [Redo Replacement Picking (384)](./121d15-2-384)\n
\n
\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\n\n```\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n```\n\n---\n\n", - "internal": "121d15\n", - "labware": "* Custom 48-tuberack\n* [Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L](https://shop.gbo.com/en/row/products/bioscience/microplates/polypropylene-storage-plates/96-well-masterblock-0-5ml/786201.html)\n* [Opentrons 300\u00b5L Tips](https://shop.opentrons.com/opentrons-300ul-tips-1000-refills/)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)\n\n---\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "title": "Redo Replacement Picking (96)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single Channel Electronic Pipette (GEN2)\n\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "title": "Redo Replacement Picking (96)" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2-96/metadata.json b/protoBuilds/121d15-2-96/metadata.json deleted file mode 100644 index 6b3b15abb5..0000000000 --- a/protoBuilds/121d15-2-96/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "redoreplacementpicking.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/121d15-2-96", - "slug": "121d15-2-96", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2-96/redoreplacementpicking.ot2.apiv2.py.json b/protoBuilds/121d15-2-96/redoreplacementpicking.ot2.apiv2.py.json deleted file mode 100644 index bbf6b8e744..0000000000 --- a/protoBuilds/121d15-2-96/redoreplacementpicking.ot2.apiv2.py.json +++ /dev/null @@ -1,16904 +0,0 @@ -{ - "content": "# metadata\nmetadata = {\n 'protocolName': 'Redo Replacement Picking (96)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [input_file, default_disposal_vol, default_transfer_vol,\n p300_mount] = get_values( # noqa: F821\n 'input_file', 'default_disposal_vol', 'default_transfer_vol',\n 'p300_mount')\n\n # load labware\n rack = ctx.load_labware('eurofins_96x2ml_tuberack', '2', 'tuberack')\n plate = ctx.load_labware('greinermasterblock_96_wellplate_500ul', '1')\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['4', '7']]\n\n # pipette\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n # parse\n data = [\n [val.strip() for val in line.split(',')]\n for line in input_file.splitlines()[3:]\n if line and line.split(',')[0].strip()]\n\n tubes_ordered = [\n well for i in range(2) for col in rack.columns()\n for well in col[i*8:(i+1)*8]]\n\n for line in data:\n tube = tubes_ordered[int(line[0])-1]\n well = plate.wells()[int(line[1])-1]\n if len(line) >= 3 and line[2]:\n disposal_vol = float(line[2])\n else:\n disposal_vol = default_disposal_vol\n if len(line) >= 4 and line[3]:\n transfer_vol = float(line[3])\n else:\n transfer_vol = default_transfer_vol\n\n # remove contents of well\n p300.pick_up_tip()\n ctx.max_speeds['A'] = 100 # slow descent\n ctx.max_speeds['Z'] = 100 # slow descent\n\n p300.aspirate(disposal_vol, well.bottom(0.2))\n del ctx.max_speeds['A'] # reset to default\n del ctx.max_speeds['Z'] # reset to default\n p300.drop_tip()\n\n # transfer tube to well\n p300.transfer(transfer_vol, tube, well.top(-1))\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Greiner Masterblock", - "brandId": [ - "781270" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 22 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "I2", - "J2", - "K2", - "L2", - "M2", - "N2", - "O2", - "P2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "I3", - "J3", - "K3", - "L3", - "M3", - "N3", - "O3", - "P3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "I4", - "J4", - "K4", - "L4", - "M4", - "N4", - "O4", - "P4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "I5", - "J5", - "K5", - "L5", - "M5", - "N5", - "O5", - "P5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "I6", - "J6", - "K6", - "L6", - "M6", - "N6", - "O6", - "P6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "I7", - "J7", - "K7", - "L7", - "M7", - "N7", - "O7", - "P7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "I8", - "J8", - "K8", - "L8", - "M8", - "N8", - "O8", - "P8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "I9", - "J9", - "K9", - "L9", - "M9", - "N9", - "O9", - "P9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "I10", - "J10", - "K10", - "L10", - "M10", - "N10", - "O10", - "P10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "I11", - "J11", - "K11", - "L11", - "M11", - "N11", - "O11", - "P11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12", - "I12", - "J12", - "K12", - "L12", - "M12", - "N12", - "O12", - "P12", - "A13", - "B13", - "C13", - "D13", - "E13", - "F13", - "G13", - "H13", - "I13", - "J13", - "K13", - "L13", - "M13", - "N13", - "O13", - "P13", - "A14", - "B14", - "C14", - "D14", - "E14", - "F14", - "G14", - "H14", - "I14", - "J14", - "K14", - "L14", - "M14", - "N14", - "O14", - "P14", - "A15", - "B15", - "C15", - "D15", - "E15", - "F15", - "G15", - "H15", - "I15", - "J15", - "K15", - "L15", - "M15", - "N15", - "O15", - "P15", - "A16", - "B16", - "C16", - "D16", - "E16", - "F16", - "G16", - "H16", - "I16", - "J16", - "K16", - "L16", - "M16", - "N16", - "O16", - "P16", - "A17", - "B17", - "C17", - "D17", - "E17", - "F17", - "G17", - "H17", - "I17", - "J17", - "K17", - "L17", - "M17", - "N17", - "O17", - "P17", - "A18", - "B18", - "C18", - "D18", - "E18", - "F18", - "G18", - "H18", - "I18", - "J18", - "K18", - "L18", - "M18", - "N18", - "O18", - "P18", - "A19", - "B19", - "C19", - "D19", - "E19", - "F19", - "G19", - "H19", - "I19", - "J19", - "K19", - "L19", - "M19", - "N19", - "O19", - "P19", - "A20", - "B20", - "C20", - "D20", - "E20", - "F20", - "G20", - "H20", - "I20", - "J20", - "K20", - "L20", - "M20", - "N20", - "O20", - "P20", - "A21", - "B21", - "C21", - "D21", - "E21", - "F21", - "G21", - "H21", - "I21", - "J21", - "K21", - "L21", - "M21", - "N21", - "O21", - "P21", - "A22", - "B22", - "C22", - "D22", - "E22", - "F22", - "G22", - "H22", - "I22", - "J22", - "K22", - "L22", - "M22", - "N22", - "O22", - "P22", - "A23", - "B23", - "C23", - "D23", - "E23", - "F23", - "G23", - "H23", - "I23", - "J23", - "K23", - "L23", - "M23", - "N23", - "O23", - "P23", - "A24", - "B24", - "C24", - "D24", - "E24", - "F24", - "G24", - "H24", - "I24", - "J24", - "K24", - "L24", - "M24", - "N24", - "O24", - "P24" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Greiner Masterblock 384 Well Plate 225 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1" - ], - 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"x": 77.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - }, - "H9": { - "depth": 39.23, - "shape": "rectangular", - "totalLiquidVolume": 2200, - "x": 86.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - } - } - } - ], - "fields": [ - { - "default": "Number of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n", - "label": "input file", - "name": "input_file", - "type": "textFile" - }, - { - "default": 200.0, - "label": "default initial disposal volume (\u00b5l)", - "name": "default_disposal_vol", - "type": "float" - }, - { - "default": 200.0, - "label": "default new transfer volume (\u00b5l)", - "name": "default_transfer_vol", - "type": "float" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L on 1", - "share": false, - "slot": "1", - "type": "greinermasterblock_96_wellplate_500ul" - }, - { - "name": "tuberack on 2", - "share": false, - "slot": "2", - "type": "eurofins_96x2ml_tuberack" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "Redo Replacement Picking (96)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/121d15-2/README.json b/protoBuilds/121d15-2/README.json deleted file mode 100644 index 23498780bb..0000000000 --- a/protoBuilds/121d15-2/README.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Sample Prep": [ - "Cherrypicking" - ] - }, - "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* Redo Replacement Picking\n\n\n* HPLC Picking\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n9\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n9,219\n...\n", - "internal": "121d15", - "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 384 Well Plate 225 \u00b5L\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Sample Prep\n\t* Cherrypicking\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/121d15/deck2-v2.png)\n\n---\n\n", - "description": "\nLinks:\n* [Manual Cleave](./121d15)\n
\n
\n* [Manual Cleave Elution (Off-deck Vacuum)](./121d15-4)\n
\n
\n* [Manual Cleave, ACN + Elution (Off-deck Vacuum)](./121d15-5)\n
\n
\n* [Manual Cleave, ACN + Elution (On-deck Vacuum)](./121d15-6)\n
\n
\n* [Redo Replacement Picking](./121d15-2)\n
\n
\n* [HPLC Picking](./121d15-3)\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\n\n```\nNumber of Redo\n9\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n9,219\n...\n```\n\n---\n\n", - "internal": "121d15\n", - "labware": "* Custom 48-tuberack\n* [Greiner MASTERBLOCK 384 Well Plate 225 \u00b5L](https://shop.gbo.com/en/row/products/bioscience/microplates/polypropylene-storage-plates/384-deep-well-masterblock/781270.html)\n* [Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L](https://shop.gbo.com/en/row/products/bioscience/microplates/polypropylene-storage-plates/96-well-masterblock-0-5ml/786201.html)\n* [Opentrons 300\u00b5L Tips](https://shop.opentrons.com/opentrons-300ul-tips-1000-refills/)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)\n\n---\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "title": "Redo Replacement Picking" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single Channel Electronic Pipette (GEN2)\n\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "title": "Redo Replacement Picking" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2/metadata.json b/protoBuilds/121d15-2/metadata.json deleted file mode 100644 index cf0579d83f..0000000000 --- a/protoBuilds/121d15-2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "redoreplacementpicking.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/121d15-2", - "slug": "121d15-2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/121d15-2/redoreplacementpicking.ot2.apiv2.py.json b/protoBuilds/121d15-2/redoreplacementpicking.ot2.apiv2.py.json deleted file mode 100644 index ec0ae32187..0000000000 --- a/protoBuilds/121d15-2/redoreplacementpicking.ot2.apiv2.py.json +++ /dev/null @@ -1,16919 +0,0 @@ -{ - "content": "# metadata\nmetadata = {\n 'protocolName': 'Redo Replacement Picking',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [input_file, default_disposal_vol, default_transfer_vol, plate_type,\n p300_mount] = get_values( # noqa: F821\n 'input_file', 'default_disposal_vol', 'default_transfer_vol',\n 'plate_type', 'p300_mount')\n\n # load labware\n rack = ctx.load_labware('eurofins_96x2ml_tuberack', '2', 'tuberack')\n plate = ctx.load_labware(plate_type, '1')\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['4', '7']]\n\n # pipette\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n # parse\n data = [\n [val.strip() for val in line.split(',')]\n for line in input_file.splitlines()[3:]\n if line and line.split(',')[0].strip()]\n\n tubes_ordered = [\n well for i in range(2) for col in rack.columns()\n for well in col[i*8:(i+1)*8]]\n\n for line in data:\n tube = tubes_ordered[int(line[0])-1]\n well = plate.wells()[int(line[1])-1]\n if len(line) >= 3 and line[2]:\n disposal_vol = float(line[2])\n else:\n disposal_vol = default_disposal_vol\n if len(line) >= 4 and line[3]:\n transfer_vol = float(line[3])\n else:\n transfer_vol = default_transfer_vol\n\n # remove contents of well\n p300.pick_up_tip()\n ctx.max_speeds['A'] = 100 # slow descent\n ctx.max_speeds['Z'] = 100 # slow descent\n\n p300.aspirate(disposal_vol, well.bottom(0.2))\n del ctx.max_speeds['A'] # reset to default\n del ctx.max_speeds['Z'] # reset to default\n p300.drop_tip()\n\n # transfer tube to well\n p300.transfer(transfer_vol, tube, well.top(-1))\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Greiner Masterblock", - "brandId": [ - "781270" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 22 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "I2", - "J2", - "K2", - "L2", - "M2", - "N2", - "O2", - "P2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "I3", - "J3", - "K3", - "L3", - "M3", - "N3", - "O3", - "P3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "I4", - "J4", - "K4", - "L4", - "M4", - "N4", - "O4", - "P4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "I5", - "J5", - "K5", - "L5", - "M5", - "N5", - "O5", - "P5", - "A6", - "B6", - "C6", - 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"x": 77.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - }, - "H9": { - "depth": 39.23, - "shape": "rectangular", - "totalLiquidVolume": 2200, - "x": 86.38, - "xDimension": 8.24, - "y": 11.26, - "yDimension": 8.24, - "z": 4.97 - } - } - } - ], - "fields": [ - { - "default": "Number of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n", - "label": "input file", - "name": "input_file", - "type": "textFile" - }, - { - "default": 200.0, - "label": "default initial disposal volume (\u00b5l)", - "name": "default_disposal_vol", - "type": "float" - }, - { - "default": 200.0, - "label": "default new transfer volume (\u00b5l)", - "name": "default_transfer_vol", - "type": "float" - }, - { - "label": "plate type", - "name": "plate_type", - "options": [ - { - "label": "Greiner MASTERBLOCK 384 Well Plate 225 \u00b5L", - "value": "greinermasterblock_384_wellplate_225ul" - }, - { - "label": "Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L", - "value": "greinermasterblock_96_wellplate_500ul" - } - ], - "type": "dropDown" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "Greiner Masterblock 384 Well Plate 225 \u00b5L on 1", - "share": false, - "slot": "1", - "type": "greinermasterblock_384_wellplate_225ul" - }, - { - "name": "tuberack on 2", - "share": false, - "slot": "2", - "type": "eurofins_96x2ml_tuberack" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "Redo Replacement Picking", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json b/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json index 140d790c5b..eb9b57a345 100644 --- a/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json +++ b/protoBuilds/121d15-4/manual_cleave.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import json\nimport os\n\n# metadata\nmetadata = {\n 'protocolName': 'Manual Cleave Elution',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3, reagent_scan,\n slot_scan, transfer_vol, m300_mount, p300_mount,\n tip_track] = get_values( # noqa: F821\n 'occupied_well_csv1', 'occupied_well_csv2', 'occupied_well_csv3',\n 'reagent_scan', 'slot_scan', 'transfer_vol', 'm300_mount',\n 'p300_mount', 'tip_track')\n\n # load labware\n racks = [\n ctx.load_labware('custom_96_tuberack_500ul', f'{slot}', f'plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot,\n '300ul tiprack')\n for slot in ['10', '11']]\n\n reagent_map = {\n 'WATER': {\n 'slot': '9',\n 'tips': tips300[1].columns()[5:6],\n 'flow-rate-asp': 100,\n 'flow-rate-disp': 100,\n 'flow-rate-blow-out': 100,\n 'blow-out': True,\n 'dispense-delay': 0,\n 'drop-tip': False\n }\n }\n\n # check for barcode scan\n reagent_scan_type = reagent_scan.split('_')[-1].upper().strip()\n slot_scan_type = slot_scan.upper().strip()\n if reagent_scan_type == 'REPLACE WITH SCAN' \\\n or slot_scan_type == 'REPLACE WITH SCAN':\n pass\n else:\n if not reagent_scan_type:\n raise Exception('Rescan reagent (empty reagent_scan)')\n if not slot_scan_type:\n raise Exception('Rescan slot (empty slot scan)')\n if not reagent_scan_type == slot_scan_type[:3]:\n raise Exception(f'Reagent mismatch: {reagent_scan_type} in slot \\\n {slot_scan_type}')\n if slot_scan_type not in reagent_map.keys():\n raise Exception(f'Invalid slot scan: {slot_scan_type}')\n\n reagent_type = slot_scan_type\n reagent = ctx.load_labware(\n 'test_1_reservoir_300000ul', reagent_map[reagent_type]['slot'],\n reagent_type).wells()[0]\n\n def all_tips_full():\n for rack in tips300:\n for well in rack.wells():\n well.has_tip = True\n\n folder_path = '/data/manual_cleave'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n tip_data = json.load(json_file)\n for slot in tip_data.keys():\n for well, tip_bool in tip_data[slot].items():\n ctx.loaded_labwares[int(slot)].wells_by_name()[\n well].has_tip = tip_bool\n else:\n all_tips_full()\n else:\n all_tips_full()\n\n # load pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n p300 = ctx.load_instrument(\n 'p300_single_gen2', p300_mount, tip_racks=tips300)\n\n # samples and reagents\n def slide_window(num_tips, col):\n num_slides = 9 - num_tips\n for slide in range(num_slides):\n window_start_index = 8 + -1*num_tips - slide\n window = col[window_start_index:(window_start_index+num_tips)]\n window_full = True\n for tip in window:\n if not tip.has_tip:\n window_full = False\n if window_full:\n return window[0]\n return False\n\n def scan_racks(num_tips, reagent_type):\n all_columns = reagent_map[reagent_type]['tips']\n for col in all_columns:\n pick_up_loc = slide_window(num_tips, col)\n if pick_up_loc:\n return pick_up_loc\n return False\n\n per_tip_pickup_current = .1\n\n def pick_up(num_tips, reagent_type):\n if not 1 <= num_tips <= 8:\n raise Exception(f'INVALID NUMBER OF TIPS: {num_tips}.')\n if num_tips > 1:\n pip = m300\n pick_up_current = num_tips*per_tip_pickup_current\n ctx._implementation._hw_manager.hardware._attached_instruments[\n pip._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n else:\n pip = p300\n scan_result = scan_racks(num_tips, reagent_type)\n if scan_result:\n pip.pick_up_tip(scan_result)\n else:\n ctx.pause('REFILL TIPRACKS BEFORE RESUMING.')\n [rack.reset() for rack in tips300]\n scan_result = scan_racks(num_tips, reagent_type)\n pip.pick_up_tip(scan_result)\n return scan_result, pip\n\n def return_tip(pip, tip_loc, chunk_len, reagent_type):\n pip.drop_tip(tip_loc)\n all_tips = [\n well\n for col in reagent_map[reagent_type]['tips'] for well in col]\n tip_ind = all_tips.index(tip_loc)\n for tip in all_tips[tip_ind:tip_ind+chunk_len]:\n tip.has_tip = True\n\n # parse wells into chunks\n chunk_map = {num: [] for num in range(1, 9)}\n for csv, rack in zip(\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3],\n racks):\n occupied_wells = [\n rack.wells_by_name()[line.upper()]\n for line in csv.splitlines() if line]\n for col in rack.columns():\n running = None\n chunk_length = 0\n for well in col[::-1]:\n if well in occupied_wells:\n running = well\n chunk_length += 1\n else:\n if running:\n chunk_map[chunk_length].append(running)\n running = None\n chunk_length = 0\n if running:\n chunk_map[chunk_length].append(running)\n\n ctx.home()\n first_col = 0\n for i, col in enumerate(reagent_map[reagent_type]['tips']):\n if col[0].has_tip:\n first_col = i\n break\n col = reagent_map[\n reagent_type]['tips'][first_col][0].display_name.split(' ')[0][1:]\n ctx.pause(f'Ensure tips are in column {col}')\n\n num_chunks = len(\n [key for key, vals in chunk_map.items()\n if len(vals) > 0])\n accessed = 0\n num_centrifugations = 4\n\n for elution in range(num_centrifugations):\n for num_tips, dests in chunk_map.items():\n if len(dests) > 0:\n accessed += 1\n pick_up_loc, pip = pick_up(num_tips, reagent_type)\n for dest in dests:\n pip.aspirate(transfer_vol, reagent.bottom(2))\n pip.dispense(transfer_vol, dest.top(-1))\n ctx.delay(seconds=reagent_map[\n reagent_type]['dispense-delay'])\n if reagent_map[reagent_type]['blow-out']:\n pip.blow_out(dest.top(-1))\n\n if elution == num_centrifugations - 1 and \\\n reagent_map[reagent_type]['drop-tip'] and \\\n accessed == num_chunks:\n pip.drop_tip()\n else:\n # return tip and reset has_tip attribute\n return_tip(pip, pick_up_loc, num_tips, reagent_type)\n func = ctx.pause if elution < num_centrifugations - 1 \\\n else ctx.comment\n func('Centrifuge all plates. Replace and resume when finished.')\n\n # track final used tip\n # void partially full tip column\n for tiprack in tips300:\n for col in tiprack.columns():\n for well in col:\n if not well.has_tip:\n for well in col:\n well.has_tip = False\n break\n tip_data = {\n str(rack.parent):\n {well.display_name.split(' ')[0]: well.has_tip\n for well in rack.wells()}\n for rack in tips300\n }\n if not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n with open(tip_file_path, 'w') as outfile:\n json.dump(tip_data, outfile)\n\n ctx._implementation._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 1.0)\n", + "content": "import json\nimport os\n\n# metadata\nmetadata = {\n 'protocolName': 'Manual Cleave Elution',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3, reagent_scan,\n slot_scan, transfer_vol, m300_mount, p300_mount,\n tip_track] = get_values( # noqa: F821\n 'occupied_well_csv1', 'occupied_well_csv2', 'occupied_well_csv3',\n 'reagent_scan', 'slot_scan', 'transfer_vol', 'm300_mount',\n 'p300_mount', 'tip_track')\n\n # load labware\n racks = [\n ctx.load_labware('custom_96_tuberack_500ul', f'{slot}', f'plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n tips300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot,\n '300ul tiprack')\n for slot in ['10', '11']]\n\n reagent_map = {\n 'WATER': {\n 'slot': '9',\n 'tips': tips300[1].columns()[5:6],\n 'flow-rate-asp': 100,\n 'flow-rate-disp': 100,\n 'flow-rate-blow-out': 100,\n 'blow-out': True,\n 'dispense-delay': 0,\n 'drop-tip': False\n }\n }\n\n # check for barcode scan\n reagent_scan_type = reagent_scan.split('_')[-1].upper().strip()\n slot_scan_type = slot_scan.upper().strip()\n if reagent_scan_type == 'REPLACE WITH SCAN' \\\n or slot_scan_type == 'REPLACE WITH SCAN':\n pass\n else:\n if not reagent_scan_type:\n raise Exception('Rescan reagent (empty reagent_scan)')\n if not slot_scan_type:\n raise Exception('Rescan slot (empty slot scan)')\n if not reagent_scan_type == slot_scan_type[:3]:\n raise Exception(f'Reagent mismatch: {reagent_scan_type} in slot \\\n {slot_scan_type}')\n if slot_scan_type not in reagent_map.keys():\n raise Exception(f'Invalid slot scan: {slot_scan_type}')\n\n reagent_type = slot_scan_type\n reagent = ctx.load_labware(\n 'test_1_reservoir_300000ul', reagent_map[reagent_type]['slot'],\n reagent_type).wells()[0]\n\n def all_tips_full():\n for rack in tips300:\n for well in rack.wells():\n well.has_tip = True\n\n folder_path = '/data/manual_cleave'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n tip_data = json.load(json_file)\n for slot in tip_data.keys():\n for well, tip_bool in tip_data[slot].items():\n ctx.loaded_labwares[int(slot)].wells_by_name()[\n well].has_tip = tip_bool\n else:\n all_tips_full()\n else:\n all_tips_full()\n\n # load pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n p300 = ctx.load_instrument(\n 'p300_single_gen2', p300_mount, tip_racks=tips300)\n\n # samples and reagents\n def slide_window(num_tips, col):\n num_slides = 9 - num_tips\n for slide in range(num_slides):\n window_start_index = 8 + -1*num_tips - slide\n window = col[window_start_index:(window_start_index+num_tips)]\n window_full = True\n for tip in window:\n if not tip.has_tip:\n window_full = False\n if window_full:\n return window[0]\n return False\n\n def scan_racks(num_tips, reagent_type):\n all_columns = reagent_map[reagent_type]['tips']\n for col in all_columns:\n pick_up_loc = slide_window(num_tips, col)\n if pick_up_loc:\n return pick_up_loc\n return False\n\n per_tip_pickup_current = .1\n\n def pick_up(num_tips, reagent_type):\n if not 1 <= num_tips <= 8:\n raise Exception(f'INVALID NUMBER OF TIPS: {num_tips}.')\n if num_tips > 1:\n pip = m300\n pick_up_current = num_tips*per_tip_pickup_current\n ctx._hw_manager.hardware._attached_instruments[\n pip._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n else:\n pip = p300\n scan_result = scan_racks(num_tips, reagent_type)\n if scan_result:\n pip.pick_up_tip(scan_result)\n else:\n ctx.pause('REFILL TIPRACKS BEFORE RESUMING.')\n [rack.reset() for rack in tips300]\n scan_result = scan_racks(num_tips, reagent_type)\n pip.pick_up_tip(scan_result)\n return scan_result, pip\n\n def return_tip(pip, tip_loc, chunk_len, reagent_type):\n pip.drop_tip(tip_loc)\n all_tips = [\n well\n for col in reagent_map[reagent_type]['tips'] for well in col]\n tip_ind = all_tips.index(tip_loc)\n for tip in all_tips[tip_ind:tip_ind+chunk_len]:\n tip.has_tip = True\n\n # parse wells into chunks\n chunk_map = {num: [] for num in range(1, 9)}\n for csv, rack in zip(\n [occupied_well_csv1, occupied_well_csv2, occupied_well_csv3],\n racks):\n occupied_wells = [\n rack.wells_by_name()[line.upper()]\n for line in csv.splitlines() if line]\n for col in rack.columns():\n running = None\n chunk_length = 0\n for well in col[::-1]:\n if well in occupied_wells:\n running = well\n chunk_length += 1\n else:\n if running:\n chunk_map[chunk_length].append(running)\n running = None\n chunk_length = 0\n if running:\n chunk_map[chunk_length].append(running)\n\n ctx.home()\n first_col = 0\n for i, col in enumerate(reagent_map[reagent_type]['tips']):\n if col[0].has_tip:\n first_col = i\n break\n col = reagent_map[\n reagent_type]['tips'][first_col][0].display_name.split(' ')[0][1:]\n ctx.pause(f'Ensure tips are in column {col}')\n\n num_chunks = len(\n [key for key, vals in chunk_map.items()\n if len(vals) > 0])\n accessed = 0\n num_centrifugations = 4\n\n for elution in range(num_centrifugations):\n for num_tips, dests in chunk_map.items():\n if len(dests) > 0:\n accessed += 1\n pick_up_loc, pip = pick_up(num_tips, reagent_type)\n for dest in dests:\n pip.aspirate(transfer_vol, reagent.bottom(2))\n pip.dispense(transfer_vol, dest.top(-1))\n ctx.delay(seconds=reagent_map[\n reagent_type]['dispense-delay'])\n if reagent_map[reagent_type]['blow-out']:\n pip.blow_out(dest.top(-1))\n\n if elution == num_centrifugations - 1 and \\\n reagent_map[reagent_type]['drop-tip'] and \\\n accessed == num_chunks:\n pip.drop_tip()\n else:\n # return tip and reset has_tip attribute\n return_tip(pip, pick_up_loc, num_tips, reagent_type)\n func = ctx.pause if elution < num_centrifugations - 1 \\\n else ctx.comment\n func('Centrifuge all plates. Replace and resume when finished.')\n\n # track final used tip\n # void partially full tip column\n for tiprack in tips300:\n for col in tiprack.columns():\n for well in col:\n if not well.has_tip:\n for well in col:\n well.has_tip = False\n break\n tip_data = {\n str(rack.parent):\n {well.display_name.split(' ')[0]: well.has_tip\n for well in rack.wells()}\n for rack in tips300\n }\n if not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n with open(tip_file_path, 'w') as outfile:\n json.dump(tip_data, outfile)\n\n ctx._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 1.0)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/12213d/12213d.ot2.apiv2.py.json b/protoBuilds/12213d/12213d.ot2.apiv2.py.json index 621deb13da..af0bfb714c 100644 --- a/protoBuilds/12213d/12213d.ot2.apiv2.py.json +++ b/protoBuilds/12213d/12213d.ot2.apiv2.py.json @@ -81,5 +81,12 @@ "protocolName": "Ethanol Transfer with User", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json b/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json index 1acad9eb2f..3d49dad3ca 100644 --- a/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json +++ b/protoBuilds/13c0b8/13c0b8.ot2.apiv2.py.json @@ -1146,7 +1146,7 @@ ], "labware": [ { - "name": "96-well BRANDplate with V-bottom on Temperature Module GEN1 on 1", + "name": "96-well BRANDplate with V-bottom on Temperature Module on 1", "share": false, "slot": "1", "type": "brandplates_96_wellplate_360ul" @@ -1206,5 +1206,12 @@ "protocolName": "Non-Sterile Cell Analysis", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 1 lw 96-well BRANDplate with V-bottom on Temperature Module on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/13ea1e-part1/13ea1e-part1.ot2.apiv2.py.json b/protoBuilds/13ea1e-part1/13ea1e-part1.ot2.apiv2.py.json deleted file mode 100644 index 83c721bd2f..0000000000 --- a/protoBuilds/13ea1e-part1/13ea1e-part1.ot2.apiv2.py.json +++ /dev/null @@ -1,139 +0,0 @@ -{ - "content": "metadata = {\n 'protodestName': 'Extraction Prep with Kingfisher Flex Extractor',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protodest Request',\n 'apiLevel': '2.7'\n}\n\n\ndef run(ctx):\n\n [num_samp, mix_reps, p300_mount, p1000_mount] = get_values( # noqa: F821\n \"num_samp\", \"mix_reps\", \"p300_mount\", \"p1000_mount\")\n\n if not 0 <= num_samp <= 96:\n raise Exception(\"Enter a sample number between 1-96\")\n\n # load labware\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', '1')\n reservoir2 = ctx.load_labware('nest_12_reservoir_15ml', '2')\n npw4_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '3')\n sample_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '4')\n elution_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '5')\n ethanol_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '6')\n npw3_block = ctx.load_labware('nest_96_wellplate_2ml_deep', '7')\n\n tiprack300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['9', '8']]\n tiprack1000 = [ctx.load_labware('opentrons_96_tiprack_1000ul', '10')]\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11')\n\n # load instrument\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tiprack1000)\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=tiprack300)\n\n num_channels_per_pickup = 1 # (only pickup tips on front-most channel)\n tips_ordered = [\n tip for rack in tiprack300\n for row in rack.rows()[\n len(rack.rows())-num_channels_per_pickup::-1*num_channels_per_pickup]\n for tip in row]\n tip_count = 0\n\n def pick_up(pip):\n nonlocal tip_count\n pip.pick_up_tip(tips_ordered[tip_count])\n tip_count += 1\n\n # reagents\n mag_beads = reservoir.rows()[0][:4]\n ethanol = reservoir.rows()[0][4:8]\n npw3 = reservoir.rows()[0][8:12]\n npw4 = reservoir2.rows()[0][:4]\n\n proteinase_k = tuberack.rows()[0][:2]\n ntc = tuberack.rows()[1][0]\n hsc = tuberack.rows()[2][0]\n elution_buffer = tuberack.rows()[3][:4]\n\n # add controls\n p1000.pick_up_tip()\n p1000.transfer(400, ntc, sample_block.wells()[0], new_tip='never')\n p1000.drop_tip()\n\n p1000.pick_up_tip()\n p1000.transfer(400, hsc, sample_block.wells()[1], new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # add proteinase k and incubate for 15 minutes\n for s, d in zip(proteinase_k*num_samp, sample_block.wells()[:num_samp]):\n pick_up(p300)\n p300.aspirate(24, s)\n p300.dispense(24, d)\n p300.mix(mix_reps, 300, d)\n p300.drop_tip()\n ctx.delay(minutes=15)\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # add magnetic beads\n p1000.pick_up_tip()\n for mag_well, dest in zip(mag_beads*num_samp,\n sample_block.wells()[:num_samp]):\n p1000.mix(5, 1000, mag_well)\n p1000.transfer(595, mag_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # make npw3, npw4 and ethanol npw3_block\n # ethanol\n p1000.pick_up_tip()\n for ethanol_well, dest in zip(ethanol*num_samp,\n ethanol_block.wells()[:num_samp]):\n p1000.transfer(600, ethanol_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # npw3\n p1000.pick_up_tip()\n for npw3_well, dest in zip(npw3*num_samp,\n npw3_block.wells()[:num_samp]):\n p1000.transfer(600, npw3_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n ctx.comment('\\n\\n\\n\\n\\n')\n\n # npw4\n p1000.pick_up_tip()\n for npw4_well, dest in zip(npw4*num_samp, npw4_block.wells()[:num_samp]):\n p1000.transfer(600, npw4_well, dest.top(), new_tip='never')\n p1000.drop_tip()\n\n # elution buffer\n pick_up(p300)\n for elution_tubes, elution_well in zip(elution_buffer*num_samp,\n elution_block.wells()[:num_samp]):\n p300.aspirate(50, elution_tubes)\n p300.dispense(50, elution_well.top())\n p300.drop_tip()\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of wells (1-96)", - "name": "num_samp", - "type": "int" - }, - { - "default": 15, - "label": "Mix Repetitions to Re-suspend beads", - "name": "mix_reps", - "type": "int" - }, - { - "label": "P1000 Single Channel Mount (GEN2)", - "name": "p1000_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P300 Multi Channel Mount (GEN2)", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p1000_single_gen2" - } - ], - "labware": [ - { - "name": "NEST 12 Well Reservoir 15 mL on 1", - "share": false, - "slot": "1", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "NEST 12 Well Reservoir 15 mL on 2", - "share": false, - "slot": "2", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 3", - "share": false, - "slot": "3", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 4", - "share": false, - "slot": "4", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 5", - "share": false, - "slot": "5", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 6", - "share": false, - "slot": "6", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "NEST 96 Deepwell Plate 2mL on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons 96 Tip Rack 1000 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_1000ul" - }, - { - "name": "Opentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap on 11", - "share": false, - "slot": "11", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.7", - "author": "Rami Farawi ", - "protodestName": "Extraction Prep with Kingfisher Flex Extractor", - "source": "Custom Protodest Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/13ea1e-part1/README.json b/protoBuilds/13ea1e-part1/README.json deleted file mode 100644 index 022def7780..0000000000 --- a/protoBuilds/13ea1e-part1/README.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Sample Prep": [ - "Plate Filling" - ] - }, - "deck-setup": "\nDeck setup with samples loaded into all wells except A1 and B1.\n\n", - "description": "This protocol preps a sample plate as well as an ethanol, NPW3, NPW4, and elution buffer plate for further use in a Kingfisher Flex Extractor. Samples are pre-loaded onto the sample plate before the protocol begins. Mag beads are then added to sample, and after an incubation step, all other reagent plates are prepped. \nThe protocol is broken down into 3 main parts:\n Controls are added to sample plate\n Proteinase K is added to samples\n Magnetic Beads are added, incubate\n Sample blocks made\nNote: For all transfers between reservoirs/tubes to well plate, transfers will always iterate over all wells in the source. For example, magnetic beads will be transferred from A1 to plate, A2 to plate, A3 to plate, A4 to plate, A1 to plate, etc. Consequently, all reaction volumes should be split equally into respective wells as seen in the deck layout.\nExplanation of complex parameters below:\n Number of samples: Specify the number of populated wells (1-96, include controls) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n Mix repetitions to resuspend beads: Specify the amount of mix steps to re-suspend beads each time the pipette returns to the reservoir.\n P1000 Single Channel Mount (GEN2): Specify which mount the P1000 Single Channel pipette will be mounted.\n P300 Multi Channel Mount (GEN2): Specify which mount the P300 Multi Channel pipette will be mounted.\n", - "internal": "13ea1e", - "labware": "\nKingfisher 96 Well Plate\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\nOpentrons 4-in-1 tube rack with 1.5mL tubes\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Sample Prep\n\t* Plate Filling\n\n", - "deck-setup": "* Deck setup with samples loaded into all wells except A1 and B1.\n\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-26+at+11.24.55+AM.png)\n\n", - "description": "This protocol preps a sample plate as well as an ethanol, NPW3, NPW4, and elution buffer plate for further use in a Kingfisher Flex Extractor. Samples are pre-loaded onto the sample plate before the protocol begins. Mag beads are then added to sample, and after an incubation step, all other reagent plates are prepped. \n\nThe protocol is broken down into 3 main parts:\n* Controls are added to sample plate\n* Proteinase K is added to samples\n* Magnetic Beads are added, incubate\n* Sample blocks made\n\nNote: For all transfers between reservoirs/tubes to well plate, transfers will always iterate over all wells in the source. For example, magnetic beads will be transferred from A1 to plate, A2 to plate, A3 to plate, A4 to plate, A1 to plate, etc. Consequently, all reaction volumes should be split equally into respective wells as seen in the deck layout.\n\nExplanation of complex parameters below:\n* `Number of samples`: Specify the number of populated wells (1-96, include controls) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n* `Mix repetitions to resuspend beads`: Specify the amount of mix steps to re-suspend beads each time the pipette returns to the reservoir.\n* `P1000 Single Channel Mount (GEN2)`: Specify which mount the P1000 Single Channel pipette will be mounted.\n* `P300 Multi Channel Mount (GEN2)`: Specify which mount the P300 Multi Channel pipette will be mounted.\n---\n\n", - "internal": "13ea1e\n", - "labware": "* Kingfisher 96 Well Plate\n* [NEST 12-Well Reservoirs, 15 mL](https://shop.opentrons.com/collections/reservoirs/products/nest-12-well-reservoir-15-ml)\n* [Opentrons 20\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n* [Opentrons 300\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons 4-in-1 tube rack with 1.5mL tubes](https://shop.opentrons.com/collections/racks-and-adapters/products/tube-rack-set-1)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "partner": "[Partner Name](partner website link)\n\n", - "pipettes": "* [P1000 GEN2 Single Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/single-channel-electronic-pipette)\n* [P300 GEN2 Multi-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n\n\n---\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "protocol-steps": "1. Controls are added to sample plate\n2. Proteinase K is added to samples\n3. Magnetic beads are added to samples\n4. Incubate 15 minutes\n5. Ethanol block is prepped.\n6. NPW3 block is prepped.\n7. NPW4 block is prepped.\n10. Elution buffer block is prepped.\n\n", - "reagent-setup": "\n* Reservoir 1: Slot 1\n\n![reservoir 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-24+at+9.08.52+AM.png)\n* Reservoir 2: Slot 2\n\n![reservoir 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-24+at+9.14.53+AM.png)\n* Tube rack: Slot 11\n\n![tube rack](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/13ea1e/pt1/Screen+Shot+2021-05-24+at+9.09.13+AM.png)\n\n---\n\n", - "title": "Extraction Prep with Kingfisher Flex Extractor" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Partner Name", - "pipettes": "\nP1000 GEN2 Single Channel Pipette\nP300 GEN2 Multi-Channel Pipette\n\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "protocol-steps": "\nControls are added to sample plate\nProteinase K is added to samples\nMagnetic beads are added to samples\nIncubate 15 minutes\nEthanol block is prepped.\nNPW3 block is prepped.\nNPW4 block is prepped.\nElution buffer block is prepped.\n", - "reagent-setup": "\nReservoir 1: Slot 1\n\n\n* Reservoir 2: Slot 2\n\n* Tube rack: Slot 11\n\n", - "title": "Extraction Prep with Kingfisher Flex Extractor" -} \ No newline at end of file diff --git a/protoBuilds/13ea1e-part1/metadata.json b/protoBuilds/13ea1e-part1/metadata.json deleted file mode 100644 index f9c279f16e..0000000000 --- a/protoBuilds/13ea1e-part1/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "13ea1e-part1.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/13ea1e-part1", - "slug": "13ea1e-part1", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json b/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json index 88926a10c3..c194bf9097 100644 --- a/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json +++ b/protoBuilds/13fd88/13fd88.ot2.apiv2.py.json @@ -2341,5 +2341,12 @@ "protocolName": "Protein Purification with Magnetic NI Resin", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw Greiner BioOne 96 Well Microplate on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json b/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json index 5e7e4cdeeb..a0f4528fc8 100644 --- a/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json +++ b/protoBuilds/141a1a/141a1a.ot2.apiv2.py.json @@ -4825,5 +4825,12 @@ "protocolName": "Cell-Free Gene Expression (TXTL) Test", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json b/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json index 853d5ac913..1c7e3e790e 100644 --- a/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json +++ b/protoBuilds/1440ad/1440ad.ot2.apiv2.py.json @@ -225,5 +225,24 @@ "protocolName": "Extraction with Mag-Bind TotalPure NGS kit", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw MAG PLATE on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw SAMPLES on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 6 lw COOL REAGENTS on Temperature Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/14b685/14b685.ot2.apiv2.py.json b/protoBuilds/14b685/14b685.ot2.apiv2.py.json index 4c634f51b8..3ab0c65e69 100644 --- a/protoBuilds/14b685/14b685.ot2.apiv2.py.json +++ b/protoBuilds/14b685/14b685.ot2.apiv2.py.json @@ -150,5 +150,12 @@ "protocolName": "PCR Clean-Up for Illumina 16S", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 10 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json b/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json index 17b305c6a3..8ecd36d51d 100644 --- a/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json +++ b/protoBuilds/1577-v2/custom_chip_PCR_prep.ot2.apiv2.py.json @@ -1523,7 +1523,7 @@ "type": "opentrons_96_tiprack_300ul" }, { - "name": "2ml Eppendorf snapcap reagent tubes on Temperature Module GEN1 on 6", + "name": "2ml Eppendorf snapcap reagent tubes on Temperature Module on 6", "share": false, "slot": "6", "type": "opentrons_24_aluminumblock_nest_2ml_snapcap" @@ -1547,5 +1547,18 @@ "protocolName": "Custom Chip PCR Preparation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw thermocycler plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 6 lw 2ml Eppendorf snapcap reagent tubes on Temperature Module on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json b/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json index bfa77b32a8..2f3a851f71 100644 --- a/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json +++ b/protoBuilds/1649b1/1649b1.ot2.apiv2.py.json @@ -1328,5 +1328,18 @@ "description": "Custom Protocol Request", "protocolName": "LGC Sbeadex Plant Maxi Kit Nucleic Acid Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json b/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json index fa032290dc..89200db461 100644 --- a/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json +++ b/protoBuilds/18d6a1/18d6a1.ot2.apiv2.py.json @@ -1315,5 +1315,12 @@ "protocolName": "MGI Easy Nucleic Acid Extraction Kit", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 10 lw Extraction Plate on Magnetic Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/19313a/19313a.ot2.apiv2.py.json b/protoBuilds/19313a/19313a.ot2.apiv2.py.json index 6ed0ee8300..7a4b114dc8 100644 --- a/protoBuilds/19313a/19313a.ot2.apiv2.py.json +++ b/protoBuilds/19313a/19313a.ot2.apiv2.py.json @@ -1386,5 +1386,18 @@ "protocolName": "RNA Extraction with Magnetic Life", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw Mag Plate on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Temperature tuberack on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json b/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json index de0b2fd510..b1b75c4153 100644 --- a/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json +++ b/protoBuilds/19fc32/19fc32.ot2.apiv2.py.json @@ -44,7 +44,7 @@ "type": "corning_384_wellplate_112ul_flat" }, { - "name": "Mag Plate on Magnetic Module GEN1 on 4", + "name": "Mag Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -98,5 +98,12 @@ "protocolName": "Library Prep Clean Up", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Mag Plate on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json b/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json index e92bc37f47..7f3081fe10 100644 --- a/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/1a2343/pcr_prep.ot2.apiv2.py.json @@ -63,7 +63,7 @@ "type": "opentrons_96_tiprack_20ul" }, { - "name": "reagent plate on Temperature Module GEN1 on 4", + "name": "reagent plate on Temperature Module on 4", "share": false, "slot": "4", "type": "usascientific_96_wellplate_2.4ml_deep" @@ -113,7 +113,7 @@ "type": "thermocycler" }, { - "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw reagent plate on Temperature Module GEN1 on 4", + "name": "TemperatureModuleContext at Temperature Module on 4 lw reagent plate on Temperature Module on 4", "share": false, "slot": "4", "type": "tempdeck" diff --git a/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json b/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json index b61d3b8c10..67dc2e2c67 100644 --- a/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json +++ b/protoBuilds/1bcd67/normalization.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Normalization',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n ] = get_values( # noqa: F821\n 'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n 'final_vol')\n\n # labware\n dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n 'deepwell plate')\n final_dilution_plates = [\n ctx.load_labware('nunc_96_wellplate_500ul', slot,\n f'final dilution plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n '9', 'diluent').wells()[0]\n tipracks1000 = [\n ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n for slot in ['10']]\n tipracks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['7']]\n\n # pipettes\n if p1000_mount == m300_mount:\n raise Exception('Pipette mounts cannot match.')\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tipracks1000)\n p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for rack in tipracks300[::-1]\n for col in rack.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n def extract_well_name(well_obj):\n return well_obj.display_name.split(' ')[0]\n\n def custom_transfer(vol, source, dest, pip=p300):\n num_trans = math.ceil(vol/pip.max_volume)\n vol_per_trans = vol/num_trans\n for n in range(num_trans):\n pip.aspirate(vol_per_trans, source)\n pip.dispense(vol_per_trans, dest)\n\n def determine_dil(col):\n rows = 'ABCDEFGH'\n col = dw_plate.rows()[0].index(col)\n dict = [dict1, dict2, dict3][col % 3]\n wells_to_check = [row + str(col+1) for row in rows]\n for well in wells_to_check:\n if dict[well]:\n return True\n return False\n\n # pre-parse `None` to `null`\n dil_json_1 = dil_json_1.replace('None', 'null')\n dil_json_2 = dil_json_2.replace('None', 'null')\n dil_json_3 = dil_json_3.replace('None', 'null')\n\n # read .json files as dictionaries\n dict1 = json.loads(dil_json_1)\n dict2 = json.loads(dil_json_2)\n dict3 = json.loads(dil_json_3)\n\n map_dil_wells = {\n well_set[0]: {\n well_set[0]: dict1[extract_well_name(well_set[0])],\n well_set[1]: dict2[extract_well_name(well_set[1])],\n well_set[2]: dict3[extract_well_name(well_set[2])]\n }\n for well_set in [\n row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n }\n\n final_locations = []\n for key, dict in map_dil_wells.items():\n final_well = None\n for well, vol in dict.items():\n if vol:\n final_well = well\n final_locations.append(final_well)\n\n # pre-add diluent\n pickup_p300('multi')\n for col in dw_plate.rows()[0]:\n if determine_dil(col):\n for _ in range(4): # 4x 200ul = 800ul\n p300.transfer(200, diluent, col, new_tip='never')\n p300.drop_tip()\n\n # prompt user to transfer neat sample\n display_wells = [\n well for well, vol in dict1.items() if vol]\n display_vols = [\n round(vol, 2) for vol in dict1.values() if vol]\n sample_str = '\\n'.join([\n f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n for display_well, display_vol in zip(display_wells, display_vols)])\n ctx.pause(msg=sample_str)\n\n # perform dilutions\n for set in map_dil_wells.values():\n for i, (well, vol) in enumerate(set.items()):\n if i > 0 and vol: # neat is manually added\n if vol <= 200:\n pip = p300\n pickup_p300('single')\n else:\n pip = p1000\n p1000.pick_up_tip()\n custom_transfer(vol, list(set.keys())[i-1], well, pip)\n pip.mix(5, 200, well)\n pip.drop_tip()\n\n # final transfer\n final_targets = [\n well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n for source, dest in zip(final_locations, final_targets):\n if source:\n col = int(source.display_name.split(' ')[0][1:])\n if col % 3 == 1:\n pip.mix(5, 200, source)\n p1000.transfer(final_vol, source, dest)\n", + "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Normalization',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n ] = get_values( # noqa: F821\n 'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n 'final_vol')\n\n # labware\n dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n 'deepwell plate')\n final_dilution_plates = [\n ctx.load_labware('nunc_96_wellplate_500ul', slot,\n f'final dilution plate {i+1}')\n for i, slot in enumerate(['4', '5', '6'])]\n diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n '9', 'diluent').wells()[0]\n tipracks1000 = [\n ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n for slot in ['10']]\n tipracks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['7']]\n\n # pipettes\n if p1000_mount == m300_mount:\n raise Exception('Pipette mounts cannot match.')\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=tipracks1000)\n p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for rack in tipracks300[::-1]\n for col in rack.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n def extract_well_name(well_obj):\n return well_obj.display_name.split(' ')[0]\n\n def custom_transfer(vol, source, dest, pip=p300):\n num_trans = math.ceil(vol/pip.max_volume)\n vol_per_trans = vol/num_trans\n for n in range(num_trans):\n pip.aspirate(vol_per_trans, source)\n pip.dispense(vol_per_trans, dest)\n\n def determine_dil(col):\n rows = 'ABCDEFGH'\n col = dw_plate.rows()[0].index(col)\n dict = [dict1, dict2, dict3][col % 3]\n wells_to_check = [row + str(col+1) for row in rows]\n for well in wells_to_check:\n if dict[well]:\n return True\n return False\n\n # pre-parse `None` to `null`\n dil_json_1 = dil_json_1.replace('None', 'null')\n dil_json_2 = dil_json_2.replace('None', 'null')\n dil_json_3 = dil_json_3.replace('None', 'null')\n\n # read .json files as dictionaries\n dict1 = json.loads(dil_json_1)\n dict2 = json.loads(dil_json_2)\n dict3 = json.loads(dil_json_3)\n\n map_dil_wells = {\n well_set[0]: {\n well_set[0]: dict1[extract_well_name(well_set[0])],\n well_set[1]: dict2[extract_well_name(well_set[1])],\n well_set[2]: dict3[extract_well_name(well_set[2])]\n }\n for well_set in [\n row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n }\n\n final_locations = []\n for key, dict in map_dil_wells.items():\n final_well = None\n for well, vol in dict.items():\n if vol:\n final_well = well\n final_locations.append(final_well)\n\n # pre-add diluent\n pickup_p300('multi')\n for col in dw_plate.rows()[0]:\n if determine_dil(col):\n for _ in range(4): # 4x 200ul = 800ul\n p300.transfer(200, diluent, col, new_tip='never')\n p300.drop_tip()\n\n # prompt user to transfer neat sample\n display_wells = [\n well for well, vol in dict1.items() if vol]\n display_vols = [\n round(vol, 2) for vol in dict1.values() if vol]\n sample_str = '\\n'.join([\n f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n for display_well, display_vol in zip(display_wells, display_vols)])\n ctx.pause(msg=sample_str)\n\n # perform dilutions\n for set in map_dil_wells.values():\n for i, (well, vol) in enumerate(set.items()):\n if i > 0 and vol: # neat is manually added\n if vol <= 200:\n pip = p300\n pickup_p300('single')\n else:\n pip = p1000\n p1000.pick_up_tip()\n custom_transfer(vol, list(set.keys())[i-1], well, pip)\n pip.mix(5, 200, well)\n pip.drop_tip()\n\n # final transfer\n final_targets = [\n well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n for source, dest in zip(final_locations, final_targets):\n if source:\n col = int(source.display_name.split(' ')[0][1:])\n if col % 3 == 1:\n pip.mix(5, 200, source)\n p1000.transfer(final_vol, source, dest)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json b/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json index 5087349c80..d3fd2533eb 100644 --- a/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json +++ b/protoBuilds/1ccd23-station-B/extraction.ot2.apiv2.py.json @@ -205,5 +205,18 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json b/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json index d9653be3bc..0a5f68f3cc 100644 --- a/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json +++ b/protoBuilds/1eeb01/1eeb01.ot2.apiv2.py.json @@ -122,5 +122,18 @@ "protocolName": "Nucleic Acid Extraction Using 1.5mL Tubes", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 10 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 7 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json b/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json index 79bd7d7ce0..2a14552021 100644 --- a/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json +++ b/protoBuilds/1f96ca-part-2/1f96ca-part-2.ot2.apiv2.py.json @@ -149,5 +149,12 @@ "author": "Steve Plonk ", "protocolName": "NGS Library Prep: KAPA Hyper Plus 96rx, cat#07962428001,\n ROCHE - part 2 of 2: post-PCR clean up and pooling" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json b/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json index fa5aee0029..2421aa72a7 100644 --- a/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json +++ b/protoBuilds/1f96ca/1f96ca.ot2.apiv2.py.json @@ -2492,5 +2492,18 @@ "author": "Steve Plonk ", "protocolName": "NGS Library Prep: KAPA Hyper Plus 96rx, cat#07962428001,\n ROCHE - part 1 of 2" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/203136/203136.ot2.apiv2.py.json b/protoBuilds/203136/203136.ot2.apiv2.py.json index 70f5743293..b0ca0af608 100644 --- a/protoBuilds/203136/203136.ot2.apiv2.py.json +++ b/protoBuilds/203136/203136.ot2.apiv2.py.json @@ -69,7 +69,7 @@ "type": "opentrons_96_filtertiprack_200ul" }, { - "name": "Deep Well Plate on Magnetic Module GEN1 on 4", + "name": "Deep Well Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "usascientific_96_wellplate_2.4ml_deep" @@ -129,5 +129,12 @@ "protocolName": "Purification of Genomic DNA", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Deep Well Plate on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json b/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json index 47ff46c99f..07dac4eff2 100644 --- a/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json +++ b/protoBuilds/211fe1/mass_spec_sample_prep.ot2.apiv2.py.json @@ -80,5 +80,12 @@ "protocolName": "Mass Spec Sample Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json b/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json index 10e9bfbbdd..34986fd524 100644 --- a/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json +++ b/protoBuilds/21e4d8-pt2/21e4d8-pt2.ot2.apiv2.py.json @@ -1504,5 +1504,12 @@ "protocolName": "Twist Library Prep || Part 2: Ligate Adapters", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 10 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json b/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json index 7f2d5f493a..fe21fb7568 100644 --- a/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json +++ b/protoBuilds/21e4d8-pt3/21e4d8-pt3.ot2.apiv2.py.json @@ -1504,5 +1504,12 @@ "protocolName": "Twist Library Prep || Part 3: PCR Amplification", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 10 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json b/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json index c7599dfd27..eb23726ffa 100644 --- a/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json +++ b/protoBuilds/245eb2/245eb2.ot2.apiv2.py.json @@ -1240,5 +1240,12 @@ "protocolName": "Nucleic Acid Extraction", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw Axygen 96 Well Plate 300 \u00b5L on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json b/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json index 48990b5ef2..a3e4ab71e3 100644 --- a/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/269b21/pcr_prep.ot2.apiv2.py.json @@ -5513,7 +5513,7 @@ "type": "genmate_96_aluminumblock_20ul" }, { - "name": "Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN1 on 4", + "name": "Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module on 4", "share": false, "slot": "4", "type": "opentrons_24_aluminumblock_nest_1.5ml_snapcap" @@ -5543,5 +5543,12 @@ "protocolName": "PCR Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/280ea4/generic_station_C.ot2.apiv2.py.json b/protoBuilds/280ea4/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index 8b52b4cc05..0000000000 --- a/protoBuilds/280ea4/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,1280 +0,0 @@ -{ - "content": "from opentrons import protocol_api\nimport json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n [num_samples, assay, prepare_mastermix, p300_mount,\n tip_track] = get_values( # noqa: F821\n 'num_samples', 'assay', 'prepare_mastermix',\n 'p300_mount', 'tip_track')\n\n # check source (elution) labware type\n source_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '1', 'DNA source plate')\n tips300 = [\n ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['5', '6', '8', '9']]\n tips20 = []\n tempdeck = ctx.load_module('Temperature Module Gen2', '7')\n pcr_plate = tempdeck.load_labware('biorad_96_aluminumblock_200ul',\n 'PCR strips')\n tempdeck.set_temperature(4)\n tube_block = ctx.load_labware(\n 'opentrons_24_aluminumblock_nest_2ml_screwcap', '3',\n '2ml screw tube aluminum block for mastermix + reagents')\n\n # pipette\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n m20_mount = 'left' if p300_mount == 'right' else 'right'\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount)\n\n # setup up sample sources and destinations\n sources = source_plate.wells()[:num_samples]\n sample_dests = pcr_plate.wells()[:num_samples]\n\n tip_log = {'count': {}}\n folder_path = '/data/C'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip_log['count'][m20] = data['tips20']\n else:\n tip_log['count'][m20] = 0\n if 'tips300' in data:\n tip_log['count'][p300] = data['tips300']\n else:\n tip_log['count'][p300] = 0\n else:\n tip_log['count'] = {m20: 0, p300: 0}\n else:\n tip_log['count'] = {m20: 0, p300: 0}\n\n tip_log['tips'] = {\n m20: [tip for rack in tips20 for tip in rack.rows()[0]],\n p300: [tip for rack in tips300 for tip in rack.wells()]\n }\n tip_log['max'] = {\n pip: len(tip_log['tips'][pip])\n for pip in [m20, p300]\n }\n\n def pick_up(pip):\n nonlocal tip_log\n if tip_log['count'][pip] == tip_log['max'][pip]:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log['count'][pip] = 0\n pip.pick_up_tip(tip_log['tips'][pip][tip_log['count'][pip]])\n tip_log['count'][pip] += 1\n\n \"\"\" mastermix component maps \"\"\"\n mm_tubes = tube_block.wells()[:2]\n [mmx, enzyme, primer1, primer2, primer3, primer4, primer5, primer6, probe,\n other, nfh2o] = tube_block.wells()[2:13]\n mm_map = {\n '1': {\n 'sample_vol': 5,\n 'mm_vol': 50,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, enzyme, primer1, primer2, primer3, primer4, primer5,\n primer6, nfh2o],\n [25, 2, 2, 2, 2, 2, 2, 2, 11])\n }\n },\n '2': {\n 'sample_vol': 5,\n 'mm_vol': 50,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, enzyme, primer1, primer2, nfh2o],\n [25, 2, 1, 1, 21])\n }\n },\n '3': {\n 'sample_vol': 5,\n 'mm_vol': 22.5,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, primer1, primer2, nfh2o],\n [12.5, 1.25, 1.25, 8.5])\n }\n },\n '4': {\n 'sample_vol': 5,\n 'mm_vol': 17,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, enzyme, primer1, primer2, primer3, probe, nfh2o],\n [12.5, 1, 0.25, 0.25, 0.25, 0.25, 2.5])\n }\n },\n '5': {\n 'sample_vol': 5,\n 'mm_vol': 20,\n 'components': {\n tube: vol for tube, vol in zip(\n [mmx, primer1, primer2, probe, other, nfh2o],\n [6.25, 0.1, 0.2, 0.5, 1, 11.95])\n }\n }\n }\n mm_dict = mm_map[assay]\n sample_vol = mm_dict['sample_vol']\n mm_vol = mm_dict['mm_vol']\n\n vol_overage = 1.2 if num_samples > 48 else 1.1\n total_mm_vol = mm_vol*(num_samples+2)*vol_overage\n # translate total mastermix volume to starting height\n r = mm_tubes[0].diameter/2\n mm_heights = {\n tube: total_mm_vol/(math.pi*(r**2)) - 5\n for tube in mm_tubes\n }\n\n def h_track(vol, tube):\n dh = 1.1*vol/(math.pi*(r**2)) # compensate for 10% theoretical v loss\n h = mm_heights[tube]\n h = h - dh if h - dh > 2 else 2 # stop at 2mm\n mm_heights[tube] = h\n return tube.bottom(mm_heights[tube])\n\n def p300_transfer(vol, source, dest):\n if vol < 20:\n p300.air_gap(20-vol)\n p300.aspirate(vol, source)\n p300.dispense(vol, dest)\n p300.dispense(p300.current_volume, dest.top())\n else:\n num_trans = math.ceil(vol/260)\n vol_per_trans = vol/num_trans\n for _ in range(num_trans):\n p300.air_gap(20)\n p300.aspirate(vol_per_trans, source)\n ctx.delay(seconds=2)\n p300.touch_tip(source)\n p300.air_gap(20)\n p300.dispense(20, dest.top()) # void air gap\n p300.dispense(vol_per_trans, dest.bottom(2))\n p300.dispense(20, dest.top()) # void pre-loaded air gap\n # p300.blow_out(mm_tube.top())\n p300.touch_tip(dest)\n\n if prepare_mastermix:\n p300.flow_rate.aspirate = 15\n p300.flow_rate.dispense = 30\n vol_overage = 1.2 if num_samples > 48 else 1.1\n if mm_dict['mm_vol']*num_samples*vol_overage > 1700:\n num_mm_tubes = 2\n else:\n num_mm_tubes = 1\n for i, (tube, vol) in enumerate(mm_dict['components'].items()):\n comp_vol = vol*num_samples*vol_overage/num_mm_tubes\n pick_up(p300)\n for mm_tube in mm_tubes[:num_mm_tubes]:\n p300_transfer(comp_vol, tube, mm_tube)\n if i < len(mm_dict['components'].items()) - 1:\n p300.drop_tip()\n mm_total_vol_per_tube = mm_vol*(num_samples)*vol_overage/num_mm_tubes\n if not p300.hw_pipette['has_tip']:\n pick_up(p300)\n if mm_total_vol_per_tube / 2 <= 300:\n mix_vol = mm_total_vol_per_tube / 2\n else:\n mix_vol = 300\n for tube in mm_tubes[:num_mm_tubes]:\n if num_samples > 48:\n mix_loc = mm_tube.bottom(20)\n else:\n mix_loc = mm_tube.bottom(5)\n p300.mix(7, mix_vol, mix_loc)\n # p300.blow_out(mm_tube.top())\n p300.touch_tip()\n\n # transfer mastermix to plate\n if num_mm_tubes == 1:\n sample_dest_sets = [sample_dests]\n else:\n split_ind = math.ceil(num_samples/2)\n sample_dest_sets = [sample_dests[:split_ind], sample_dests[split_ind:]]\n for mm_tube, dest_set in zip(mm_tubes, sample_dest_sets):\n p300.distribute(mm_dict['mm_vol'], mm_tube, dest_set,\n new_tip='never')\n p300.drop_tip()\n\n # transfer samples to corresponding locations\n for s, d in zip(sources, sample_dests):\n pick_up(p300)\n p300_transfer(sample_vol, s, d)\n p300.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {\n 'tips20': tip_log['count'][m20],\n 'tips300': tip_log['count'][p300]\n }\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Bio-Rad", - "brandId": [ - "TBS0201" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 20 - }, - "groups": [ - { - "metadata": { - "displayCategory": "tubeRack", - "wellBottomShape": "flat" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Bio-Rad 96 Aluminum Block 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "biorad_96_aluminumblock_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.25, - "z": 5 - }, - "A10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 74.25, - "z": 5 - }, - "A11": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 74.25, - "z": 5 - }, - "A12": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 74.25, - "z": 5 - }, - "A2": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 74.25, - "z": 5 - }, - "A3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 74.25, - "z": 5 - }, - "A4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 74.25, - "z": 5 - }, - "A5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 74.25, - "z": 5 - }, - "A6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 74.25, - "z": 5 - }, - "A7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 74.25, - "z": 5 - }, - "A8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 74.25, - "z": 5 - }, - "A9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 74.25, - "z": 5 - }, - "B1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 65.25, - "z": 5 - }, - "B10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 65.25, - "z": 5 - }, - "B11": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 65.25, - "z": 5 - }, - "B12": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 65.25, - "z": 5 - }, - "B2": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 65.25, - "z": 5 - }, - "B3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 65.25, - "z": 5 - }, - "B4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 65.25, - "z": 5 - }, - "B5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 65.25, - "z": 5 - }, - "B6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 65.25, - "z": 5 - }, - "B7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 65.25, - "z": 5 - }, - "B8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 65.25, - "z": 5 - }, - "B9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 65.25, - "z": 5 - }, - "C1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 56.25, - "z": 5 - }, - "C10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 56.25, - "z": 5 - }, - "C11": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 56.25, - "z": 5 - }, - "C12": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 56.25, - "z": 5 - }, - "C2": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 56.25, - "z": 5 - }, - "C3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 56.25, - "z": 5 - }, - "C4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 56.25, - "z": 5 - }, - "C5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 56.25, - "z": 5 - }, - "C6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 56.25, - "z": 5 - }, - "C7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 56.25, - "z": 5 - }, - "C8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 56.25, - "z": 5 - }, - "C9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 56.25, - "z": 5 - }, - "D1": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 47.25, - "z": 5 - }, - "D10": { - "depth": 15, - "diameter": 6, - "shape": "circular", - 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11.25, - "z": 5 - }, - "H3": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 11.25, - "z": 5 - }, - "H4": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 11.25, - "z": 5 - }, - "H5": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 11.25, - "z": 5 - }, - "H6": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 11.25, - "z": 5 - }, - "H7": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 11.25, - "z": 5 - }, - "H8": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 11.25, - "z": 5 - }, - "H9": { - "depth": 15, - "diameter": 6, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 11.25, - "z": 5 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "Number of Samples", - "name": "num_samples", - "type": "int" - }, - { - "label": "assay type (see image above for reference)", - "name": "assay", - "options": [ - { - "label": "1", - "value": "1" - }, - { - "label": "2", - "value": "2" - }, - { - "label": "3", - "value": "3" - }, - { - "label": "4", - "value": "4" - }, - { - "label": "5", - "value": "5" - } - ], - "type": "dropDown" - }, - { - "label": "prepare mastermix", - "name": "prepare_mastermix", - "options": [ - { - "label": "yes", - "value": true - }, - { - "label": "no", - "value": false - } - ], - "type": "dropDown" - }, - { - "label": "P300 single-channel pipette GEN2 mount", - "name": "p300_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "DNA source plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "2ml screw tube aluminum block for mastermix + reagents on 3", - "share": false, - "slot": "3", - "type": "opentrons_24_aluminumblock_nest_2ml_screwcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "PCR strips on Temperature Module GEN2 on 7", - "share": false, - "slot": "7", - "type": "biorad_96_aluminumblock_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.9", - "author": "Nick ", - "protocolName": "PCR Prep", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json b/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json index 05f51d1594..847e694846 100644 --- a/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json +++ b/protoBuilds/2905a4/2905a4.ot2.apiv2.py.json @@ -2381,5 +2381,24 @@ "description": "Custom Protocol Request", "protocolName": "RNA Purification with Magnetic Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Origin RNA Sample Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 6 lw Recipient Cooled Plate on Temperature Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw Mag Deck Plate on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/295c73/295c73.ot2.apiv2.py.json b/protoBuilds/295c73/295c73.ot2.apiv2.py.json index 90463a474e..c89e96f4f4 100644 --- a/protoBuilds/295c73/295c73.ot2.apiv2.py.json +++ b/protoBuilds/295c73/295c73.ot2.apiv2.py.json @@ -86,5 +86,24 @@ "author": "Steve Plonk ", "protocolName": "swiftbiosci.com accel-amplicon-plus-egfr-pathway-panel" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 6 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json b/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json index eb6a2cac3b..d515e10971 100644 --- a/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json +++ b/protoBuilds/29effa-mastermix/29effa-mastermix.ot2.apiv2.py.json @@ -62,5 +62,12 @@ "protocolName": "Lyra Direct Covid-19 Mastermix Distribution", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json b/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json index 91598f77bf..8d6ca8a833 100644 --- a/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json +++ b/protoBuilds/2a370c/2a370c.ot2.apiv2.py.json @@ -117,5 +117,12 @@ "description": "Custom Protocol Request", "protocolName": "Omega Mag-Bind Bacterial DNA 96 Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2aee74-2/README.json b/protoBuilds/2aee74-2/README.json deleted file mode 100644 index 0eace6f499..0000000000 --- a/protoBuilds/2aee74-2/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Proteins & Proteomics": [ - "Olink Target 96" - ] - }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n green on reservoir (slot 5): 10562.0\u00b5l extension mix\n blue on incubation plate (slot 2): samples\n", - "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 2/3: Extension for the Olink Target 96 protocol for protein biomarker discovery.\n", - "internal": "2aee74", - "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoir, 15 mL\nOpentrons Filter Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Proteins & Proteomics\n\t* Olink Target 96\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/deck2.png)\nNote: all volumes for 96 samples (including controls)\n* green on reservoir (slot 5): 10562.0\u00b5l extension mix\n* blue on incubation plate (slot 2): samples\n\n---\n\n", - "description": "\nLinks:\n* [Part 1: Incubation](./2aee74)\n* [Part 2: Extension](./2aee74-2)\n* [Part 3: Detection](./2aee74-3)\n\nThis protocol accomplishes part 2/3: Extension for the [Olink Target 96 protocol](https://www.olink.com/products-services/target/) for protein biomarker discovery.\n\n---\n\n", - "internal": "2aee74\n", - "labware": "* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [NEST 12-Well Reservoir, 15 mL](https://shop.opentrons.com/collections/verified-labware/products/nest-12-well-reservoir-15-ml)\n* [Opentrons Filter Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 8-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Olink Target 96](https://www.olink.com/products-services/target/)\n\n---\n\n", - "title": "Olink Target 96 Part 2/3: Extension" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 8-Channel Electronic Pipette (GEN2)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Olink Target 96" - ], - "title": "Olink Target 96 Part 2/3: Extension" -} diff --git a/protoBuilds/2aee74-2/metadata.json b/protoBuilds/2aee74-2/metadata.json deleted file mode 100644 index ff28ad11ff..0000000000 --- a/protoBuilds/2aee74-2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "olink.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/2aee74-2", - "slug": "2aee74-2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/2aee74-2/olink.ot2.apiv2.py.json b/protoBuilds/2aee74-2/olink.ot2.apiv2.py.json deleted file mode 100644 index 3caeaeb19b..0000000000 --- a/protoBuilds/2aee74-2/olink.ot2.apiv2.py.json +++ /dev/null @@ -1,1208 +0,0 @@ -{ - "content": "import math\n\nmetadata = {\n 'protocolName': 'Olink Target 96 Part 2/3: Extension',\n 'author': 'Nick ',\n 'description': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, plate_type, m300_mount = get_values( # noqa: F821\n 'num_samples', 'plate_type', 'm300_mount')\n\n if not 1 <= num_samples <= 96:\n raise Exception('Invalid number of samples (1-96)')\n\n ext_mix = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5',\n 'reservoir for extension mix (channel 1)').wells()[0]\n inc_plate = ctx.load_labware(plate_type, '2', 'incubation plate')\n tipracks300 = [ctx.load_labware('opentrons_96_tiprack_300ul', '6')]\n\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tipracks300)\n\n num_cols = math.ceil(num_samples/8)\n\n ctx.comment('Bring the Incubation Plate to room temperature, spin at 400 x \\\ng for 1 min. Preheat the PCR machine.')\n ctx.comment('Vortex the Extension mix and pour into a multi-channel \\\npipette reservoir.')\n\n m300.pick_up_tip()\n m300.aspirate(20, ext_mix)\n for col in inc_plate.rows()[0][:num_cols]:\n m300.aspirate(96, ext_mix)\n m300.dispense(96, col.top(-1))\n m300.drop_tip()\n\n ctx.comment('Seal the plate with an adhesive plastic film, vortex \\\nthoroughly ensuring that all wells are mixed, and spin down.')\n ctx.comment('Place the Incubation Plate in the thermal cycler, and start \\\nthe PEA program (50\u00b0C 20 min, 95\u00b0C 5 min (95\u00b0C 30s, 54\u00b0C 1 min, 60\u00b0C 1 min) \\\nx17, 10\u00b0C hold).')\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Generic", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 25 - }, - "groups": [ - { - "metadata": { - "displayCategory": "wellPlate", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Generic 96 Aluminum Block 350 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "generic_96_aluminumblock_350ul", - 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"y": 20.25, - "z": 3 - }, - "G10": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 95.38, - "y": 20.25, - "z": 3 - }, - "G11": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 104.38, - "y": 20.25, - "z": 3 - }, - "G12": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 113.38, - "y": 20.25, - "z": 3 - }, - "G2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 20.25, - "z": 3 - }, - "G3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 20.25, - "z": 3 - }, - "G4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 20.25, - "z": 3 - }, - "G5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 20.25, - "z": 3 - }, - "G6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 20.25, - "z": 3 - }, - "G7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 20.25, - "z": 3 - }, - "G8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 20.25, - "z": 3 - }, - "G9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 20.25, - "z": 3 - }, - "H1": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 14.38, - "y": 11.25, - "z": 3 - }, - "H10": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 95.38, - "y": 11.25, - "z": 3 - }, - "H11": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 104.38, - "y": 11.25, - "z": 3 - }, - "H12": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 113.38, - "y": 11.25, - "z": 3 - }, - "H2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 11.25, - "z": 3 - }, - "H3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 11.25, - "z": 3 - }, - "H4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 11.25, - "z": 3 - }, - "H5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 11.25, - "z": 3 - }, - "H6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 11.25, - "z": 3 - }, - "H7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 11.25, - "z": 3 - }, - "H8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 11.25, - "z": 3 - }, - "H9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 11.25, - "z": 3 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "number of samples (1-96)", - "name": "num_samples", - "type": "int" - }, - { - "label": "PCR plate type", - "name": "plate_type", - "options": [ - { - "label": "NEST", - "value": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "label": "Custom on aluminum block", - "value": "generic_96_aluminumblock_350ul" - } - ], - "type": "dropDown" - }, - { - "label": "P300 multi-channel pipette mount", - "name": "m300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - } - ], - "labware": [ - { - "name": "incubation plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "reservoir for extension mix (channel 1) on 5", - "share": false, - "slot": "5", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Tip Rack 300 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_300ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "description": "Custom Protocol Request", - "protocolName": "Olink Target 96 Part 2/3: Extension" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2aee74-3/README.json b/protoBuilds/2aee74-3/README.json deleted file mode 100644 index b902102302..0000000000 --- a/protoBuilds/2aee74-3/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Proteins & Proteomics": [ - "Olink Target 96" - ] - }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n purple on primer plate (slot 1): samples\n blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n", - "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 3/3: Detection for the Olink Target 96 protocol for protein biomarker discovery. Primers are transferred to the left 96 wells of the Fluidigm detection plate, and samples are transferred to the right 96 wells. The transfer mapping for these plates is shown in the following images:\n\n\n", - "internal": "2aee74", - "labware": "\nFluidigm 96.96 Dynamic Array\u2122 IFC for Gene Expression\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Proteins & Proteomics\n\t* Olink Target 96\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/deck3-5.png)\nNote: all volumes for 96 samples (including controls)\n* purple on primer plate (slot 1): samples\n* blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n\n---\n\n", - "description": "\nLinks:\n* [Part 1: Incubation](./2aee74)\n* [Part 2: Extension](./2aee74-2)\n* [Part 3: Detection](./2aee74-3)\n\nThis protocol accomplishes part 3/3: Detection for the [Olink Target 96 protocol](https://www.olink.com/products-services/target/) for protein biomarker discovery. Primers are transferred to the left 96 wells of the Fluidigm detection plate, and samples are transferred to the right 96 wells. The transfer mapping for these plates is shown in the following images: \n![scheme1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/scheme1-2.png)\n![scheme2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/scheme2-2.png)\n\n---\n\n", - "internal": "2aee74\n", - "labware": "* [Fluidigm 96.96 Dynamic Array\u2122 IFC for Gene Expression](https://store.fluidigm.com/Genomics/ApplicationsGenomics/GeneExpression/96-96%20Dynamic%20Array%E2%84%A2%20IFC%20for%20Gene%20Expression)\n* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 4-in-1 Tube Rack Set](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Screwcap Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-1-5-ml-sample-vial) or equivalent\n* [Opentrons Filter Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette?variant=5984549109789)\n* [P20 8-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Olink Target 96](https://www.olink.com/products-services/target/)\n\n---\n\n", - "title": "Olink Target 96 Part 3/3: Detection" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single-Channel Electronic Pipette (GEN2)\nP20 8-Channel Electronic Pipette (GEN2)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Olink Target 96" - ], - "title": "Olink Target 96 Part 3/3: Detection" -} diff --git a/protoBuilds/2aee74-3/metadata.json b/protoBuilds/2aee74-3/metadata.json deleted file mode 100644 index 699cdc8704..0000000000 --- a/protoBuilds/2aee74-3/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "olink.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/2aee74-3", - "slug": "2aee74-3", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/2aee74-3/olink.ot2.apiv2.py.json b/protoBuilds/2aee74-3/olink.ot2.apiv2.py.json deleted file mode 100644 index 2e6a4448f7..0000000000 --- a/protoBuilds/2aee74-3/olink.ot2.apiv2.py.json +++ /dev/null @@ -1,4794 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Olink Target 96 Part 3/3: Detection',\n 'author': 'Nick ',\n 'description': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, p300_mount, m20_mount = get_values( # noqa: F821\n 'num_samples', 'p300_mount', 'm20_mount')\n\n if not 1 <= num_samples <= 96:\n raise Exception('Invalid number of samples (1-96)')\n\n det_mix = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '9',\n 'tuberack for detection mix (A3)').wells_by_name()['A3']\n inc_plate = ctx.load_labware('generic_96_aluminumblock_350ul', '5',\n 'incubation plate')\n sample_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '3', 'sample plate')\n strip = ctx.load_labware(\n 'genericstrips_96_wellplate_200ul', '6',\n 'strip for distribution (column 7)').columns_by_name()['7']\n primer_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '1', 'primer plate')\n fluidigm = ctx.load_labware('fluidigm_192_wellplate_96x10ul_96x10ul', '2',\n 'Fluidigm 96.96 Dynamic Array')\n tipracks300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '10')]\n tipracks20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['7', '8', '11']]\n stationary_rack = ctx.load_labware('opentrons_96_filtertiprack_20ul', '4')\n\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tipracks300)\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount,\n tip_racks=tipracks20)\n num_cols = math.ceil(num_samples/8)\n tip_track = True\n tip_count = 0\n\n folder_path = '/data/olink'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n if 'm20' in data:\n tip_count = data['m20']\n\n def m20_pick_up():\n nonlocal tip_count\n if tip_count == 12:\n ctx.pause('\\n\\n\\n\\n\\nPlease refill 20ul filter tiprack on slot 6 \\\nbefore resuming.\\n\\n\\n\\n\\n')\n m20.pick_up_tip(stationary_rack.rows()[0][tip_count])\n tip_count += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=30*side))\n pip.drop_tip(drop_loc)\n side = -1*side\n\n p300.default_speed = 100\n m20.default_speed = 100\n ctx.home()\n ctx.comment('\\n\\n\\n\\n\\nPrepare and prime a 96.96 Dynamic ArrayTM \\\nIntegrated Fluidic Circuit (IFC) according to the manufacturer\u2019s instructions.\\\n Briefly,inject one control line fluid syringe into each accumulator on the \\\nchip, and then prime the chip on the IFC Controller for approximately 20 \\\nminutes.\\n\\n\\n\\n\\n')\n ctx.comment('\\n\\n\\n\\n\\nThaw the Primer Plate, vortex and spin \\\nbriefly.\\n\\n\\n\\n\\n')\n ctx.pause(f'\\n\\n\\n\\n\\nP20 multi transfer will begin at column \\\n{tip_count+1} of tiprack on slot 6.\\n\\n\\n\\n\\n')\n\n # transfer detection mix to strip with reverse pipetting\n p300.pick_up_tip()\n p300.aspirate(5, det_mix)\n for well in strip:\n p300.aspirate(95, det_mix)\n p300.dispense(95, well)\n p300.dispense(p300.current_volume, det_mix)\n drop(p300)\n\n # transfer from strip to plate\n m20_pick_up()\n m20.aspirate(5, strip[0])\n for col in sample_plate.rows()[0][:num_cols]:\n m20.aspirate(7.2, strip[0])\n m20.dispense(7.2, col)\n drop(m20)\n\n # transfer samples\n for s, d in zip(inc_plate.rows()[0][:num_cols],\n sample_plate.rows()[0][:num_cols]):\n m20.pick_up_tip()\n m20.transfer(2.8, s, d, new_tip='never')\n drop(m20)\n\n ctx.pause('\\n\\n\\n\\n\\nSeal the plate with an adhesive plastic film, vortex \\\nand spin at 400 x g, 1 min at room temperature.\\n\\n\\n\\n\\n')\n\n # transfer primer and sample to fluidigm plate\n sample_destinations = [\n well for row in fluidigm.rows()[:2] for well in row[6:]]\n primer_destinations = [\n well for col in fluidigm.rows()[:2] for well in col[:6]]\n\n for source, dest in zip(\n primer_plate.rows()[0] + sample_plate.rows()[0][:num_cols],\n primer_destinations + sample_destinations[:num_cols]):\n m20.pick_up_tip()\n m20.aspirate(7, source.bottom(0.5))\n m20.dispense(5, dest.bottom(1))\n drop(m20)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {'m20': tip_count}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "generic strips", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 20 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Generic Strips 96 Well Plate 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ 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"totalLiquidVolume": 350, - "x": 41.38, - "y": 29.25, - "z": 3 - }, - "F5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 29.25, - "z": 3 - }, - "F6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 29.25, - "z": 3 - }, - "F7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 29.25, - "z": 3 - }, - "F8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 29.25, - "z": 3 - }, - "F9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 29.25, - "z": 3 - }, - "G1": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 14.38, - "y": 20.25, - "z": 3 - }, - "G10": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 95.38, - "y": 20.25, - "z": 3 - }, - "G11": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 104.38, - "y": 20.25, - "z": 3 - }, - "G12": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 113.38, - "y": 20.25, - "z": 3 - }, - "G2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 20.25, - "z": 3 - }, - "G3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 20.25, - "z": 3 - }, - "G4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 20.25, - "z": 3 - }, - "G5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 20.25, - "z": 3 - }, - "G6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 20.25, - "z": 3 - }, - "G7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 20.25, - "z": 3 - }, - "G8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 20.25, - "z": 3 - }, - "G9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 20.25, - "z": 3 - }, - "H1": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 14.38, - "y": 11.25, - "z": 3 - }, - "H10": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 95.38, - "y": 11.25, - "z": 3 - }, - "H11": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 104.38, - "y": 11.25, - "z": 3 - }, - "H12": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 113.38, - "y": 11.25, - "z": 3 - }, - "H2": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 23.38, - "y": 11.25, - "z": 3 - }, - "H3": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 32.38, - "y": 11.25, - "z": 3 - }, - "H4": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 41.38, - "y": 11.25, - "z": 3 - }, - "H5": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 50.38, - "y": 11.25, - "z": 3 - }, - "H6": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 59.38, - "y": 11.25, - "z": 3 - }, - "H7": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 68.38, - "y": 11.25, - "z": 3 - }, - "H8": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 77.38, - "y": 11.25, - "z": 3 - }, - "H9": { - "depth": 22, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 350, - "x": 86.38, - "y": 11.25, - "z": 3 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "number of samples (1-96)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P20 multi-channel pipette mount", - "name": "m20_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "primer plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Fluidigm 96.96 Dynamic Array on 2", - "share": false, - "slot": "2", - "type": "fluidigm_192_wellplate_96x10ul_96x10ul" - }, - { - "name": "sample plate on 3", - "share": false, - "slot": "3", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "incubation plate on 5", - "share": false, - "slot": "5", - "type": "generic_96_aluminumblock_350ul" - }, - { - "name": "strip for distribution (column 7) on 6", - "share": false, - "slot": "6", - "type": "genericstrips_96_wellplate_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "tuberack for detection mix (A3) on 9", - "share": false, - "slot": "9", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "description": "Custom Protocol Request", - "protocolName": "Olink Target 96 Part 3/3: Detection" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2aee74/README.json b/protoBuilds/2aee74/README.json deleted file mode 100644 index d2c828e68d..0000000000 --- a/protoBuilds/2aee74/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Proteins & Proteomics": [ - "Olink Target 96" - ] - }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n blue on sample plate (slot 7): starting samples\n green on tuberack (slot 8): 400.0\u00b5l incubation mix\n", - "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 1/3: Incubation for the Olink Target 96 protocol for protein biomarker discovery.\n", - "internal": "2aee74", - "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Proteins & Proteomics\n\t* Olink Target 96\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/2aee74/deck1-5.png)\nNote: all volumes for 96 samples (including controls)\n* blue on sample plate (slot 7): starting samples\n* green on tuberack (slot 8): 400.0\u00b5l incubation mix\n\n---\n\n", - "description": "\nLinks:\n* [Part 1: Incubation](./2aee74)\n* [Part 2: Extension](./2aee74-2)\n* [Part 3: Detection](./2aee74-3)\n\nThis protocol accomplishes part 1/3: Incubation for the [Olink Target 96 protocol](https://www.olink.com/products-services/target/) for protein biomarker discovery.\n\n---\n\n", - "internal": "2aee74\n", - "labware": "* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 4-in-1 Tube Rack Set](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Screwcap Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-1-5-ml-sample-vial) or equivalent\n* [Opentrons Filter Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300 Single-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette?variant=5984549109789)\n* [P20 8-Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Olink Target 96](https://www.olink.com/products-services/target/)\n\n---\n\n", - "title": "Olink Target 96 Part 1/3: Incubation" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300 Single-Channel Electronic Pipette (GEN2)\nP20 8-Channel Electronic Pipette (GEN2)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Olink Target 96" - ], - "title": "Olink Target 96 Part 1/3: Incubation" -} diff --git a/protoBuilds/2aee74/metadata.json b/protoBuilds/2aee74/metadata.json deleted file mode 100644 index bc53b1b577..0000000000 --- a/protoBuilds/2aee74/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "olink.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/2aee74", - "slug": "2aee74", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/2aee74/olink.ot2.apiv2.py.json b/protoBuilds/2aee74/olink.ot2.apiv2.py.json deleted file mode 100644 index 58e22e07c4..0000000000 --- a/protoBuilds/2aee74/olink.ot2.apiv2.py.json +++ /dev/null @@ -1,2361 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Olink Target 96 Part 1/3: Incubation',\n 'author': 'Nick ',\n 'description': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, p300_mount, m20_mount = get_values( # noqa: F821\n 'num_samples', 'p300_mount', 'm20_mount')\n\n if not 1 <= num_samples <= 96:\n raise Exception('Invalid number of samples (1-96)')\n\n inc_mix = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '8',\n 'tuberack for incubation mix (A1)').wells()[0]\n inc_plate = ctx.load_labware('generic_96_aluminumblock_350ul', '10',\n 'incubation plate')\n sample_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '7', 'sample plate')\n strip = ctx.load_labware('genericstrips_96_wellplate_200ul', '11',\n 'strip for distribution (column 1)').columns()[0]\n tipracks300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')]\n tipracks20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['1']]\n stationary_rack = ctx.load_labware('opentrons_96_filtertiprack_20ul', '4')\n\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tipracks300)\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount,\n tip_racks=tipracks20)\n\n num_cols = math.ceil(num_samples/8)\n tip_track = True\n tip_count = 0\n\n folder_path = '/data/olink'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n if 'm20' in data:\n tip_count = data['m20']\n\n def m20_pick_up():\n nonlocal tip_count\n if tip_count == 12:\n ctx.pause('\\n\\n\\n\\n\\nPlease refill 20ul filter tiprack on slot 6 \\\nbefore resuming.\\n\\n\\n\\n\\n')\n m20.pick_up_tip(stationary_rack.rows()[0][tip_count])\n tip_count += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=30*side))\n pip.drop_tip(drop_loc)\n side = -1*side\n\n p300.default_speed = 100\n m20.default_speed = 100\n\n ctx.home()\n ctx.pause(f'P20 multi transfer will begin at column {tip_count+1} of \\\ntiprack on slot 6.')\n\n # transfer incubation mix to strip with reverse pipetting\n p300.pick_up_tip()\n p300.aspirate(5, inc_mix)\n for well in strip:\n p300.aspirate(47, inc_mix)\n p300.dispense(47, well)\n p300.dispense(p300.current_volume, inc_mix)\n drop(p300)\n\n # transfer from strip to plate\n m20_pick_up()\n m20.aspirate(5, strip[0])\n for col in inc_plate.rows()[0][:num_cols]:\n m20.aspirate(3, strip[0])\n m20.dispense(3, col)\n # m20.dispense(m20.current_volume, strip[0])\n drop(m20)\n\n # transfer samples\n for s, d in zip(sample_plate.rows()[0][:num_samples],\n inc_plate.rows()[0][:num_samples]):\n m20.pick_up_tip()\n m20.transfer(1, s, d, new_tip='never')\n m20.blow_out(d.bottom(1))\n drop(m20)\n\n ctx.comment('\\n\\n\\n\\n\\nSeal the plate with an adhesive plastic film, spin \\\nat 400 x g, 1 min at room temperature. Incubate overnight at +4\u00b0C.\\n\\n\\n\\n\\n')\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {'m20': tip_count}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "generic strips", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 20 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Generic Strips 96 Well Plate 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "genericstrips_96_wellplate_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.24, - "z": 4 - }, - "A10": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 74.24, - "z": 4 - }, - "A11": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 74.24, - "z": 4 - }, - "A12": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 74.24, - "z": 4 - }, - "A2": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 74.24, - "z": 4 - }, - "A3": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 74.24, - "z": 4 - }, - "A4": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 74.24, - "z": 4 - }, - "A5": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 74.24, - "z": 4 - }, - "A6": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 74.24, - "z": 4 - }, - "A7": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 74.24, - "z": 4 - }, - "A8": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 74.24, - "z": 4 - }, - "A9": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 74.24, - "z": 4 - }, - "B1": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 65.24, - "z": 4 - }, - "B10": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 65.24, - "z": 4 - }, - "B11": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 65.24, - "z": 4 - }, - "B12": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 65.24, - "z": 4 - }, - "B2": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 65.24, - "z": 4 - }, - "B3": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 65.24, - "z": 4 - }, - "B4": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 65.24, - "z": 4 - }, - "B5": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 65.24, - "z": 4 - }, - "B6": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 65.24, - "z": 4 - }, - "B7": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 65.24, - "z": 4 - }, - "B8": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 65.24, - "z": 4 - }, - "B9": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 65.24, - "z": 4 - }, - "C1": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 56.24, - "z": 4 - }, - "C10": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 56.24, - "z": 4 - }, - "C11": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 56.24, - "z": 4 - }, - "C12": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 56.24, - "z": 4 - }, - "C2": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 56.24, - "z": 4 - }, - "C3": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 56.24, - "z": 4 - }, - "C4": { - "depth": 16, - "diameter": 5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 56.24, - "z": 4 - }, - "C5": { - "depth": 16, - "diameter": 5, - "shape": 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"right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_single_gen2" - } - ], - "labware": [ - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 1", - "share": false, - "slot": "1", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "sample plate on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "tuberack for incubation mix (A1) on 8", - "share": false, - "slot": "8", - "type": "opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "incubation plate on 10", - "share": false, - "slot": "10", - "type": "generic_96_aluminumblock_350ul" - }, - { - "name": "strip for distribution (column 1) on 11", - "share": false, - "slot": "11", - "type": "genericstrips_96_wellplate_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "description": "Custom Protocol Request", - "protocolName": "Olink Target 96 Part 1/3: Incubation" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json b/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json index 789fb8191f..6717c90238 100644 --- a/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json +++ b/protoBuilds/2b3642/2b3642.ot2.apiv2.py.json @@ -159,5 +159,24 @@ "description": "Custom Protocol Request", "protocolName": "NEBNext Ultra II DNA Library Preparation Kit\n for Illumina E7645S" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json b/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json index a057a46b77..58631de434 100644 --- a/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json +++ b/protoBuilds/2b9486/ngs_prep.ot2.apiv2.py.json @@ -4623,5 +4623,12 @@ "protocolName": "NGS Library Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw ABGene 96 Well Plate 200\u00b5l on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json b/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json index 3c050aa7da..194a93fe03 100644 --- a/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json +++ b/protoBuilds/2c83f7/2c83f7.ot2.apiv2.py.json @@ -128,5 +128,12 @@ "protocolName": "Zymo Research Direct-zol-96 RNA MagPrep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw deepwell block on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json b/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json index de5a652534..11df18c6b5 100644 --- a/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json +++ b/protoBuilds/2d9a0c/2d9a0c.ot2.apiv2.py.json @@ -1257,5 +1257,12 @@ "protocolName": "PCR Workflow With Thermocycler", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Thermo Scientific Non Skirted 96 Well Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json b/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json index dddc5511a1..4d0965aee3 100644 --- a/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json +++ b/protoBuilds/2e84cc/2e84cc.ot2.apiv2.py.json @@ -81,5 +81,24 @@ "protocolName": "TG Nextera XT index kit v2 Set A to D", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json b/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json index 2e297b5766..115b541e2c 100644 --- a/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json +++ b/protoBuilds/2ed4de-2/fluribogreen.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nfrom opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'FluRibogreen Assay',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n standard_type, p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'standard_type', 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[5]\n assay_buffer_1 = reagent_labware.wells()[6:9]\n starting_samples = sample_rack.wells()[:num_samples]\n num_sets = math.ceil(num_samples/8)\n all_samples = [\n deepplate.columns()[i*3:(i+1)*3]\n for i in range(1, 1+num_sets)]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for vol, dest in zip([100, 300, 500, 700, 900, 950, 1000],\n dilution_col):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[0], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_sets, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n print(dil_vol)\n for j, set in enumerate(dil_sets):\n for k, well in enumerate(set[i]):\n if j*k+k < num_samples:\n p1000.pick_up_tip()\n p1000.transfer(dil_vol,\n buffer[1+int((j*8+k)//(num_samples/2))],\n well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n p300.flow_rate.dispense = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n print(sample_vol)\n pickup_p300('single')\n well = dil_sets[i//8][0][i % 8]\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, well.bottom(3))\n p300.mix(1, 20, well.bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n p300.flow_rate.dispense = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n for set in dil_sets:\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, set[i][0])\n else:\n print(sample_vol*(i+1))\n p300.transfer(sample_vol*(i+1), set[i-1][0].bottom(3),\n set[i][0].bottom(3),\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return int(len(factors)-1)\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # standard preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE or TR)\n sample_1_final_ind = dilute(standard_type, all_samples, assay_buffer_1)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n sources = [deepplate.rows_by_name()['A'][0]] + [\n set[sample_1_final_ind][0] for set in all_samples]\n for i, source in enumerate(sources):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", + "content": "import math\nfrom opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'FluRibogreen Assay',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n standard_type, p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'standard_type', 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[5]\n assay_buffer_1 = reagent_labware.wells()[6:9]\n starting_samples = sample_rack.wells()[:num_samples]\n num_sets = math.ceil(num_samples/8)\n all_samples = [\n deepplate.columns()[i*3:(i+1)*3]\n for i in range(1, 1+num_sets)]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for vol, dest in zip([100, 300, 500, 700, 900, 950, 1000],\n dilution_col):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[0], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_sets, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n print(dil_vol)\n for j, set in enumerate(dil_sets):\n for k, well in enumerate(set[i]):\n if j*k+k < num_samples:\n p1000.pick_up_tip()\n p1000.transfer(dil_vol,\n buffer[1+int((j*8+k)//(num_samples/2))],\n well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n p300.flow_rate.dispense = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n print(sample_vol)\n pickup_p300('single')\n well = dil_sets[i//8][0][i % 8]\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, well.bottom(3))\n p300.mix(1, 20, well.bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n p300.flow_rate.dispense = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n for set in dil_sets:\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, set[i][0])\n else:\n print(sample_vol*(i+1))\n p300.transfer(sample_vol*(i+1), set[i-1][0].bottom(3),\n set[i][0].bottom(3),\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return int(len(factors)-1)\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # standard preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE or TR)\n sample_1_final_ind = dilute(standard_type, all_samples, assay_buffer_1)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n sources = [deepplate.rows_by_name()['A'][0]] + [\n set[sample_1_final_ind][0] for set in all_samples]\n for i, source in enumerate(sources):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", "custom_labware_defs": [], "fields": [ { diff --git a/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json b/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json index f81e3405c5..ad2c1bde61 100644 --- a/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json +++ b/protoBuilds/2ed4de/fluribogreen.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'Ribogreen Assay - 2 Standards and up to 8 Samples',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[0]\n assay_buffer_1 = reagent_labware.wells()[1:3]\n working_standard_2 = reagent_labware.wells()[9]\n assay_buffer_2 = reagent_labware.wells()[10:12]\n starting_samples = sample_rack.wells()[:num_samples]\n samples_1 = deepplate.columns()[3:6]\n samples_2 = deepplate.columns()[9:]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for i, (vol, dest) in enumerate(\n zip([100, 300, 500, 700, 900, 950, 1000], dilution_col)):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[i//5], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_set, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n for j, well in enumerate(dil_set[i][:num_samples]):\n p1000.pick_up_tip()\n p1000.transfer(dil_vol, buffer[j//5], well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n pickup_p300('single')\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, dil_set[0][i].bottom(3))\n p300.mix(1, 20, dil_set[0][i].bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, dil_set[i][0])\n else:\n p300.transfer(sample_vol*(i+1), dil_set[i-1][0].bottom(3),\n dil_set[i][0].bottom(3),\n\n\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return dil_set[len(factors)-1][0]\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # TE preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n # TR preparation\n standard_prep(working_standard_2, assay_buffer_2,\n deepplate.columns()[6])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE)\n sample_1_final_loc = dilute(2.5, samples_1, assay_buffer_1)\n\n # sample normalization (TR)\n sample_2_final_loc = dilute(0.5, samples_2, assay_buffer_2)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n for i, source in enumerate(\n [deepplate.rows_by_name()['A'][0], sample_1_final_loc,\n deepplate.rows_by_name()['A'][6], sample_2_final_loc]):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", + "content": "from opentrons.types import Point\n\n\nmetadata = {\n 'protocolName': 'Ribogreen Assay - 2 Standards and up to 8 Samples',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n [num_samples, reagent_labware, starting_conc, prepare_standard,\n p1000_mount, p300_mount] = get_values( # noqa: F821\n 'num_samples', 'reagent_labware', 'starting_conc', 'prepare_standard',\n 'p1000_mount', 'p300_mount')\n\n final_transfer_vol = 100\n sample_vol = 25\n max_working_vol = 1000\n mix_reps = 10\n max_factor_1_dil = max_working_vol/sample_vol\n\n # load labwarex\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '11',\n 'sample tuberack')\n deepplate = ctx.load_labware('nest_96_wellplate_2ml_deep', '5',\n 'standard preparation plate')\n flatplate = ctx.load_labware('corning_96_wellplate_360ul_flat', '2',\n 'final plate')\n reagent_labware = ctx.load_labware(reagent_labware, '8',\n 'standards and buffers')\n tipracks1000 = ctx.load_labware('opentrons_96_filtertiprack_1000ul', '7')\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '6')\n tiprack200m = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # load pipettes\n p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n tip_racks=[tipracks1000])\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tiprack200m])\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()[::-1]\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': tipracks200.rows()[0]\n }\n }\n\n def pickup_p300(mode='single'):\n current = 0.1 if mode == 'single' else 0.5\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', current)\n\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n side = 1\n\n def drop(pip):\n nonlocal side\n center = ctx.loaded_labwares[12].wells()[0].top()\n pip.drop_tip(center.move(Point(x=side*20)))\n side = side * -1\n\n working_standard_1 = reagent_labware.wells()[0]\n assay_buffer_1 = reagent_labware.wells()[1:3]\n working_standard_2 = reagent_labware.wells()[9]\n assay_buffer_2 = reagent_labware.wells()[10:12]\n starting_samples = sample_rack.wells()[:num_samples]\n samples_1 = deepplate.columns()[3:6]\n samples_2 = deepplate.columns()[9:]\n\n def standard_prep(standard, buffer, column):\n dilution_col = column[:7]\n for vol, dest in zip([900, 700, 500, 300, 100], dilution_col[:5]):\n p1000.pick_up_tip()\n p1000.transfer(vol, standard, dest, new_tip='never')\n drop(p1000)\n\n for i, (vol, dest) in enumerate(\n zip([100, 300, 500, 700, 900, 950, 1000], dilution_col)):\n p1000.pick_up_tip()\n p1000.transfer(vol, buffer[i//5], dest, mix_after=(5, 800),\n new_tip='never')\n drop(p1000)\n pickup_p300('single')\n p300.aspirate(50, standard.bottom(2))\n p300.dispense(50, dilution_col[5].bottom(3))\n p300.mix(1, 100, dilution_col[5].bottom(3))\n drop(p300)\n p1000.pick_up_tip()\n p1000.mix(mix_reps, 800, dilution_col[5])\n drop(p1000)\n\n def dilute(final_conc, dil_set, buffer):\n dil_factor = starting_conc/final_conc\n # find necessary dilution factor(s)\n if dil_factor > max_factor_1_dil:\n factors = [10, dil_factor/10]\n else:\n factors = [dil_factor]\n\n # pre add diluent\n for i, factor in enumerate(factors):\n dil_vol = (factor-1)*sample_vol*(i+1)\n for j, well in enumerate(dil_set[i][:num_samples]):\n p1000.pick_up_tip()\n p1000.transfer(dil_vol, buffer[j//5], well, new_tip='never')\n drop(p1000)\n\n p300.flow_rate.aspirate = 40\n # transfer sample\n for i, s in enumerate(starting_samples):\n pickup_p300('single')\n p300.aspirate(sample_vol, s.bottom(2))\n p300.dispense(sample_vol, dil_set[0][i].bottom(3))\n p300.mix(1, 20, dil_set[0][i].bottom(3))\n drop(p300)\n p300.flow_rate.aspirate = 94\n\n # perform dilution\n for i, factor in enumerate(factors):\n pickup_p300('multi')\n total_vol = sample_vol*(i+1)*factor\n mix_vol = total_vol*0.8 if total_vol*0.8 <= 175 else 175\n if i == 0:\n p300.mix(mix_reps, mix_vol, dil_set[i][0])\n else:\n p300.transfer(sample_vol*(i+1), dil_set[i-1][0].bottom(3),\n dil_set[i][0].bottom(3),\n\n\n mix_after=(5, mix_vol),\n new_tip='never')\n drop(p300)\n\n return dil_set[len(factors)-1][0]\n\n \"\"\" PART 1 \"\"\"\n if prepare_standard:\n\n # TE preparation\n standard_prep(working_standard_1, assay_buffer_1,\n deepplate.columns()[0])\n\n # TR preparation\n standard_prep(working_standard_2, assay_buffer_2,\n deepplate.columns()[6])\n\n \"\"\" PART 2 \"\"\"\n\n # sample normalization (TE)\n sample_1_final_loc = dilute(2.5, samples_1, assay_buffer_1)\n\n # sample normalization (TR)\n sample_2_final_loc = dilute(0.5, samples_2, assay_buffer_2)\n\n \"\"\" PART 3 \"\"\"\n\n # transfer to final black plate\n for i, source in enumerate(\n [deepplate.rows_by_name()['A'][0], sample_1_final_loc,\n deepplate.rows_by_name()['A'][6], sample_2_final_loc]):\n dest_set = flatplate.rows()[0][i*3:(i+1)*3]\n for dest in dest_set:\n p300.pick_up_tip()\n p300.transfer(final_transfer_vol, source.bottom(3), dest.bottom(3),\n mix_before=(mix_reps, 0.8*final_transfer_vol),\n new_tip='never')\n drop(p300)\n", "custom_labware_defs": [], "fields": [ { diff --git a/protoBuilds/313086-logixsmart-station-C/README.json b/protoBuilds/313086-logixsmart-station-C/README.json deleted file mode 100644 index dd9984253a..0000000000 --- a/protoBuilds/313086-logixsmart-station-C/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Covid Workstation": [ - "qPCR Setup" - ] - }, - "deck-setup": "\ngreen: mastermix\npink: positive control\npurple: negative control \nblue: starting samples\n\n\n", - "description": "Links:\n Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below:\n\n", - "internal": "313086", - "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 24 tuberack with NEST 1.5 mL Microcentrifuge Tubes\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 10\u00b5l tipracks\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Covid Workstation\n\t* qPCR Setup\n\n", - "deck-setup": "* green: mastermix\n* pink: positive control\n* purple: negative control \n* blue: starting samples\n![deck setup](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/313086-station-C/deck_setup2.png)\n\n---\n\n", - "description": "Links: \n* [Logix Smart Nasopharyngeal Covid-19 Plating (Station A)](./313086)\n* [Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)](./313086-station-C)\n\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below: \n![order](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/demo/order.png)\n\n---\n\n", - "internal": "313086\n", - "labware": "* [NEST 2 mL 96-Well Deep Well Plate, V Bottom](https://shop.opentrons.com/collections/verified-labware/products/nest-0-2-ml-96-well-deep-well-plate-v-bottom)\n* [Opentrons 24 tuberack](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Microcentrifuge Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-microcentrifuge-tubes)\n* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 10\u00b5l tipracks](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P10 Single-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette)\n* [P10 Multi-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Logix Smart Nasopharyngeal Covid-19 Kit](https://codiagnostics.com/products/diagnostic-solutions/logix-smart-covid19/)\n\n---\n\n", - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP10 Single-channel electronic pipette\nP10 Multi-channel electronic pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Logix Smart Nasopharyngeal Covid-19 Kit" - ], - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" -} \ No newline at end of file diff --git a/protoBuilds/313086-logixsmart-station-C/generic_station_C.ot2.apiv2.py.json b/protoBuilds/313086-logixsmart-station-C/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index d46d1195cb..0000000000 --- a/protoBuilds/313086-logixsmart-station-C/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,163 +0,0 @@ -{ - "content": "import json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep \\\n(Station C)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.10'\n}\n\n\ndef run(ctx):\n\n [sample_type, num_samples, p10_mount, m10_mount,\n tip_track] = get_values( # noqa: F821\n 'sample_type', 'num_samples', 'p10_mount', 'm10_mount', 'tip_track')\n\n # load labware\n source_plate = ctx.load_labware('nest_96_wellplate_2ml_deep', '1',\n '96-deepwell sample plate')\n dest_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2', '96-well PCR plate')\n tuberack = ctx.load_labware('opentrons_24_tuberack_nest_2ml_screwcap',\n '4', 'reagent tuberack')\n tipracks10s = [\n ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '300\u00b5l tiprack')\n for slot in ['7', '8', '10', '11']]\n tipracks10m = [ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '10\u00b5l tiprack')\n for slot in ['3', '5', '6', '9']]\n\n # load pipette\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tipracks10s)\n m10 = ctx.load_instrument('p10_multi', m10_mount, tip_racks=tipracks10m)\n\n # setup samples and reagents\n source_multi = source_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n all_dests = dest_plate.wells()[:2+num_samples]\n all_dests_multi = dest_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n mm, pos_control, neg_control = tuberack.wells()[:3]\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n if sample_type == 'nasopharyngeal':\n vol_mm = 5\n vol_sample = 5\n else:\n vol_mm = 10\n vol_sample = 10\n\n # transfer mastermix\n _pick_up(p10)\n for d in all_dests:\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_mm, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # transfer sample\n for s, d in zip(source_multi, all_dests_multi):\n _pick_up(m10)\n if vol_mm <= 7:\n m10.air_gap(2)\n m10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n m10.air_gap(1)\n m10.dispense(p10.current_volume, d.bottom(1))\n m10.drop_tip()\n\n # transfer controls\n for s, d in zip([pos_control, neg_control], dest_plate.wells()[:2]):\n _pick_up(p10)\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "sample type", - "name": "sample_type", - "options": [ - { - "label": "nasopharyngeal (5\u00b5l sample, 5\u00b5l mix)", - "value": "nasopharyngeal" - }, - { - "label": "saliva (10\u00b5l sample, 10\u00b5l mix)", - "value": "saliva" - } - ], - "type": "dropDown" - }, - { - "default": 94, - "label": "number of samples (1-94)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P10 single-channel GEN1 mount", - "name": "p10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN2 mount", - "name": "m10_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_multi" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "96-deepwell sample plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "96-well PCR plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "10\u00b5l tiprack on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "reagent tuberack on 4", - "share": false, - "slot": "4", - "type": "opentrons_24_tuberack_nest_2ml_screwcap" - }, - { - "name": "10\u00b5l tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Nick ", - "protocolName": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/313086-logixsmart-station-C/metadata.json b/protoBuilds/313086-logixsmart-station-C/metadata.json deleted file mode 100644 index c15f027d09..0000000000 --- a/protoBuilds/313086-logixsmart-station-C/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "generic_station_C.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/313086-logixsmart-station-C", - "slug": "313086-logixsmart-station-C", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-B/README.json b/protoBuilds/313086-station-B/README.json deleted file mode 100644 index 0d0a247ca9..0000000000 --- a/protoBuilds/313086-station-B/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Covid Workstation": [ - "Sample Plating" - ] - }, - "deck-setup": "\ngreen: lysis/binding buffer (13ml per channel)\npink: elution buffer: (9ml per channel)\nblue: starting samples\n\n\n", - "description": "This protocol plates lysis/binding buffer, samples, and elution buffer in a NEST 96-deepwell plate. Samples should be arranged in up to 4x Opentrons tuberacks, and buffers should be loaded in a NEST 12-channel reservoir. The transfer order is as shown below:\n\nDeepwells A1 and B1 are left empty for controls to be added later on.\n", - "internal": "313086", - "labware": "\nLabware name\nNick is working on auto-filling these sections from the protocol (3/28/2021)\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Covid Workstation\n\t* Sample Plating\n\n\n", - "deck-setup": "* green: lysis/binding buffer (13ml per channel)\n* pink: elution buffer: (9ml per channel)\n* blue: starting samples \n![deck setup](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/313086/deck_setup.png)\n\n---\n\n", - "description": "This protocol plates lysis/binding buffer, samples, and elution buffer in a NEST 96-deepwell plate. Samples should be arranged in up to 4x Opentrons tuberacks, and buffers should be loaded in a NEST 12-channel reservoir. The transfer order is as shown below: \n![order](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/demo/order.png)\n\nDeepwells A1 and B1 are left empty for controls to be added later on.\n\n---\n\n", - "internal": "313086\n", - "labware": "* [Labware name](link to labware on shop.opentrons.com when applicable)\n* Nick is working on auto-filling these sections from the protocol (3/28/2021)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P300](link to pipette on shop.opentrons.com)\n* Nick is working on auto-filling these sections from the protocol (3/28/2021)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Logix Smart Nasopharyngeal Covid-19 Kit](https://codiagnostics.com/products/diagnostic-solutions/logix-smart-covid19/)\n\n---\n\n", - "title": "Logix Smart Nasopharyngeal Covid-19 Plating (Station A)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP300\nNick is working on auto-filling these sections from the protocol (3/28/2021)\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Logix Smart Nasopharyngeal Covid-19 Kit" - ], - "title": "Logix Smart Nasopharyngeal Covid-19 Plating (Station A)" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-B/generic_station_B.ot2.apiv2.py.json b/protoBuilds/313086-station-B/generic_station_B.ot2.apiv2.py.json deleted file mode 100644 index 099a86a1ca..0000000000 --- a/protoBuilds/313086-station-B/generic_station_B.ot2.apiv2.py.json +++ /dev/null @@ -1,2741 +0,0 @@ -{ - "content": "import json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'Logix Smart Nasopharyngeal Covid-19 PCR Prep (Station B)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.10'\n}\n\n\ndef run(ctx):\n\n [sample_type, num_samples, p10_mount, m10_mount,\n tip_track] = get_values( # noqa: F821\n 'sample_type', 'num_samples', 'p10_mount', 'm10_mount', 'tip_track')\n\n # load labware\n source_plate = ctx.load_labware('nest_96_wellplate_2ml_deep', '1',\n '96-deepwell sample plate')\n dest_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2', '96-well PCR plate')\n tuberack = ctx.load_labware('opentrons_24_tuberack_nest_1.5ml_screwcap',\n '4', 'reagent tuberack')\n tipracks10s = [\n ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '300\u00b5l tiprack')\n for slot in ['7', '8', '10', '11']]\n tipracks10m = [ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '10\u00b5l tiprack')\n for slot in ['3', '5', '6', '9']]\n\n # load pipette\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tipracks10s)\n m10 = ctx.load_instrument('p10_multi', m10_mount, tip_racks=tipracks10m)\n\n # setup samples and reagents\n source_multi = source_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n all_dests = dest_plate.wells()[:2+num_samples]\n all_dests_multi = dest_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n mm, pos_control, neg_control = tuberack.wells()[:3]\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n folder_path = '/data/tip_track'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n if sample_type == 'nasopharyngeal':\n vol_mm = 5\n vol_sample = 5\n else:\n vol_mm = 10\n vol_sample = 10\n\n # transfer mastermix\n _pick_up(p10)\n for d in all_dests:\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_mm, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # transfer sample\n for s, d in zip(source_multi, all_dests_multi):\n _pick_up(m10)\n if vol_mm <= 7:\n m10.air_gap(2)\n m10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n m10.air_gap(1)\n m10.dispense(p10.current_volume, d.bottom(1))\n m10.drop_tip()\n\n # transfer controls\n for s, d in zip([pos_control, neg_control], dest_plate.wells()[:2]):\n _pick_up(p10)\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "", - "brandId": [], - "links": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.47, - "zDimension": 85.35 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "A2", - "B2", - "C2", - "D2", - "A3", - "B3", - "C3", - "D3", - "A4", - "B4", - "C4", - "D4", - "A5", - "B5", - "C5", - "D5", - "A6", - "B6", - "C6", - "D6" - ] - } - ], - "metadata": { - "displayCategory": "tubeRack", - "displayName": "Opentrons 24 Tube Rack with Blood Tube 5mL Conical", - "displayVolumeUnits": "mL", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1" - ], - [ - "A2", - "B2", - "C2", - "D2" - ], - [ - "A3", - "B3", - "C3", - "D3" - ], - [ - "A4", - "B4", - "C4", - "D4" - ], - [ - "A5", - "B5", - "C5", - "D5" - ], - [ - "A6", - "B6", - "C6", - "D6" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "custom_24_tuberack_5ml" - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 73, - "diameter": 10, - "shape": "circular", - "totalLiquidVolume": 5000, - "x": 13.88, - "y": 72.72, - "z": 5 - }, - "A2": { - "depth": 73, - "diameter": 10, - "shape": "circular", - "totalLiquidVolume": 5000, - "x": 33.88, - "y": 72.72, - "z": 5 - }, - "A3": { - "depth": 73, - "diameter": 10, - "shape": "circular", - "totalLiquidVolume": 5000, - "x": 53.88, - "y": 72.72, - "z": 5 - }, - "A4": { - "depth": 73, - "diameter": 10, - "shape": "circular", - "totalLiquidVolume": 5000, - "x": 73.88, - "y": 72.72, - "z": 5 - }, - "A5": { - "depth": 73, - "diameter": 10, - "shape": "circular", - "totalLiquidVolume": 5000, - "x": 93.88, - "y": 72.72, - "z": 5 - }, - "A6": { - "depth": 73, - "diameter": 10, - "shape": "circular", - "totalLiquidVolume": 5000, - "x": 113.88, - "y": 72.72, - "z": 5 - }, - 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"y": 20.25, - "z": 5.02 - }, - "G4": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 20.25, - "z": 5.02 - }, - "G5": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 20.25, - "z": 5.02 - }, - "G6": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 20.25, - "z": 5.02 - }, - "G7": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 20.25, - "z": 5.02 - }, - "G8": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 20.25, - "z": 5.02 - }, - "G9": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 20.25, - "z": 5.02 - }, - "H1": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 11.25, - "z": 5.02 - }, - "H10": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 11.25, - "z": 5.02 - }, - "H11": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 11.25, - "z": 5.02 - }, - "H12": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 11.25, - "z": 5.02 - }, - "H2": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 11.25, - "z": 5.02 - }, - "H3": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 11.25, - "z": 5.02 - }, - "H4": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 11.25, - "z": 5.02 - }, - "H5": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 11.25, - "z": 5.02 - }, - "H6": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 11.25, - "z": 5.02 - }, - "H7": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 11.25, - "z": 5.02 - }, - "H8": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 11.25, - "z": 5.02 - }, - "H9": { - "depth": 14.48, - "diameter": 5.46, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 11.25, - "z": 5.02 - } - } - } - ], - "fields": [ - { - "label": "sample type", - "name": "sample_type", - "options": [ - { - "label": "nasopharyngeal (5\u00b5l sample, 5\u00b5l mix)", - "value": "nasopharyngeal" - }, - { - "label": "saliva (10\u00b5l sample, 10\u00b5l mix)", - "value": "saliva" - } - ], - "type": "dropDown" - }, - { - "default": 94, - "label": "number of samples (1-94)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P10 single-channel GEN1 mount", - "name": "p10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN2 mount", - "name": "m10_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_multi" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "96-deepwell sample plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "96-well PCR plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "10\u00b5l tiprack on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "reagent tuberack on 4", - "share": false, - "slot": "4", - "type": "opentrons_24_tuberack_nest_1.5ml_screwcap" - }, - { - "name": "10\u00b5l tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Nick ", - "protocolName": "Logix Smart Nasopharyngeal Covid-19 PCR Prep (Station B)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/313086-station-B/metadata.json b/protoBuilds/313086-station-B/metadata.json deleted file mode 100644 index e46d9af958..0000000000 --- a/protoBuilds/313086-station-B/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "generic_station_B.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/313086-station-B", - "slug": "313086-station-B", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-C/README.json b/protoBuilds/313086-station-C/README.json deleted file mode 100644 index dd9984253a..0000000000 --- a/protoBuilds/313086-station-C/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "Covid Workstation": [ - "qPCR Setup" - ] - }, - "deck-setup": "\ngreen: mastermix\npink: positive control\npurple: negative control \nblue: starting samples\n\n\n", - "description": "Links:\n Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below:\n\n", - "internal": "313086", - "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 24 tuberack with NEST 1.5 mL Microcentrifuge Tubes\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 10\u00b5l tipracks\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* Covid Workstation\n\t* qPCR Setup\n\n", - "deck-setup": "* green: mastermix\n* pink: positive control\n* purple: negative control \n* blue: starting samples\n![deck setup](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/313086-station-C/deck_setup2.png)\n\n---\n\n", - "description": "Links: \n* [Logix Smart Nasopharyngeal Covid-19 Plating (Station A)](./313086)\n* [Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)](./313086-station-C)\n\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below: \n![order](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/demo/order.png)\n\n---\n\n", - "internal": "313086\n", - "labware": "* [NEST 2 mL 96-Well Deep Well Plate, V Bottom](https://shop.opentrons.com/collections/verified-labware/products/nest-0-2-ml-96-well-deep-well-plate-v-bottom)\n* [Opentrons 24 tuberack](https://shop.opentrons.com/collections/verified-labware/products/tube-rack-set-1) with [NEST 1.5 mL Microcentrifuge Tubes](https://shop.opentrons.com/collections/verified-consumables/products/nest-microcentrifuge-tubes)\n* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/verified-labware/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 10\u00b5l tipracks](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P10 Single-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette)\n* [P10 Multi-channel electronic pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "reagents": "* [Logix Smart Nasopharyngeal Covid-19 Kit](https://codiagnostics.com/products/diagnostic-solutions/logix-smart-covid19/)\n\n---\n\n", - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" - }, - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP10 Single-channel electronic pipette\nP10 Multi-channel electronic pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagents": [ - "Logix Smart Nasopharyngeal Covid-19 Kit" - ], - "title": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)" -} \ No newline at end of file diff --git a/protoBuilds/313086-station-C/generic_station_C.ot2.apiv2.py.json b/protoBuilds/313086-station-C/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index d46d1195cb..0000000000 --- a/protoBuilds/313086-station-C/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,163 +0,0 @@ -{ - "content": "import json\nimport os\nimport math\n\n# metadata\nmetadata = {\n 'protocolName': 'Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep \\\n(Station C)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.10'\n}\n\n\ndef run(ctx):\n\n [sample_type, num_samples, p10_mount, m10_mount,\n tip_track] = get_values( # noqa: F821\n 'sample_type', 'num_samples', 'p10_mount', 'm10_mount', 'tip_track')\n\n # load labware\n source_plate = ctx.load_labware('nest_96_wellplate_2ml_deep', '1',\n '96-deepwell sample plate')\n dest_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2', '96-well PCR plate')\n tuberack = ctx.load_labware('opentrons_24_tuberack_nest_2ml_screwcap',\n '4', 'reagent tuberack')\n tipracks10s = [\n ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '300\u00b5l tiprack')\n for slot in ['7', '8', '10', '11']]\n tipracks10m = [ctx.load_labware('opentrons_96_tiprack_10ul', slot,\n '10\u00b5l tiprack')\n for slot in ['3', '5', '6', '9']]\n\n # load pipette\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tipracks10s)\n m10 = ctx.load_instrument('p10_multi', m10_mount, tip_racks=tipracks10m)\n\n # setup samples and reagents\n source_multi = source_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n all_dests = dest_plate.wells()[:2+num_samples]\n all_dests_multi = dest_plate.rows()[0][:math.ceil((num_samples+2)/8)]\n mm, pos_control, neg_control = tuberack.wells()[:3]\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n if sample_type == 'nasopharyngeal':\n vol_mm = 5\n vol_sample = 5\n else:\n vol_mm = 10\n vol_sample = 10\n\n # transfer mastermix\n _pick_up(p10)\n for d in all_dests:\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_mm, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # transfer sample\n for s, d in zip(source_multi, all_dests_multi):\n _pick_up(m10)\n if vol_mm <= 7:\n m10.air_gap(2)\n m10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n m10.air_gap(1)\n m10.dispense(p10.current_volume, d.bottom(1))\n m10.drop_tip()\n\n # transfer controls\n for s, d in zip([pos_control, neg_control], dest_plate.wells()[:2]):\n _pick_up(p10)\n if vol_mm <= 7:\n p10.air_gap(2)\n p10.aspirate(vol_sample, mm)\n if vol_mm <= 7:\n p10.air_gap(1)\n p10.dispense(p10.current_volume, d.bottom(1))\n p10.drop_tip()\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "sample type", - "name": "sample_type", - "options": [ - { - "label": "nasopharyngeal (5\u00b5l sample, 5\u00b5l mix)", - "value": "nasopharyngeal" - }, - { - "label": "saliva (10\u00b5l sample, 10\u00b5l mix)", - "value": "saliva" - } - ], - "type": "dropDown" - }, - { - "default": 94, - "label": "number of samples (1-94)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P10 single-channel GEN1 mount", - "name": "p10_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "label": "P10 multi-channel GEN2 mount", - "name": "m10_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "track tips across protocol runs", - "name": "tip_track", - "options": [ - { - "label": "no", - "value": false - }, - { - "label": "yes", - "value": true - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p10_multi" - }, - { - "mount": "right", - "name": "p10_single" - } - ], - "labware": [ - { - "name": "96-deepwell sample plate on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_2ml_deep" - }, - { - "name": "96-well PCR plate on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "10\u00b5l tiprack on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "reagent tuberack on 4", - "share": false, - "slot": "4", - "type": "opentrons_24_tuberack_nest_2ml_screwcap" - }, - { - "name": "10\u00b5l tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "10\u00b5l tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "300\u00b5l tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_10ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Nick ", - "protocolName": "Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station C)", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/313086-station-C/metadata.json b/protoBuilds/313086-station-C/metadata.json deleted file mode 100644 index 947784f1b6..0000000000 --- a/protoBuilds/313086-station-C/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "generic_station_C.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/313086-station-C", - "slug": "313086-station-C", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json b/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json index 3455574df0..8a062e94f6 100644 --- a/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json +++ b/protoBuilds/33900b/protein_purification.ot2.apiv2.py.json @@ -2726,7 +2726,7 @@ ], "labware": [ { - "name": "Greiner Bio-One 96-Deepwell Plate 2ml on Magnetic Module GEN1 on 1", + "name": "Greiner Bio-One 96-Deepwell Plate 2ml on Magnetic Module on 1", "share": false, "slot": "1", "type": "greinerbioone_96_wellplate_2ml_deep" @@ -2804,5 +2804,12 @@ "protocolName": "Promega MagneHis\u2122 Protein Purification System", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Greiner Bio-One 96-Deepwell Plate 2ml on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/343001/343001.ot2.apiv2.py.json b/protoBuilds/343001/343001.ot2.apiv2.py.json index 27ff5cef5e..d189f8c43e 100644 --- a/protoBuilds/343001/343001.ot2.apiv2.py.json +++ b/protoBuilds/343001/343001.ot2.apiv2.py.json @@ -2345,7 +2345,7 @@ "type": "opentrons_6_tuberack_falcon_50ml_conical" }, { - "name": "Zymo 96-Well Block on Magnetic Module GEN1 on 4", + "name": "Zymo 96-Well Block on Magnetic Module on 4", "share": false, "slot": "4", "type": "zymo_96_wellblock" @@ -2405,5 +2405,12 @@ "protocolName": "Zymo Extraction Protocol", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Zymo 96-Well Block on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/35269b/35269b.ot2.apiv2.py.json b/protoBuilds/35269b/35269b.ot2.apiv2.py.json index f9cae73706..2721b9e094 100644 --- a/protoBuilds/35269b/35269b.ot2.apiv2.py.json +++ b/protoBuilds/35269b/35269b.ot2.apiv2.py.json @@ -1328,5 +1328,12 @@ "description": "Custom Protocol Request", "protocolName": "MAI VIRAL ISOLATION" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw Extraction Plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3607d5-3/extraction1.ot2.apiv2.py.json b/protoBuilds/3607d5-3/extraction1.ot2.apiv2.py.json deleted file mode 100644 index 41e2f7ed38..0000000000 --- a/protoBuilds/3607d5-3/extraction1.ot2.apiv2.py.json +++ /dev/null @@ -1,4698 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'SPRI 3',\n 'author': 'Opentrons ',\n 'apiLevel': '2.10'\n}\n\n\n# Start protocol\ndef run(ctx):\n [num_samples, m20_mount, m300_mount, mag_height, sample_vol,\n binding_buffer_vol, wash1_vol, wash2_vol, elution_vol,\n settling_time] = get_values( # noqa: F821\n 'num_samples', 'm20_mount', 'm300_mount', 'mag_height', 'sample_vol',\n 'binding_buffer_vol', 'wash1_vol', 'wash2_vol', 'elution_vol',\n 'settling_time')\n\n # num_samples = 96\n # m20_mount = 'left'\n # m300_mount = 'right'\n # mag_height = 10.5\n # sample_vol = 45.0\n # binding_buffer_vol = 45.0\n # wash1_vol = 200.0\n # wash2_vol = 200.0\n # elution_vol = 50.0\n # settling_time = 5.0\n park_tips = False\n tip_track = False\n radial_offset = 0.3\n z_offset = 0.5\n air_gap_vol = 0\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n pcr_plate = ctx.load_labware('eppendorfmetaladapter_96_wellplate_200ul',\n '7', 'sample plate')\n magdeck = ctx.load_module('magnetic module gen2', '10')\n magdeck.disengage()\n magplate = magdeck.load_labware('abgenemidi_96_wellplate_800ul',\n 'deepwell wash plate')\n elutionplate = ctx.load_labware('eppendorfmetaladapter_96_wellplate_200ul',\n '2', 'elution plate')\n waste = ctx.loaded_labwares[12].wells()[0].top()\n res1 = ctx.load_labware('nest_12_reservoir_15ml', '6', 'reagent reservoir')\n num_cols = math.ceil(num_samples/6) # offset\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200ul tiprack')\n for slot in ['4', '9', '11']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '5',\n '20ul tiprack')]\n if park_tips:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '1', '200ul tiprack')\n parking_spots = rack.rows()[0][:num_cols]\n else:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '1', '200ul tiprack')\n parking_spots = [None for none in range(12)]\n tips300.insert(0, rack)\n\n # load pipettes\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tips20)\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', m300_mount, tip_racks=tips300)\n\n m300.default_speed = 180\n m20.default_speed = 180\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n binding_buffer = res1.rows()[0][:1]\n wash1 = res1.rows()[0][1:4]\n wash2 = res1.rows()[0][4:7]\n elution_solution = res1.rows()[0][-1]\n\n starting_samples = pcr_plate.rows()[0][:num_cols]\n mag_samples_m = magplate.rows()[0][:num_cols]\n elution_samples_m = elutionplate.rows()[0][:num_cols]\n radius = mag_samples_m[0].diameter/2\n\n magdeck.disengage() # just in case\n\n m300.flow_rate.aspirate = 20\n m300.flow_rate.dispense = 50\n m300.flow_rate.blow_out = 150\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[2]] # offset\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + 'ul tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip):\n nonlocal switch\n nonlocal drop_count\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n # Setup for flashing lights notification to empty trash\n ctx.home() # home before continuing with protocol\n drop_count = 0\n\n waste_vol = 0\n waste_threshold = 185000\n\n def remove_supernatant(vol, pip=m300, park=False):\n \"\"\"\n `remove_supernatant` will transfer supernatant from the deepwell\n extraction plate to the liquid waste reservoir.\n :param vol (float): The amount of volume to aspirate from all deepwell\n sample wells and dispense in the liquid waste.\n :param park (boolean): Whether to pick up sample-corresponding tips\n in the 'parking rack' or to pick up new tips.\n \"\"\"\n def _waste_track(vol):\n nonlocal waste_vol\n if waste_vol + vol >= waste_threshold:\n # Setup for flashing lights notification to empty liquid waste\n ctx.home()\n waste_vol = 0\n waste_vol += vol\n\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if park:\n _pick_up(pip, spot)\n else:\n _pick_up(pip)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side*radius*radial_offset,\n z=z_offset))\n _waste_track(vol)\n pip.move_to(m.center())\n # if pip == m300:\n # air_gap_vol = 20\n # else:\n # air_gap_vol = pip.max_volume - vol\n pip.transfer(vol, loc, waste, new_tip='never',\n air_gap=(air_gap_vol))\n # pip.blow_out(waste)\n _drop(pip)\n\n def bind(vol, park=True):\n \"\"\"\n `bind` will perform magnetic bead binding on each sample in the\n deepwell plate. Each channel of binding beads will be mixed before\n transfer, and the samples will be mixed with the binding beads after\n the transfer. The magnetic deck activates after the addition to all\n samples, and the supernatant is removed after bead binding.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n m300.flow_rate.aspirate = 30\n latest_chan = -1\n _pick_up(m300)\n for i, (well, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n asp_per_chan = (\n 0.95*res1.rows()[0][0].max_volume)//(vol_per_trans*8)\n for t in range(num_trans):\n chan_ind = int((i*num_trans + t)//asp_per_chan)\n source = binding_buffer[chan_ind]\n if m300.current_volume > 0:\n # void air gap if necessary\n m300.dispense(m300.current_volume, source.top())\n if chan_ind > latest_chan: # mix if accessing new channel\n for _ in range(5):\n m300.aspirate(180, source.bottom(0.1))\n m300.dispense(180, source.bottom(5))\n latest_chan = chan_ind\n m300.transfer(vol_per_trans, source, well.bottom(0.1),\n air_gap=20, new_tip='never')\n m300.blow_out(well.bottom(2))\n m300.air_gap(20)\n # m300.mix(10, 200, well)\n # m300.blow_out(well.top(-2))\n _drop(m300)\n\n m300.flow_rate.aspirate = 80\n\n # transfer samples\n for source, dest, spot in zip(starting_samples, mag_samples_m,\n parking_spots):\n if not m300.has_tip:\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n # _drop(m300)\n # _pick_up(m300)\n m300.transfer(sample_vol, source.bottom(0.1), dest,\n mix_after=(10, sample_vol),\n air_gap=air_gap_vol, new_tip='never')\n m300.air_gap(air_gap_vol)\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n ctx.delay(minutes=5, msg='Incubating off magnet for 5 minutes.')\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=settling_time, msg=f'Incubating on MagDeck for \\\n{settling_time} minutes.')\n\n # remove initial supernatant\n remove_supernatant(150, park=park)\n\n def wash(vol, source, mix_reps=15, park=True, blow_out=False,\n resuspend=False):\n \"\"\"\n `wash` will perform bead washing for the extraction protocol.\n :param vol (float): The amount of volume to aspirate from each\n source and dispense to each well containing beads.\n :param source (List[Well]): A list of wells from where liquid will be\n aspirated. If the length of the source list\n > 1, `wash` automatically calculates\n the index of the source that should be\n accessed.\n :param mix_reps (int): The number of repititions to mix the beads with\n specified wash buffer (ignored if resuspend is\n False).\n :param park (boolean): Whether to save sample-corresponding tips\n between adding wash buffer and removing\n supernatant.\n :param resuspend (boolean): Whether to resuspend beads in wash buffer.\n \"\"\"\n\n if resuspend and magdeck.status == 'engaged':\n magdeck.disengage()\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n src = source[int(i//(12/len(source)))]\n for n in range(num_trans):\n if m300.current_volume > 0:\n m300.dispense(m300.current_volume, src.top())\n m300.transfer(vol_per_trans, src, m.top(), air_gap=air_gap_vol,\n new_tip='never')\n if blow_out:\n m300.blow_out(m.top(-1))\n if n < num_trans - 1: # only air_gap if going back to source\n m300.air_gap(air_gap_vol)\n if resuspend:\n m300.mix(mix_reps, 150, loc)\n m300.blow_out(m.top())\n m300.air_gap(air_gap_vol)\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n if magdeck.status == 'disengaged':\n magdeck.engage(height=mag_height)\n\n ctx.delay(seconds=60, msg='Incubating on MagDeck for 60s seconds.')\n remove_supernatant(vol, park=park)\n\n def elute(vol, park=True):\n \"\"\"\n `elute` will perform elution from the deepwell extraciton plate to the\n final clean elutions PCR plate to complete the extraction protocol.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n\n # resuspend beads in elution\n magdeck.disengage()\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.aspirate(vol+2.5, elution_solution)\n m300.move_to(m.center())\n m300.dispense(vol, loc)\n m300.mix(10, 0.8*vol, loc)\n m300.blow_out(m.bottom(5))\n m300.air_gap(air_gap_vol)\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n magdeck.engage(height=mag_height)\n ctx.delay(minutes=settling_time, msg=f'Incubating on MagDeck for \\\n{settling_time} minutes.')\n\n for i, (m, e, spot) in enumerate(\n zip(mag_samples_m, elution_samples_m, parking_spots)):\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.transfer(vol, loc, e.bottom(5), air_gap=air_gap_vol,\n new_tip='never')\n m300.blow_out(e.top(-2))\n m300.air_gap(air_gap_vol)\n m300.drop_tip()\n\n \"\"\"\n Here is where you can call the methods defined above to fit your specific\n protocol. The normal sequence is:\n \"\"\"\n bind(binding_buffer_vol, park=park_tips)\n wash(wash1_vol, wash1, park=park_tips, blow_out=True)\n wash(wash2_vol, wash2, park=park_tips)\n remove_supernatant(18, pip=m20)\n elute(elution_vol, park=park_tips)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Axygen", - "brandId": [ - "14-222-327" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 15.51 - }, - "groups": [ - { - "brand": { - "brand": "Axygen", - "brandId": [ - "14-222-327" - ] - }, - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Axygen 96 Well Plate 200ul", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Axygen 96 Well Plate 200ul", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "axygen_96_wellplate_200ul", - 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"value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "P300 multi-channel GEN2 pipette mount", - "name": "m300_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "default": 6.8, - "label": "magnetic engage height (in mm)", - "name": "mag_height", - "type": "float" - }, - { - "default": 0.5, - "label": "height offset from bottom of deepwell plate (in mm)", - "name": "z_offset", - "type": "float" - }, - { - "default": 0.3, - "label": "lateral offset (as fraction of deepwell radius)", - "name": "radial_offset", - "type": "float" - }, - { - "default": 45.0, - "label": "sample volume", - "name": "sample_vol", - "type": "float" - }, - { - "default": 45.0, - "label": "initial binding buffer volume (in ul)", - "name": "binding_buffer_vol", - "type": "float" - }, - { - "default": 200.0, - "label": "wash 1 volume (in ul, up to 500ul)", - "name": "wash1_vol", - "type": "float" - }, - { - "default": 200.0, - "label": "wash 2 volume (in ul, up to 500ul)", - "name": "wash2_vol", - "type": "float" - }, - { - "default": 50.0, - "label": "initial elution volume (in ul)", - "name": "elution_vol", - "type": "float" - }, - { - "default": 2.0, - "label": "bead settling time (in minutes)", - "name": "settling_time", - "type": "float" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - }, - { - "mount": "right", - "name": "p300_multi_gen2" - } - ], - "labware": [ - { - "name": "200ul tiprack on 1", - "share": false, - "slot": "1", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "elution plate on 2", - "share": false, - "slot": "2", - "type": "eppendorfmetaladapter_96_wellplate_200ul" - }, - { - "name": "200ul tiprack on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "20ul tiprack on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "reagent reservoir on 6", - "share": false, - "slot": "6", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "sample plate on 7", - "share": false, - "slot": "7", - "type": "eppendorfmetaladapter_96_wellplate_200ul" - }, - { - "name": "200ul tiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "deepwell wash plate on Magnetic Module GEN2 on 10", - "share": false, - "slot": "10", - "type": "abgenemidi_96_wellplate_800ul" - }, - { - "name": "200ul tiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.10", - "author": "Opentrons ", - "protocolName": "SPRI 3" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json b/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json index 917d58bb04..f2931972c8 100644 --- a/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json +++ b/protoBuilds/3633ca/3633ca.ot2.apiv2.py.json @@ -87,5 +87,12 @@ "protocolName": "Ethanol Transfer", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json b/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json index 430ebd935e..15a6e67c02 100644 --- a/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json +++ b/protoBuilds/39b4c7/39b4c7.ot2.apiv2.py.json @@ -5620,5 +5620,12 @@ "description": "Custom Protocol Request", "protocolName": "Reformat 96 Well Plates to 384 Well Plate for qPCR" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json b/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json index a198f04bc5..c0c9ab4536 100644 --- a/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json +++ b/protoBuilds/3a49b6/3a49b6.ot2.apiv2.py.json @@ -105,5 +105,12 @@ "protocolName": "Normalization", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json b/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json index 6187da0f63..e9dbfaeb92 100644 --- a/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json +++ b/protoBuilds/3b0db0/3b0db0.ot2.apiv2.py.json @@ -1524,5 +1524,12 @@ "protocolName": "Temperature Controlled PCR Prep With Tube Strips", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json b/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json index 52faf03f55..32bfd8ce78 100644 --- a/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json +++ b/protoBuilds/3b3d2f/3b3d2f.ot2.apiv2.py.json @@ -106,5 +106,12 @@ "protocolName": "Plate Loading for ddPCR", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Tube Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json b/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json index 933d9e8fd9..25d8654dd9 100644 --- a/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json +++ b/protoBuilds/3cf31f/3cf31f.ot2.apiv2.py.json @@ -2295,5 +2295,12 @@ "description": "Custom Protocol Request", "protocolName": "BioFluid Mix and Transfer - Part 1/2 - APIv2" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 10 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN1 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json b/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json index 2832a981bc..3b0f38e821 100644 --- a/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json +++ b/protoBuilds/3fad82-part-2/3fad82-part-2.ot2.apiv2.py.json @@ -163,5 +163,18 @@ "author": "Steve Plonk ", "protocolName": "Quarter Volume NEBNext Ultra II DNA Library Prep Kit\n for Illumina: part 2 - purification of samples and PCR" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw Sample Plate on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Sample Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json b/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json index 1c44293714..44e57aae6a 100644 --- a/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json +++ b/protoBuilds/3fad82-part-3/3fad82-part-3.ot2.apiv2.py.json @@ -157,5 +157,18 @@ "author": "Steve Plonk ", "protocolName": "Quarter Volume NEBNext Ultra II DNA Library Prep Kit\n for Illumina: part 3 - final purification" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw Sample Plate on Magnetic Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw None", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json b/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json index f45a8a4e1b..7744372fdf 100644 --- a/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json +++ b/protoBuilds/3fad82/3fad82.ot2.apiv2.py.json @@ -114,5 +114,12 @@ "author": "Steve Plonk ", "protocolName": "Quarter Volume NEBNext Ultra II DNA Library Prep Kit for\n Illumina: part 1" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Sample Plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json b/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json index ea811d088b..eb3a40a61e 100644 --- a/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json +++ b/protoBuilds/407d5e/407d5e.ot2.apiv2.py.json @@ -162,5 +162,12 @@ "protocolName": "Protein Labeling with Incubation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4175de/4175de.ot2.apiv2.py.json b/protoBuilds/4175de/4175de.ot2.apiv2.py.json index ce6d5a432e..c25e8b2340 100644 --- a/protoBuilds/4175de/4175de.ot2.apiv2.py.json +++ b/protoBuilds/4175de/4175de.ot2.apiv2.py.json @@ -1233,5 +1233,12 @@ "description": "Custom Protocol Request", "protocolName": "Cherrypicking PCR/qPCR prep" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Applied Biosystems 96 Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json b/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json index 8ce7b7a40d..d8e505ee6c 100644 --- a/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json +++ b/protoBuilds/44b1ac/44b1ac.ot2.apiv2.py.json @@ -185,5 +185,24 @@ "description": "Custom Protocol Request", "protocolName": ": QIAseq Targeted RNAscan Panel for Illumina Instruments" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json b/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json index 5ec826d1be..56d5484e47 100644 --- a/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/453b5a/nuc_acid_pcr_prep.ot2.apiv2.py.json @@ -1620,7 +1620,7 @@ "type": "opentrons_96_tiprack_300ul" }, { - "name": "PCR plate on Temperature Module GEN1 on 10", + "name": "PCR plate on Temperature Module on 10", "share": false, "slot": "10", "type": "biozym_96_aluminumblock_200ul" @@ -1644,5 +1644,12 @@ "protocolName": "Nucleic Acid Purification and PCR Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 10 lw PCR plate on Temperature Module on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json b/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json index 7d1a5d5b1f..975452eebb 100644 --- a/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json +++ b/protoBuilds/4568fa-2/fa_workflow.ot2.apiv2.py.json @@ -1267,5 +1267,18 @@ "protocolName": "FA Workflow", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw None", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw None", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json b/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json index ab9b85a7a4..4d059b2ec0 100644 --- a/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json +++ b/protoBuilds/4568fa/fa_workflow.ot2.apiv2.py.json @@ -2452,5 +2452,18 @@ "protocolName": "FA Workflow", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw None", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw None", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4568fa/normalization.ot2.apiv2.py.json b/protoBuilds/4568fa/normalization.ot2.apiv2.py.json deleted file mode 100644 index 7dabd038ae..0000000000 --- a/protoBuilds/4568fa/normalization.ot2.apiv2.py.json +++ /dev/null @@ -1,1271 +0,0 @@ -{ - "content": "metadata = {\n 'protocolName': 'FA Workflow',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\nTEST_MODE = True\n\n\ndef run(ctx):\n\n [dil_csv_1, desired_conc, fill_plate_blank, p300_mount,\n p20_mount] = get_values( # noqa: F821\n 'dil_csv_1', 'desired_conc', 'fill_plate_blank', 'p300_mount',\n 'p20_mount')\n\n if TEST_MODE:\n mix_reps = 1\n else:\n mix_reps = 8\n\n tempdeck1 = ctx.load_module('temperature module gen2', '1')\n tempdeck1.set_temperature(4)\n dil_plate_final = ctx.load_labware(\n 'microampenduraplate_96_aluminumblock_200ul', '3', 'dilution plate 2')\n dil_plate_1 = ctx.load_labware(\n 'microampenduraplate_96_aluminumblock_200ul', '2',\n 'dilution plate 1')\n reservoir = ctx.load_labware('nest_12_reservoir_15ml', '9',\n 'reagent reservoir')\n tempdeck2 = ctx.load_module('temperature module gen2', '10')\n tempdeck2.set_temperature(70)\n tuberacks = [\n ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', slot,\n f'sample tuberack {i+1}')\n for i, slot in enumerate(['5', '6'])]\n tipracks200 = [\n ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['4', '7']]\n tipracks20 = [\n ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['8', '11']]\n\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tipracks200)\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tipracks20)\n\n sample_sources = [\n well for tuberack in tuberacks for well in tuberack.wells()]\n water = reservoir.wells()[0]\n hs_dil = tuberacks[-1].columns()[-1][1:]\n blank_solution = reservoir.wells()[1]\n\n data = [\n [val.strip() for val in line.split(',')]\n for line in dil_csv_1.splitlines()\n if line and line.split(',')[0].strip()][1:]\n num_samples = len(data)\n\n # dilute 2x to 4\u00b5g/ml\n dils_1 = dil_plate_1.wells()[:num_samples]\n dils_2 = dil_plate_1.wells()[48:48+num_samples] # use half of plate\n\n # pre-allocate water for dilution to 100\u00b5g/ml\n p300.pick_up_tip()\n for dil, line in zip(dils_1, data):\n conc = float(line[2])\n sample_vol = 10/conc\n dil_1_vol = 100 - sample_vol\n p300.transfer(dil_1_vol, water, dil, new_tip='never')\n\n # pre-allocate water for final desired dilution\n for well in dils_2:\n p300.transfer(100-desired_conc, water, well, new_tip='never')\n p300.drop_tip()\n\n # perform dilutions\n for sample, dil1, dil2, line in zip(sample_sources, dils_1, dils_2, data):\n conc = float(line[2])\n sample_vol = 10/conc\n p20.pick_up_tip()\n p20.transfer(sample_vol, sample, dil1,\n new_tip='never')\n p20.drop_tip()\n\n for dil1 in dils_1:\n p300.pick_up_tip()\n p300.mix(mix_reps, 80, dil1)\n p300.drop_tip()\n\n for sample, dil1, dil2, line in zip(sample_sources, dils_1, dils_2, data):\n p20.pick_up_tip()\n p20.transfer(desired_conc, dil1, dil2, new_tip='never')\n p20.drop_tip()\n\n for dil2 in dils_2:\n p300.pick_up_tip()\n p300.mix(mix_reps, 80, dil2)\n p300.drop_tip()\n\n # determine transfer scheme depending on number of samples\n if 1 <= num_samples <= 15:\n dests = dil_plate_final.rows_by_name()['A'] + [\n dil_plate_final.wells_by_name()[well]\n for well in ['D1', 'D4', 'D7']]\n dests = dests[:num_samples]\n triplicates = [col[:3] for col in dil_plate_final.columns()] + [\n dil_plate_final.rows_by_name()['D'][i*3:(i+1)*3] for i in range(3)]\n triplicate_sets = triplicates[:num_samples]\n dils_final = dests[:num_samples]\n final_dest = dil_plate_final.wells_by_name()['D12']\n # final_set = dil_plate_final.rows_by_name()['D'][9:]\n blank_wells = [\n well for well in [\n well for row in dil_plate_final.rows()[:4] for well in row]\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n\n elif 15 < num_samples <= 31:\n dests = dil_plate_final.rows()['A'] + dil_plate_final.rows()['D'] + [\n dil_plate_final.wells_by_name()[well]\n for well in ['G1', 'G4', 'G7', 'G10', 'H1', 'H4', 'H7']]\n dests = dests[:num_samples]\n triplicates = [col[:3] for col in dil_plate_final.columns()] + [\n col[4:6] for col in dil_plate_final.columns()] + [\n dil_plate_final.rows_by_name()['G'][i*3:(i+1)*3]\n for i in range(4)] + [\n dil_plate_final.rows_by_name()['H'][i*3:(i+1)*3] for i in range(3)]\n triplicate_sets = triplicates[:num_samples]\n dils_final = dests[:num_samples]\n final_dest = dil_plate_final.wells_by_name()['H12']\n # final_set = dil_plate_final.rows_by_name()['H'][9:]\n blank_wells = [\n well for well in dil_plate_final.wells()\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n else:\n raise Exception(f'Invalid number of samples given ({num_samples}). \\\nMust be 1-31 samples.')\n\n if num_samples > 15 or fill_plate_blank:\n blank_wells = [\n well for well in dil_plate_final.wells()\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n else:\n blank_wells = [\n well for well in [\n well for row in dil_plate_final.rows()[:4] for well in row]\n if well not in [\n well for set in [*triplicate_sets, *[[final_dest]]]\n for well in set]]\n\n # pre-add HS diluent\n p300.pick_up_tip()\n\n for i, d in enumerate(dests):\n p300.transfer(135, hs_dil[i//11], d, new_tip='never')\n p300.transfer(27, hs_dil[0], final_dest, new_tip='never')\n p300.drop_tip()\n\n # transfer sample\n for s, d in zip(dils_2, dils_final):\n p20.transfer(15, s, d)\n\n # transfer RNA ladder\n # p20.transfer(3, rna_ladder, final_dest)\n final_well_display = final_dest.display_name.split(' ')[0]\n ctx.pause(f'Add 3ul RNA ladder to well {final_well_display}')\n\n # mix all samples with diluent\n for set in triplicate_sets:\n p300.pick_up_tip()\n p300.mix(mix_reps, 120, set[0])\n # transfer triplicates\n p300.transfer(50, set[0], set[1:], new_tip='never')\n p300.drop_tip()\n\n # mix RNA ladder with diluent\n p300.pick_up_tip()\n p300.mix(mix_reps, 20, final_dest)\n p300.drop_tip()\n\n # heat samples\n ctx.pause('Seal the plate in slot 3 and place on the temperature module on \\\nslot 10. Resume when finished.')\n ctx.home()\n if not TEST_MODE:\n ctx.delay(minutes=2)\n ctx.home()\n ctx.pause('Move the plate from temperature module on slot 10 to temperature \\\nmodule on slot 1.')\n if not TEST_MODE:\n ctx.delay(minutes=5)\n ctx.home()\n [td.deactivate() for td in [tempdeck1, tempdeck2]]\n ctx.pause('Centrifuge the plate on temperature module on slot 1. Replace \\\non temperature module on slot 3 when complete.')\n\n # transfer water to blank wells\n p300.transfer(50, blank_solution, blank_wells)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "MicroAmp EnduraPlate", - "brandId": [ - "4483352" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 21.2 - }, - "groups": [ - { - "metadata": { - "displayCategory": "wellPlate", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "MicroAmp EnduraPlate 96 Aluminum Block 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "microampenduraplate_96_aluminumblock_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 74.25, - "z": 1.1 - }, - "A10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 74.25, - "z": 1.1 - }, - "A11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 74.25, - "z": 1.1 - }, - "A12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 74.25, - "z": 1.1 - }, - "A2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 74.25, - "z": 1.1 - }, - "A3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 74.25, - "z": 1.1 - }, - "A4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 74.25, - "z": 1.1 - }, - "A5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 74.25, - "z": 1.1 - }, - "A6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 74.25, - "z": 1.1 - }, - "A7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 74.25, - "z": 1.1 - }, - "A8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 74.25, - "z": 1.1 - }, - "A9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 74.25, - "z": 1.1 - }, - "B1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 65.25, - "z": 1.1 - }, - "B10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 65.25, - "z": 1.1 - }, - "B11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 65.25, - "z": 1.1 - }, - "B12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 65.25, - "z": 1.1 - }, - "B2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 65.25, - "z": 1.1 - }, - "B3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 65.25, - "z": 1.1 - }, - "B4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 65.25, - "z": 1.1 - }, - "B5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 65.25, - "z": 1.1 - }, - "B6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 65.25, - "z": 1.1 - }, - "B7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 65.25, - "z": 1.1 - }, - "B8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 65.25, - "z": 1.1 - }, - "B9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 65.25, - "z": 1.1 - }, - "C1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 56.25, - "z": 1.1 - }, - "C10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 56.25, - "z": 1.1 - }, - "C11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 56.25, - "z": 1.1 - }, - "C12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 56.25, - "z": 1.1 - }, - "C2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 56.25, - "z": 1.1 - }, - "C3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 56.25, - "z": 1.1 - }, - "C4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 56.25, - "z": 1.1 - }, - "C5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 56.25, - "z": 1.1 - }, - "C6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 56.25, - "z": 1.1 - }, - "C7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 56.25, - "z": 1.1 - }, - "C8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 56.25, - "z": 1.1 - }, - "C9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 56.25, - "z": 1.1 - }, - "D1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 47.25, - "z": 1.1 - }, - "D10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 47.25, - "z": 1.1 - }, - "D11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 47.25, - "z": 1.1 - }, - "D12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 47.25, - "z": 1.1 - }, - "D2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 47.25, - "z": 1.1 - }, - "D3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 47.25, - "z": 1.1 - }, - "D4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 47.25, - "z": 1.1 - }, - "D5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 47.25, - "z": 1.1 - }, - "D6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 47.25, - "z": 1.1 - }, - "D7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 47.25, - "z": 1.1 - }, - "D8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 47.25, - "z": 1.1 - }, - "D9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 47.25, - "z": 1.1 - }, - "E1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 38.25, - "z": 1.1 - }, - "E10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 38.25, - "z": 1.1 - }, - "E11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 38.25, - "z": 1.1 - }, - "E12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 38.25, - "z": 1.1 - }, - "E2": { - 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"x": 59.38, - "y": 20.25, - "z": 1.1 - }, - "G7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 20.25, - "z": 1.1 - }, - "G8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 20.25, - "z": 1.1 - }, - "G9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 20.25, - "z": 1.1 - }, - "H1": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 14.38, - "y": 11.25, - "z": 1.1 - }, - "H10": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 95.38, - "y": 11.25, - "z": 1.1 - }, - "H11": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 104.38, - "y": 11.25, - "z": 1.1 - }, - "H12": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 113.38, - "y": 11.25, - "z": 1.1 - }, - "H2": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 23.38, - "y": 11.25, - "z": 1.1 - }, - "H3": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 32.38, - "y": 11.25, - "z": 1.1 - }, - "H4": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 41.38, - "y": 11.25, - "z": 1.1 - }, - "H5": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 50.38, - "y": 11.25, - "z": 1.1 - }, - "H6": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 59.38, - "y": 11.25, - "z": 1.1 - }, - "H7": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 68.38, - "y": 11.25, - "z": 1.1 - }, - "H8": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 77.38, - "y": 11.25, - "z": 1.1 - }, - "H9": { - "depth": 20.1, - "diameter": 5.49, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 86.38, - "y": 11.25, - "z": 1.1 - } - } - } - ], - "fields": [ - { - "default": "sample number,sample name,sample concentration (mg/ml)\n1,007007009-403-1,1.569\n2,007007009-403-2,0.984\n3,007007009-403-3,2.128\n4,007007009-403-4,2.413\n", - "label": "input .csv for normalization", - "name": "dil_csv_1", - "type": "textFile" - }, - { - "default": 4.0, - "label": "desired final concentration (ug/ml)", - "name": "desired_conc", - "type": "float" - }, - { - "label": "fill entire plate with blank if necessary", - "name": "fill_plate_blank", - "options": [ - { - "label": "yes", - "value": true - }, - { - "label": "no", - "value": false - } - ], - "type": "dropDown" - }, - { - "label": "P300 single-channel pipette mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "P20 single-channel pipette mount", - "name": "p20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - }, - { - "mount": "right", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "dilution plate 1 on 2", - "share": false, - "slot": "2", - "type": "microampenduraplate_96_aluminumblock_200ul" - }, - { - "name": "dilution plate 2 on 3", - "share": false, - "slot": "3", - "type": "microampenduraplate_96_aluminumblock_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "sample tuberack 1 on 5", - "share": false, - "slot": "5", - "type": "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap" - }, - { - "name": "sample tuberack 2 on 6", - "share": false, - "slot": "6", - "type": "opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "reagent reservoir on 9", - "share": false, - "slot": "9", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "FA Workflow", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json b/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json index a7421ea837..459b51d291 100644 --- a/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json +++ b/protoBuilds/459a55/mass_spec_prep.ot2.apiv2.py.json @@ -51,7 +51,7 @@ ], "labware": [ { - "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 1", + "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 1", "share": false, "slot": "1", "type": "opentrons_96_aluminumblock_nest_wellplate_100ul" @@ -87,5 +87,12 @@ "protocolName": "Mass Spec Sample Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 1 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/48648f/48648f.ot2.apiv2.py.json b/protoBuilds/48648f/48648f.ot2.apiv2.py.json index a45fb5de72..8402e86541 100644 --- a/protoBuilds/48648f/48648f.ot2.apiv2.py.json +++ b/protoBuilds/48648f/48648f.ot2.apiv2.py.json @@ -1554,5 +1554,12 @@ "subcategory": "None", "tags": "None" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Extraction Plate on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json b/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json index 9e778e9ba7..d0717bf963 100644 --- a/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json +++ b/protoBuilds/49de51-pt2/49de51-pt2.ot2.apiv2.py.json @@ -1285,5 +1285,12 @@ "protocolName": "MagMAX Plant DNA Isolation Kit [2/2]", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json b/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json index 996558100b..8b765db8c6 100644 --- a/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json +++ b/protoBuilds/49de51/thermo_magmax_plant_isolation.ot2.apiv2.py.json @@ -95,5 +95,18 @@ "protocolName": "ThermoFisher MagMAX Plant DNA Isolation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw deepwell plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw NEST 96 Deepwell Plate 2mL on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json b/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json index 2a7cc5dc8d..4a460a9f48 100644 --- a/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json +++ b/protoBuilds/4a5f32/4a5f32.ot2.apiv2.py.json @@ -1785,5 +1785,12 @@ "description": "Custom Protocol Request", "protocolName": "Nucleic Acid Purification with Magnetic Beads" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw 4ti-0960/C 96 Well Full Skirted Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json b/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json index 4e067d87c3..e93b4db719 100644 --- a/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json +++ b/protoBuilds/4b4a80-fragmentation/4b4a80-fragmentation.ot2.apiv2.py.json @@ -1241,5 +1241,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II FS DNA Library Prep Kit for Illumina\n E6177S/L (for 1-24 DNA samples): Step 2: Fragmentation" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 2 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 2", + "share": false, + "slot": "2", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Thermo-Fast 96 Well Plate 200 \u00b5L on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json b/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json index f352831b9d..63470fdec8 100644 --- a/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json +++ b/protoBuilds/4b4a80-pcr_enrichment/4b4a80-pcr_enrichment.ot2.apiv2.py.json @@ -1313,5 +1313,24 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II FS DNA Library Prep Kit for Illumina\n E6177S/L (for 1-24 DNA samples): Step 5: PCR Enrichment" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 2 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 2", + "share": false, + "slot": "2", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json b/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json index 2a426bad20..24f0b37261 100644 --- a/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json +++ b/protoBuilds/4b4a80-size_selection/4b4a80-size_selection.ot2.apiv2.py.json @@ -1289,5 +1289,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II FS DNA Library Prep Kit for Illumina\n E6177S/L (for 1-24 DNA samples): Step 4: Size Selection" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 2 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 2", + "share": false, + "slot": "2", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json b/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json index 92645f8c30..4ff1c570f9 100644 --- a/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json +++ b/protoBuilds/4b7268/4b7268.ot2.apiv2.py.json @@ -182,5 +182,12 @@ "author": "Steve Plonk ", "protocolName": "Custom Nucleic Acid Extraction and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw Deep Well Plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json b/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json index 820ac4e030..3ff469ed81 100644 --- a/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json +++ b/protoBuilds/4ee4d6-part2/4ee4d6-part2.ot2.apiv2.py.json @@ -80,5 +80,24 @@ "author": "Steve Plonk ", "protocolName": "Illumina DNA Prep with Enrichment:\n Part 2 - Clean Up and Pool Libraries, Hybridize and Capture Probes,\n Amplify Enriched Library, Clean Up Enriched Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 9 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN1 on 9", + "share": false, + "slot": "9", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json b/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json index d805639d03..38d613b26e 100644 --- a/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json +++ b/protoBuilds/4ee4d6/4ee4d6.ot2.apiv2.py.json @@ -98,5 +98,24 @@ "author": "Steve Plonk ", "protocolName": "Illumina DNA Prep with Enrichment:\n Part 1 - Tagmentation, Clean Up, Amplify Tagmented DNA" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 9 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN1 on 9", + "share": false, + "slot": "9", + "type": "tempdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json b/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json index 9df726c066..1db36ca2d3 100644 --- a/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json +++ b/protoBuilds/4fa62e/4fa62e.ot2.apiv2.py.json @@ -63,5 +63,12 @@ "description": "Custom Protocol Request", "protocolName": "PCR Preparation" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/4fc750/extraction.ot2.apiv2.py.json b/protoBuilds/4fc750/extraction.ot2.apiv2.py.json index e6fa34e970..a074cc9b5b 100644 --- a/protoBuilds/4fc750/extraction.ot2.apiv2.py.json +++ b/protoBuilds/4fc750/extraction.ot2.apiv2.py.json @@ -302,5 +302,12 @@ "author": "Opentrons ", "protocolName": "Omega Mag-Bind\u00ae Blood & Tissue DNA 96 Kit - 250\u03bcL Blood Protocol" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw deepwell plate on Magnetic Module GEN1 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/52d238/52d238.ot2.apiv2.py.json b/protoBuilds/52d238/52d238.ot2.apiv2.py.json index f86b255877..c10d2113b6 100644 --- a/protoBuilds/52d238/52d238.ot2.apiv2.py.json +++ b/protoBuilds/52d238/52d238.ot2.apiv2.py.json @@ -1285,5 +1285,24 @@ "description": "PCR, Bead Clean up, and Elution", "protocolName": "NEB Ultra II FS DNA Library Prep (Part 2)" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json b/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json index ac80136248..c10d0ff0f1 100644 --- a/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json +++ b/protoBuilds/53e6bc_mastermix_creation/antibody_mm_creation.ot2.apiv2.py.json @@ -1415,7 +1415,7 @@ ], "labware": [ { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module GEN1 on 1", + "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 1", "share": false, "slot": "1", "type": "eppendorftwin.tec_96_wellplate_150ul" @@ -1457,5 +1457,12 @@ "protocolName": "Mastermix Creation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module on 1 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json b/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json index c4ea410318..3b28e678d6 100644 --- a/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/53fec2/omega_pcr_cleanup.ot2.apiv2.py.json @@ -2541,5 +2541,12 @@ "author": "Opentrons ", "protocolName": "Beckman Coulter AMPure XP PCR Cleanup and Size Selection" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw deepwell plate on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json b/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json index cd58692cc5..9587677b69 100644 --- a/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json +++ b/protoBuilds/558d02/peptide_enrichment.ot2.apiv2.py.json @@ -1187,7 +1187,7 @@ ], "labware": [ { - "name": "USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module GEN1 on 1", + "name": "USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module on 1", "share": false, "slot": "1", "type": "usascientific_96_wellplate_2.4ml_deep" @@ -1265,5 +1265,12 @@ "protocolName": "Magbead-Based Peptide Enrichment", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json b/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json index 95b6505b21..d43cd0b5cc 100644 --- a/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json +++ b/protoBuilds/5c7384/mass_spec_sample_prep.ot2.apiv2.py.json @@ -117,5 +117,18 @@ "protocolName": "Mass Spec Sample Prep", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw sample plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json b/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json index f0596a6ca6..deeb9d9581 100644 --- a/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json +++ b/protoBuilds/5dcd88/5dcd88.ot2.apiv2.py.json @@ -193,5 +193,12 @@ "protocolName": "nCoV-2019 Lo Cost protocol", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 10 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 10", + "share": false, + "slot": "10", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json b/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json index eb7a5e7b0b..dc1810784a 100644 --- a/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json +++ b/protoBuilds/5f37a2/5fe7a2.ot2.apiv2.py.json @@ -2423,7 +2423,7 @@ "type": "eppendorf_96_deepwellplate_500ul" }, { - "name": "Eppendorf DWP 2000ul on Magnetic Module GEN1 on 10", + "name": "Eppendorf DWP 2000ul on Magnetic Module on 10", "share": false, "slot": "10", "type": "eppendorf_96_deepwellplate_2000ul" @@ -2447,5 +2447,12 @@ "protocolName": "Nucleic Acid Purification", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 10 lw Eppendorf DWP 2000ul on Magnetic Module on 10", + "share": false, + "slot": "10", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json b/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json index 340844c596..4ec7975fbc 100644 --- a/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json +++ b/protoBuilds/5f7d18/5f7d18.ot2.apiv2.py.json @@ -195,5 +195,12 @@ "protocolName": "Viral Nucleic Acid Isolation from Oral and Nasal swabs", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json b/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json index d19e37e15f..16fa5d8010 100644 --- a/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json +++ b/protoBuilds/5fa647/5fa647.ot2.apiv2.py.json @@ -422,5 +422,12 @@ "protocolName": "SuperScript III: qRT-PCR Prep with CSV File", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json b/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json index dbbbb21c65..d4a11ffb79 100644 --- a/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/640a85/pcr_prep.ot2.apiv2.py.json @@ -1244,5 +1244,12 @@ "protocolName": "PCR Prepation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw Thermo Scientific 96 Well Plate 300 \u00b5L on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json b/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json index ad1e4f60f5..8589831f0d 100644 --- a/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json +++ b/protoBuilds/65ed01/65ed01.ot2.apiv2.py.json @@ -1299,5 +1299,12 @@ "protocolName": "Nucleic Acid Purification with Magnetic Beads", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw YDP-96-2.2-SC 96_wellplate_2200ul on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/69db93/69db93.ot2.apiv2.py.json b/protoBuilds/69db93/69db93.ot2.apiv2.py.json index 0afcc823b2..ad15616c22 100644 --- a/protoBuilds/69db93/69db93.ot2.apiv2.py.json +++ b/protoBuilds/69db93/69db93.ot2.apiv2.py.json @@ -140,5 +140,12 @@ "protocolName": "RNA Extraction With Magnetic Beads (no tip waste)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a77d9/ngs_cleanup.ot2.apiv2.py.json b/protoBuilds/6a77d9/ngs_cleanup.ot2.apiv2.py.json deleted file mode 100644 index 84712e00ca..0000000000 --- a/protoBuilds/6a77d9/ngs_cleanup.ot2.apiv2.py.json +++ /dev/null @@ -1,142 +0,0 @@ -{ - "content": "from opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'Liquid Deposition on Custom Surface',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.9'\n}\n\n\ndef run(ctx):\n\n volume, loc_csv, p20_type, p20_mount = get_values( # noqa: F821\n 'volume', 'loc_csv', 'p20_type', 'p20_mount')\n\n res = ctx.load_labware('usascientific_96_wellplate_2.4ml_deep', '10')\n tiprack20 = [ctx.load_labware('opentrons_96_tiprack_20ul', '11')]\n source = res.rows()[0][0]\n plate = ctx.load_labware('custom_1_other_20ul', '1')\n\n p20 = ctx.load_instrument(p20_type, p20_mount, tip_racks=tiprack20)\n # match mount to axis\n axis_map = {\n 'right': 'A',\n 'left': 'Z'\n }\n\n # parse .csv\n offsets = [\n [float(val) for val in line.split(',')]\n for line in loc_csv.splitlines()[1:]]\n\n # grid creation methods\n x_spaces = [0, 9, 13.5, 22.5]\n y_spaces = [0, -9, -18, -27]\n ref_a1 = plate.wells()[0].top().move(Point(x=0, y=0))\n\n def create_col(ref):\n col = [ref.move(Point(y=y_space)) for y_space in y_spaces]\n return col\n\n def create_grid(x_grid, y_grid):\n grid = []\n for x_start, y_start in zip([0, -4.5], [0, -4.5]):\n for x_space in x_spaces:\n ref = ref_a1.move(Point(x=x_grid+x_space+x_start,\n y=y_grid+y_start))\n grid.append(create_col(ref))\n return grid\n\n # initialize and create grids\n grids = [create_grid(0, 0)]\n for offset in offsets:\n x, y = offset\n grid = create_grid(x, y)\n grids.append(grid)\n\n # setup destinations depending on pipette type\n if p20_type == 'p20_multi_gen2':\n dests = [col[0] for grid in grids for col in grid]\n # update when P20 multi is received\n else:\n for grid in grids:\n dests = [well for col in grid for well in col]\n p20.pick_up_tip()\n for dest in dests:\n print(dest.point)\n p20.aspirate(volume, source)\n p20.move_to(dest.move(Point(z=10)))\n ctx.max_speeds[axis_map[p20_mount]] = 10\n p20.move_to(dest)\n p20.dispense(volume, dest)\n del ctx.max_speeds[axis_map[p20_mount]]\n p20.drop_tip()\n print('\\n\\n\\n\\n')\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "custom", - "brandId": [], - "links": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 397.5, - "yDimension": 236, - "zDimension": 100 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "flat" - }, - "wells": [ - "A1" - ] - } - ], - "metadata": { - "displayCategory": "other", - "displayName": "Custom Surface", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "custom_1_other_20ul" - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 0.5, - "diameter": 4.5, - "shape": "circular", - "totalLiquidVolume": 20, - "x": 14.38, - "y": 224.77, - "z": 99.5 - } - } - } - ], - "fields": [ - { - "default": 10, - "label": "transfer volume (in \u00b5l)", - "name": "volume", - "type": "float" - }, - { - "default": "x offset (in mm),y offset (in mm)\n20, -20", - "label": "location offset .csv", - "name": "loc_csv", - "type": "textFile" - }, - { - "label": "P20 GEN2 type", - "name": "p20_type", - "options": [ - { - "label": "single", - "value": "p20_single_gen2" - } - ], - "type": "dropDown" - }, - { - "label": "P20 GEN2 pipette mount", - "name": "p20_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "Custom Surface on 1", - "share": false, - "slot": "1", - "type": "custom_1_other_20ul" - }, - { - "name": "USA Scientific 96 Deep Well Plate 2.4 mL on 10", - "share": false, - "slot": "10", - "type": "usascientific_96_wellplate_2.4ml_deep" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.9", - "author": "Nick ", - "protocolName": "Liquid Deposition on Custom Surface", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json b/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json index 5af28b39ba..f3a68d4d72 100644 --- a/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part2/6a93a2-part2.ot2.apiv2.py.json @@ -148,5 +148,18 @@ "protocolName": "Swift Rapid NGS Part 2 - Adaptase", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json b/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json index a10dea41d6..1fcbab0dcb 100644 --- a/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part3/6a93a2-part3.ot2.apiv2.py.json @@ -151,5 +151,24 @@ "protocolName": "Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json b/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json index 74ba0c1c9b..19f67dbaa7 100644 --- a/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part4/6a93a2-part4.ot2.apiv2.py.json @@ -129,5 +129,12 @@ "protocolName": "Swift Rapid NGS Part 4 - SPRI Clean", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json b/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json index 8b358d0bc4..0937a59158 100644 --- a/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2-part5/6a93a2-part5.ot2.apiv2.py.json @@ -1289,5 +1289,18 @@ "protocolName": "Swift Rapid NGS Part 5 - Indexing and SPRI Clean", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json b/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json index 31a2c34b3d..bb3b3b9641 100644 --- a/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json +++ b/protoBuilds/6a93a2/6a93a2.ot2.apiv2.py.json @@ -1277,5 +1277,24 @@ "protocolName": "Swift Rapid NGS Part 1 - Reverse Transcription", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with Generic 2 mL Screwcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6a93a3-part2/6a93a2-part2.ot2.apiv2.py.json b/protoBuilds/6a93a3-part2/6a93a2-part2.ot2.apiv2.py.json deleted file mode 100644 index 4d2be8ee35..0000000000 --- a/protoBuilds/6a93a3-part2/6a93a2-part2.ot2.apiv2.py.json +++ /dev/null @@ -1,152 +0,0 @@ -{ - "content": "import math\n\nmetadata = {\n 'protocolName': 'Swift Rapid NGS Part 2 - Adaptase',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.7'\n}\n\n\ndef run(ctx):\n\n [num_samp, tip_type, overage_percent,\n p20_mount, p300_mount] = get_values( # noqa: F821\n \"num_samp\", \"tip_type\", \"overage_percent\",\n \"p20_mount\", \"p300_mount\")\n\n # keep user in range\n num_samp = int(num_samp)\n if not 0.0 <= overage_percent <= 10.0:\n raise Exception(\"Enter a an overage percent between 5-10%\")\n overage_percent = 1+overage_percent/100\n num_cols = math.ceil(int(num_samp/8))\n\n # load labware\n thermocycler = ctx.load_module('thermocycler')\n samp_plate = thermocycler.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt')\n temperature_mod = ctx.load_module('temperature module gen2', '3')\n alum_tuberack = temperature_mod.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n tiprack20 = [ctx.load_labware(tip_type, slot) for slot in ['6', '9']]\n tiprack300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['4', '5']]\n\n # load instruments\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tiprack20)\n m300 = ctx.load_instrument('p300_multi', p300_mount, tip_racks=tiprack300)\n\n # make Adaptase Mastermix\n temperature_mod.set_temperature(4)\n mastermix = alum_tuberack.rows()[1][0]\n reagents = alum_tuberack.rows()[0][:6]\n vols = [math.ceil(num_samp*rxn_vol*overage_percent)\n for rxn_vol in [2, 2, 1.25, 0.5, 0.5, 4.25]]\n num_cols = math.ceil(int(num_samp/8))\n sample_cols = samp_plate.rows()[0][4:4+num_cols]\n\n for reagent, vol in zip(reagents, vols):\n p20.pick_up_tip()\n p20.transfer(vol, reagent, mastermix.top(), new_tip='never')\n p20.drop_tip()\n\n ctx.pause(\"\"\"Vortex mix Adaptase mix tube (tube B1)\n After placing mix tube back, thermocycler will warm up.\"\"\")\n\n # operate thermocycler - denature samples\n if thermocycler.lid_position != 'open':\n thermocycler.open_lid()\n thermocycler.set_lid_temperature(105)\n thermocycler.set_block_temperature(95)\n profile = [{'temperature': 95, 'hold_time_minutes': 2}]\n ctx.pause('''Thermocycler temperature is at 95C.\n Please add the sample plate to the thermocycler.\n Thermocycler will close lid automatically.\n Be ready to take samples and put on ice\n immediately after the 2 minute cycle has completed. ''')\n\n thermocycler.close_lid()\n thermocycler.execute_profile(steps=profile,\n repetitions=1,\n block_max_volume=10.5)\n thermocycler.open_lid()\n ctx.pause('''Immediately remove samples and put on ice for 2 minutes.\n After, put the plate back on the Thermocycler for the Adaptase Mastermix\n to be added.''')\n\n # add adaptase and mix thouroughly\n for well in samp_plate.wells()[32:32+num_samp]:\n p20.pick_up_tip()\n p20.aspirate(10.5*overage_percent, mastermix)\n p20.dispense(10.5*overage_percent, well.top())\n p20.drop_tip()\n\n for col in sample_cols:\n m300.pick_up_tip()\n m300.mix(15, 20, col)\n m300.blow_out()\n m300.drop_tip()\n\n ctx.pause('''Transfer of Adaptase Mastermix is complete -\n Solutions have been pipette-mixed 15 times.\n Spin samples, seal, and place back on thermocycler for another\n thermocycler profile.''')\n\n profile = [\n {'temperature': 37, 'hold_time_minutes': 15},\n {'temperature': 95, 'hold_time_minutes': 2},\n ]\n thermocycler.close_lid()\n thermocycler.execute_profile(steps=profile,\n repetitions=1,\n block_max_volume=20.5)\n thermocycler.set_block_temperature(4, block_max_volume=20.5)\n thermocycler.open_lid()\n ctx.comment('Protocol complete. Samples ready for extension')\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "Number of Samples", - "name": "num_samp", - "options": [ - { - "label": "8", - "value": "8" - }, - { - "label": "16", - "value": "16" - }, - { - "label": "24", - "value": "24" - } - ], - "type": "dropDown" - }, - { - "default": 7.5, - "label": "Adaptase Mastermix Overage Percent (0-10%)", - "name": "overage_percent", - "type": "float" - }, - { - "label": "Opentrons 96 Tip Rack 20ul Tip Type", - "name": "tip_type", - "options": [ - { - "label": "Filtertips", - "value": "opentrons_96_filtertiprack_20ul" - }, - { - "label": "Non-Filtertips", - "value": "opentrons_96_tiprack_20ul" - } - ], - "type": "dropDown" - }, - { - "label": "Opentrons 96 Tip Rack 20ul Tip Type", - "name": "tip_type", - "options": [ - { - "label": "Filtertips", - "value": "opentrons_96_filtertiprack_200ul" - }, - { - "label": "Non-Filtertips", - "value": "opentrons_96_tiprack_20ul" - } - ], - "type": "dropDown" - }, - { - "label": "P300 Multi GEN2 Mount", - "name": "p300_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "P20 Single GEN2 Mount", - "name": "p20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi" - }, - { - "mount": "right", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 3", - "share": false, - "slot": "3", - "type": "opentrons_24_aluminumblock_nest_1.5ml_screwcap" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.7", - "author": "Rami Farawi ", - "protocolName": "Swift Rapid NGS Part 2 - Adaptase", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/6a93a3-part2/README.json b/protoBuilds/6a93a3-part2/README.json deleted file mode 100644 index c032e17c4d..0000000000 --- a/protoBuilds/6a93a3-part2/README.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "NGS Library Prep": [ - "Swift Rapid RNA Library Kit" - ] - }, - "deck-setup": "", - "description": "This protocol is part two of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n Swift Rapid NGS Part 4 - SPRI Clean\n Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart two of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nMake Adaptase Mastermix\nRun Thermocycler Profile\nAdd Adaptase Mastermix\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n Adaptase Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", - "internal": "6a93a2-part2", - "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* NGS Library Prep\n\t* Swift Rapid RNA Library Kit\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6a93a2/pt2/Screen+Shot+2021-05-05+at+1.17.41+PM.png)\n\n", - "description": "This protocol is part two of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\n\nLinks:\n* [Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup](https://protocols.opentrons.com/protocol/6a93a2)\n* [Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation](https://protocols.opentrons.com/protocol/6a93a2-part3)\n* [Swift Rapid NGS Part 4 - SPRI Clean](https://protocols.opentrons.com/protocol/6a93a2-part4)\n* [Swift Rapid NGS Part 5 - Indexing and SPRI Clean](https://protocols.opentrons.com/protocol/6a93a2-part5)\n\nPart two of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\n* Make Adaptase Mastermix\n* Run Thermocycler Profile\n* Add Adaptase Mastermix\n\nExplanation of complex parameters below:\n* `Number of Samples`: Specify the number of samples that will be processed.\n* `Adaptase Mastermix Overage Percent (0-10%)`: Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n* `Opentrons 96 Tip Rack 20ul Tip Type`: Specify whether filter or non-filter 20ul tips will be employed.\n* `P300 Multi GEN2 Mount`: Specify which mount (left or right) to load the P300 multi channel pipette.\n* `P20 Single GEN2 Mount`: Specify which mount (left or right) to load the P20 single channel pipette.\n\n---\n\n", - "internal": "6a93a2-part2\n", - "labware": "* [NEST 0.1 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [Opentrons 20\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-10ul-tips)\n* [Opentrons 200uL Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-200ul-filter-tips)\n* [Opentrons 24-Tube Aluminum Block](https://shop.opentrons.com/collections/racks-and-adapters/products/aluminum-block-set)\n\n", - "modules": "* [Temperature Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n* [Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "partner": "[Swift Biosciences](https://swiftbiosci.com/protocols/)\n\n", - "pipettes": "* [P20 GEN2 Single Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/single-channel-electronic-pipette)\n* [P300 GEN2 Multi-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "protocol-steps": "1. Adaptase mastermix is made on ice (4C)\n2. User vortexes mix tube\n3. Samples undergo thermocycler profile\n4. User moves samples to ice for 4 minutes\n5. Adaptase mastermix is added to samples\n6. Samples undergo thermocycler profile\n7. Samples are brought back down to 4C, ready for extension.\n\n\n\n\n", - "reagent-setup": "* Aluminum Tube Rack: Slot 3\n\n![reservoir 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6a93a2/pt2/Screen+Shot+2021-05-05+at+1.17.02+PM.png)\n\n---\n\n", - "reagents": "* [Swift Rapid RNA Library Kit](https://swiftbiosci.com/wp-content/uploads/2020/04/PRT-024-Swift-Rapid-RNA-Library-Kit-Protocol-v3.0.pdf)\n\n---\n\n", - "title": "Swift Rapid NGS Part 2 - Adaptase" - }, - "modules": [ - "Temperature Module (GEN2)", - "Thermocycler Module" - ], - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Swift Biosciences", - "pipettes": "\nP20 GEN2 Single Channel Pipette\nP300 GEN2 Multi-Channel Pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "protocol-steps": "\nAdaptase mastermix is made on ice (4C)\nUser vortexes mix tube\nSamples undergo thermocycler profile\nUser moves samples to ice for 4 minutes\nAdaptase mastermix is added to samples\nSamples undergo thermocycler profile\nSamples are brought back down to 4C, ready for extension.\n", - "reagent-setup": "\nAluminum Tube Rack: Slot 3\n\n\n", - "reagents": [ - "Swift Rapid RNA Library Kit" - ], - "title": "Swift Rapid NGS Part 2 - Adaptase" -} \ No newline at end of file diff --git a/protoBuilds/6a93a3-part2/metadata.json b/protoBuilds/6a93a3-part2/metadata.json deleted file mode 100644 index 3b4542ce68..0000000000 --- a/protoBuilds/6a93a3-part2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "6a93a2-part2.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/6a93a3-part2", - "slug": "6a93a3-part2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json b/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json index 70e3f3e8d9..b0420fb75d 100644 --- a/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json +++ b/protoBuilds/6cd9d6/6cd9d6.ot2.apiv2.py.json @@ -117,5 +117,24 @@ "description": "Custom Protocol Request", "protocolName": "Custom NGS Library Prep" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw NEST 12 Well Reservoir 15 mL on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json index 44deeff161..25b6e00614 100644 --- a/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-2/6d7fc3-part-2.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit: Adapter\n Ligation" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json index bf2acdb105..31fc94e847 100644 --- a/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-3/6d7fc3-part-3.ot2.apiv2.py.json @@ -117,5 +117,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:Cleanup of Adapter-ligated DNA with\n QIAact Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json index f00b3d96b0..108fd5b23f 100644 --- a/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-4/6d7fc3-part-4.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Target Enrichment PCR" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json index 4817a30f39..6d4c1737bd 100644 --- a/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-5/6d7fc3-part-5.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Cleanup of Target Enrichment PCR with\n QIAact Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json index 1d307c213e..5375b569b4 100644 --- a/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-6/6d7fc3-part-6.ot2.apiv2.py.json @@ -93,5 +93,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Universal PCR Amplification" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json b/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json index cadb4a9594..b819938115 100644 --- a/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3-part-7/6d7fc3-part-7.ot2.apiv2.py.json @@ -111,5 +111,24 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit:\n Cleanup of Universal PCR with QIAact Beads" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json b/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json index 128ea300bd..960e291bd8 100644 --- a/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json +++ b/protoBuilds/6d7fc3/6d7fc3.ot2.apiv2.py.json @@ -87,5 +87,18 @@ "description": "Custom Protocol Request", "protocolName": "GeneRead QIAact Lung DNA UMI Panel Kit: Fragmentation,\n End-repair and A-addition" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json b/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json index f50126a067..9a7b4e646d 100644 --- a/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json +++ b/protoBuilds/6f4e2c/6f4e2c.ot2.apiv2.py.json @@ -1203,7 +1203,7 @@ ], "labware": [ { - "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Magnetic Module GEN1 on 1", + "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Magnetic Module on 1", "share": false, "slot": "1", "type": "eppendorf_96_wellplate_1000ul" @@ -1221,7 +1221,7 @@ "type": "opentrons_96_tiprack_300ul" }, { - "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Temperature Module GEN1 on 4", + "name": "Eppendorf 96 Deep Well Plate 1000\u00b5L on Temperature Module on 4", "share": false, "slot": "4", "type": "eppendorf_96_wellplate_1000ul" @@ -1275,5 +1275,18 @@ "protocolName": "DNA Isolation from Whole Blood", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Eppendorf 96 Deep Well Plate 1000\u00b5L on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Eppendorf 96 Deep Well Plate 1000\u00b5L on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json b/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json index 0f6343b516..6304634232 100644 --- a/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json +++ b/protoBuilds/6ff9e9/extraction.ot2.apiv2.py.json @@ -1393,5 +1393,12 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/701319/701319.ot2.apiv2.py.json b/protoBuilds/701319/701319.ot2.apiv2.py.json index 63ab19446a..365b4c35b8 100644 --- a/protoBuilds/701319/701319.ot2.apiv2.py.json +++ b/protoBuilds/701319/701319.ot2.apiv2.py.json @@ -2444,5 +2444,12 @@ "description": "Custom Protocol Request", "protocolName": "Peptide Mass Spec Sample Prep" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json b/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json index 826545c426..8ff341fb9d 100644 --- a/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/70567f/ngs_cleanup.ot2.apiv2.py.json @@ -209,5 +209,12 @@ "protocolName": "NGS Library Cleanup with Ampure XP Beads", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw magnetic plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json b/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json index dd50d9b921..98fb7c7ab1 100644 --- a/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json +++ b/protoBuilds/7062c9-2/extraction.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Capping Assay: Steps 3-6',\n 'author': 'Nick ',\n 'apiLevel': '2.11'\n}\n\nTEST_MODE = False\n\n\ndef run(ctx):\n [num_samples, tip_track] = get_values( # noqa: F821\n 'num_samples', 'tip_track')\n\n bead_vol = 125.0\n sample_vol = 110.0\n park_tips = True\n sample_incubation_mixing = True\n mag_height = 11.5\n z_offset = 0.0\n radial_offset = 0.3\n wash1_vol = 200.0\n wash2_vol = 200.0\n elution_vol = 100.0\n air_gap_vol = 0.0\n bead_settling_time = 1.0\n temp_time = 3.0\n mix_reps = 10\n sample_mixing_time_minutes = 15.0\n mix_volume_percentage = 0.9\n sample_mixing_blowout_height_from_bottom = 10.0\n\n if TEST_MODE:\n [bead_settling_time, mix_reps, temp_time,\n sample_incubation_mixing] = 0.0, 1, 0.0, False\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n sample_plate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul',\n '1', 'starting sample plate')\n magdeck = ctx.load_module('magnetic module gen2', '4')\n magplate = magdeck.load_labware('ge_96_wellplate_500ul',\n 'deepwell plate')\n tempdeck = ctx.load_module('Temperature Module Gen2', '7')\n heatingplate = tempdeck.load_labware(\n 'neptune_96_aluminumblock_200ul',\n 'heating plate')\n elutionplate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul', '2',\n 'final elution plate')\n waste = ctx.load_labware('nest_1_reservoir_195ml', '11',\n 'Liquid Waste').wells()[0].top()\n res = ctx.load_labware('nest_12_reservoir_15ml', '5', 'reagent reservoir')\n num_cols = math.ceil(num_samples/8)\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200\u00b5l filtertiprack')\n for slot in ['3', '6', '9', '10']]\n if park_tips:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', 'tiprack for parking')\n parking_spots = rack.rows()[0][:num_cols]\n else:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', '200\u00b5l filtertiprack')\n parking_spots = [None for none in range(12)]\n tips300.insert(0, rack)\n\n # load P300M pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', 'left', tip_racks=tips300)\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n wash1 = res.wells()[:2]\n wash2 = res.wells()[2:5]\n beads = res.wells()[10]\n elution_solution = res.wells()[-1]\n\n mag_samples_m = magplate.rows()[0][:num_cols]\n starting_samples_m = sample_plate.rows()[0][:num_cols]\n elution_samples_m = elutionplate.rows()[0][:num_cols]\n heating_samples_m = heatingplate.rows()[0][:num_cols]\n if mag_samples_m[0].width:\n radius = mag_samples_m[0].width/2\n else:\n radius = mag_samples_m[0].diameter/2\n\n magdeck.disengage() # just in case\n tempdeck.set_temperature(85)\n\n ctx._implementation._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.5)\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip=m300, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip=m300):\n nonlocal switch\n nonlocal drop_count\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n # Setup for flashing lights notification to empty trash\n ctx.home() # home before continuing with protocol\n drop_count = 0\n\n waste_vol = 0\n waste_threshold = 185000\n\n def remove_supernatant(vol, park=False, drop=True):\n \"\"\"\n `remove_supernatant` will transfer supernatant from the deepwell\n extraction plate to the liquid waste reservoir.\n :param vol (float): The amount of volume to aspirate from all deepwell\n sample wells and dispense in the liquid waste.\n :param park (boolean): Whether to pick up sample-corresponding tips\n in the 'parking rack' or to pick up new tips.\n \"\"\"\n\n def _waste_track(vol):\n nonlocal waste_vol\n if waste_vol + vol >= waste_threshold:\n # Setup for flashing lights notification to empty liquid waste\n ctx.home()\n ctx.pause('Please empty liquid waste (slot 11) before \\\nresuming.')\n\n waste_vol = 0\n waste_vol += vol\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side*radius*radial_offset,\n z=z_offset))\n for _ in range(num_trans):\n _waste_track(vol_per_trans)\n if m300.current_volume > 0:\n # void air gap if necessary\n m300.dispense(m300.current_volume, m.top())\n m300.move_to(m.center())\n m300.transfer(vol_per_trans, loc, waste, new_tip='never',\n air_gap=air_gap_vol)\n m300.blow_out(waste)\n m300.air_gap(20)\n if drop:\n _drop(m300)\n\n def wash(vol, source, change_tips_for_samples=True, mix_reps=mix_reps,\n park=True, resuspend=True, drop=True):\n \"\"\"\n `wash` will perform bead washing for the extraction protocol.\n :param vol (float): The amount of volume to aspirate from each\n source and dispense to each well containing beads.\n :param source (List[Well]): A list of wells from where liquid will be\n aspirated. If the length of the source list\n > 1, `wash` automatically calculates\n the index of the source that should be\n accessed.\n :param mix_reps (int): The number of repititions to mix the beads with\n specified wash buffer (ignored if resuspend is\n False).\n :param park (boolean): Whether to save sample-corresponding tips\n between adding wash buffer and removing\n supernatant.\n :param resuspend (boolean): Whether to resuspend beads in wash buffer.\n \"\"\"\n\n if resuspend and magdeck.status == 'engaged':\n magdeck.disengage()\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n for n in range(num_trans):\n if m300.current_volume > 0:\n m300.dispense(m300.current_volume, source.top())\n m300.transfer(vol_per_trans, source, m.top(),\n air_gap=air_gap_vol, new_tip='never')\n if n < num_trans - 1: # only air_gap if going back to source\n m300.air_gap(20)\n if resuspend:\n for _ in range(mix_reps):\n m300.aspirate(mix_volume_percentage*vol, m.bottom())\n m300.dispense(mix_volume_percentage*vol,\n m.bottom().move(\n Point(x=side*radius*radial_offset, z=3)))\n m300.blow_out(m.top())\n m300.air_gap(20)\n if change_tips_for_samples:\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n if magdeck.status == 'disengaged':\n magdeck.engage(mag_height)\n\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n remove_supernatant(vol, park=park, drop=drop)\n\n def elute(vol, park=True):\n \"\"\"\n `elute` will perform elution from the deepwell extraction plate to the\n final clean elutions PCR plate to complete the extraction protocol.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n magdeck.disengage()\n\n # pre-heat elution buffer\n _pick_up(m300)\n for h in heating_samples_m:\n m300.transfer(elution_vol*1.2, elution_solution, h,\n new_tip='never')\n m300.home()\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n # resuspend beads in elution\n m300.flow_rate.aspirate /= 5\n m300.flow_rate.dispense /= 5\n m300.flow_rate.blow_out /= 5\n for i, (m, h, spot) in enumerate(zip(mag_samples_m, heating_samples_m,\n parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.aspirate(vol*1.2, h)\n m300.move_to(m.center())\n m300.dispense(vol, loc)\n for _ in range(mix_reps):\n m300.aspirate(vol*mix_volume_percentage, m.bottom())\n m300.dispense(vol*mix_volume_percentage, m.bottom().move(Point(\n x=side*radius*radial_offset, z=3)))\n m300.transfer(vol, m.bottom(), h, new_tip='never')\n m300.blow_out(h.bottom(h.depth/2))\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n\n for m, h, spot in zip(mag_samples_m, heating_samples_m,\n parking_spots):\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n m300.transfer(vol, h, m, mix_before=(5, 0.5*vol),\n new_tip='never')\n m300.blow_out(m.bottom(m.depth/2))\n _drop(m300)\n\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n for i, (m, e, spot) in enumerate(\n zip(mag_samples_m, elution_samples_m, parking_spots)):\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset+2))\n m300.move_to(m.center())\n m300.transfer(0.8*vol, loc, e, air_gap=air_gap_vol,\n new_tip='never')\n m300.drop_tip()\n\n \"\"\"\n ACTIONS\n \"\"\"\n # beads\n _pick_up(m300)\n # add beads\n m300.mix(10, 150, beads)\n for m in mag_samples_m:\n m300.transfer(bead_vol, beads, m, new_tip='never')\n m300.home()\n\n # prewash\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg=f'Beads separating for \\\n{bead_settling_time} minutes.')\n remove_supernatant(bead_vol, drop=False)\n # keep tips for wash\n\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips, drop=False,\n change_tips_for_samples=False)\n\n # add sample and mix iteratively for ~30 minutes\n magdeck.disengage()\n for s, d, p in zip(starting_samples_m, mag_samples_m, parking_spots):\n if not m300.has_tip:\n _pick_up()\n m300.transfer(sample_vol, s, d, new_tip='never')\n m300.drop_tip(p)\n\n m300.default_speed = 200\n m300.flow_rate.aspirate = 46.43\n m300.flow_rate.dispense = 92.86\n mixes_per_min = 0.5\n num_mix_cycles = int(sample_mixing_time_minutes*mixes_per_min/num_cols)\n if TEST_MODE or not sample_incubation_mixing:\n num_mix_cycles = 5\n for i in range(num_mix_cycles):\n for j, (s, p) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300, p)\n side = 1 if j % 2 == 0 else -1\n loc = s.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset-1))\n for _ in range(mix_reps):\n m300.aspirate(sample_vol*mix_volume_percentage, loc)\n m300.dispense(sample_vol*mix_volume_percentage,\n s.bottom().move(Point(\n x=side*radius*radial_offset, z=7)))\n m300.blow_out(\n s.bottom(sample_mixing_blowout_height_from_bottom))\n m300.drop_tip(p)\n m300.default_speed = 400\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time)\n remove_supernatant(sample_vol, park=park_tips)\n\n # sample washes\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips)\n for w in range(3):\n wash(wash2_vol, wash2[w], park=park_tips)\n elute(elution_vol, park=park_tips)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "from opentrons.types import Point\nimport json\nimport os\nimport math\n\nmetadata = {\n 'protocolName': 'Capping Assay: Steps 3-6',\n 'author': 'Nick ',\n 'apiLevel': '2.11'\n}\n\nTEST_MODE = False\n\n\ndef run(ctx):\n [num_samples, tip_track] = get_values( # noqa: F821\n 'num_samples', 'tip_track')\n\n bead_vol = 125.0\n sample_vol = 110.0\n park_tips = True\n sample_incubation_mixing = True\n mag_height = 11.5\n z_offset = 0.0\n radial_offset = 0.3\n wash1_vol = 200.0\n wash2_vol = 200.0\n elution_vol = 100.0\n air_gap_vol = 0.0\n bead_settling_time = 1.0\n temp_time = 3.0\n mix_reps = 10\n sample_mixing_time_minutes = 15.0\n mix_volume_percentage = 0.9\n sample_mixing_blowout_height_from_bottom = 10.0\n\n if TEST_MODE:\n [bead_settling_time, mix_reps, temp_time,\n sample_incubation_mixing] = 0.0, 1, 0.0, False\n\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n sample_plate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul',\n '1', 'starting sample plate')\n magdeck = ctx.load_module('magnetic module gen2', '4')\n magplate = magdeck.load_labware('ge_96_wellplate_500ul',\n 'deepwell plate')\n tempdeck = ctx.load_module('Temperature Module Gen2', '7')\n heatingplate = tempdeck.load_labware(\n 'neptune_96_aluminumblock_200ul',\n 'heating plate')\n elutionplate = ctx.load_labware(\n 'neptune_96_aluminumblock_200ul', '2',\n 'final elution plate')\n waste = ctx.load_labware('nest_1_reservoir_195ml', '11',\n 'Liquid Waste').wells()[0].top()\n res = ctx.load_labware('nest_12_reservoir_15ml', '5', 'reagent reservoir')\n num_cols = math.ceil(num_samples/8)\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200\u00b5l filtertiprack')\n for slot in ['3', '6', '9', '10']]\n if park_tips:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', 'tiprack for parking')\n parking_spots = rack.rows()[0][:num_cols]\n else:\n rack = ctx.load_labware(\n 'opentrons_96_filtertiprack_200ul', '8', '200\u00b5l filtertiprack')\n parking_spots = [None for none in range(12)]\n tips300.insert(0, rack)\n\n # load P300M pipette\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', 'left', tip_racks=tips300)\n\n tip_log = {val: {} for val in ctx.loaded_instruments.values()}\n\n \"\"\"\n Here is where you can define the locations of your reagents.\n \"\"\"\n wash1 = res.wells()[:2]\n wash2 = res.wells()[2:5]\n beads = res.wells()[10]\n elution_solution = res.wells()[-1]\n\n mag_samples_m = magplate.rows()[0][:num_cols]\n starting_samples_m = sample_plate.rows()[0][:num_cols]\n elution_samples_m = elutionplate.rows()[0][:num_cols]\n heating_samples_m = heatingplate.rows()[0][:num_cols]\n if mag_samples_m[0].width:\n radius = mag_samples_m[0].width/2\n else:\n radius = mag_samples_m[0].diameter/2\n\n magdeck.disengage() # just in case\n tempdeck.set_temperature(85)\n\n ctx._hw_manager.hardware._attached_instruments[\n m300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.5)\n\n folder_path = '/data/B'\n tip_file_path = folder_path + '/tip_log.json'\n if tip_track and not ctx.is_simulating():\n if os.path.isfile(tip_file_path):\n with open(tip_file_path) as json_file:\n data = json.load(json_file)\n for pip in tip_log:\n if pip.name in data:\n tip_log[pip]['count'] = data[pip.name]\n else:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n else:\n for pip in tip_log:\n tip_log[pip]['count'] = 0\n\n for pip in tip_log:\n if pip.type == 'multi':\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.rows()[0]]\n else:\n tip_log[pip]['tips'] = [tip for rack in pip.tip_racks\n for tip in rack.wells()]\n tip_log[pip]['max'] = len(tip_log[pip]['tips'])\n\n def _pick_up(pip=m300, loc=None):\n if tip_log[pip]['count'] == tip_log[pip]['max'] and not loc:\n ctx.pause('Replace ' + str(pip.max_volume) + '\u00b5l tipracks before \\\nresuming.')\n pip.reset_tipracks()\n tip_log[pip]['count'] = 0\n if loc:\n pip.pick_up_tip(loc)\n else:\n pip.pick_up_tip(tip_log[pip]['tips'][tip_log[pip]['count']])\n tip_log[pip]['count'] += 1\n\n switch = True\n drop_count = 0\n # number of tips trash will accommodate before prompting user to empty\n drop_threshold = 120\n\n def _drop(pip=m300):\n nonlocal switch\n nonlocal drop_count\n side = 30 if switch else -18\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=side))\n pip.drop_tip(drop_loc)\n switch = not switch\n if pip.type == 'multi':\n drop_count += 8\n else:\n drop_count += 1\n if drop_count == drop_threshold:\n # Setup for flashing lights notification to empty trash\n ctx.home() # home before continuing with protocol\n drop_count = 0\n\n waste_vol = 0\n waste_threshold = 185000\n\n def remove_supernatant(vol, park=False, drop=True):\n \"\"\"\n `remove_supernatant` will transfer supernatant from the deepwell\n extraction plate to the liquid waste reservoir.\n :param vol (float): The amount of volume to aspirate from all deepwell\n sample wells and dispense in the liquid waste.\n :param park (boolean): Whether to pick up sample-corresponding tips\n in the 'parking rack' or to pick up new tips.\n \"\"\"\n\n def _waste_track(vol):\n nonlocal waste_vol\n if waste_vol + vol >= waste_threshold:\n # Setup for flashing lights notification to empty liquid waste\n ctx.home()\n ctx.pause('Please empty liquid waste (slot 11) before \\\nresuming.')\n\n waste_vol = 0\n waste_vol += vol\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom(0).move(Point(x=side*radius*radial_offset,\n z=z_offset))\n for _ in range(num_trans):\n _waste_track(vol_per_trans)\n if m300.current_volume > 0:\n # void air gap if necessary\n m300.dispense(m300.current_volume, m.top())\n m300.move_to(m.center())\n m300.transfer(vol_per_trans, loc, waste, new_tip='never',\n air_gap=air_gap_vol)\n m300.blow_out(waste)\n m300.air_gap(20)\n if drop:\n _drop(m300)\n\n def wash(vol, source, change_tips_for_samples=True, mix_reps=mix_reps,\n park=True, resuspend=True, drop=True):\n \"\"\"\n `wash` will perform bead washing for the extraction protocol.\n :param vol (float): The amount of volume to aspirate from each\n source and dispense to each well containing beads.\n :param source (List[Well]): A list of wells from where liquid will be\n aspirated. If the length of the source list\n > 1, `wash` automatically calculates\n the index of the source that should be\n accessed.\n :param mix_reps (int): The number of repititions to mix the beads with\n specified wash buffer (ignored if resuspend is\n False).\n :param park (boolean): Whether to save sample-corresponding tips\n between adding wash buffer and removing\n supernatant.\n :param resuspend (boolean): Whether to resuspend beads in wash buffer.\n \"\"\"\n\n if resuspend and magdeck.status == 'engaged':\n magdeck.disengage()\n\n num_trans = math.ceil(vol/200)\n vol_per_trans = vol/num_trans\n for i, (m, spot) in enumerate(zip(mag_samples_m, parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n for n in range(num_trans):\n if m300.current_volume > 0:\n m300.dispense(m300.current_volume, source.top())\n m300.transfer(vol_per_trans, source, m.top(),\n air_gap=air_gap_vol, new_tip='never')\n if n < num_trans - 1: # only air_gap if going back to source\n m300.air_gap(20)\n if resuspend:\n for _ in range(mix_reps):\n m300.aspirate(mix_volume_percentage*vol, m.bottom())\n m300.dispense(mix_volume_percentage*vol,\n m.bottom().move(\n Point(x=side*radius*radial_offset, z=3)))\n m300.blow_out(m.top())\n m300.air_gap(20)\n if change_tips_for_samples:\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n if magdeck.status == 'disengaged':\n magdeck.engage(mag_height)\n\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n remove_supernatant(vol, park=park, drop=drop)\n\n def elute(vol, park=True):\n \"\"\"\n `elute` will perform elution from the deepwell extraction plate to the\n final clean elutions PCR plate to complete the extraction protocol.\n :param vol (float): The amount of volume to aspirate from the elution\n buffer source and dispense to each well containing\n beads.\n :param park (boolean): Whether to save sample-corresponding tips\n between adding elution buffer and transferring\n supernatant to the final clean elutions PCR\n plate.\n \"\"\"\n magdeck.disengage()\n\n # pre-heat elution buffer\n _pick_up(m300)\n for h in heating_samples_m:\n m300.transfer(elution_vol*1.2, elution_solution, h,\n new_tip='never')\n m300.home()\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n # resuspend beads in elution\n m300.flow_rate.aspirate /= 5\n m300.flow_rate.dispense /= 5\n m300.flow_rate.blow_out /= 5\n for i, (m, h, spot) in enumerate(zip(mag_samples_m, heating_samples_m,\n parking_spots)):\n if not m300.has_tip:\n _pick_up(m300)\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset))\n m300.aspirate(vol*1.2, h)\n m300.move_to(m.center())\n m300.dispense(vol, loc)\n for _ in range(mix_reps):\n m300.aspirate(vol*mix_volume_percentage, m.bottom())\n m300.dispense(vol*mix_volume_percentage, m.bottom().move(Point(\n x=side*radius*radial_offset, z=3)))\n m300.transfer(vol, m.bottom(), h, new_tip='never')\n m300.blow_out(h.bottom(h.depth/2))\n if park:\n m300.drop_tip(spot)\n else:\n _drop(m300)\n\n ctx.delay(minutes=temp_time, msg=f'Incubating at 85C for {temp_time} \\\nminutes')\n\n for m, h, spot in zip(mag_samples_m, heating_samples_m,\n parking_spots):\n if park:\n _pick_up(m300, spot)\n else:\n _pick_up(m300)\n m300.transfer(vol, h, m, mix_before=(5, 0.5*vol),\n new_tip='never')\n m300.blow_out(m.bottom(m.depth/2))\n _drop(m300)\n\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg='Incubating on MagDeck for \\\n' + str(bead_settling_time) + ' minutes.')\n\n for i, (m, e, spot) in enumerate(\n zip(mag_samples_m, elution_samples_m, parking_spots)):\n _pick_up(m300)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset+2))\n m300.move_to(m.center())\n m300.transfer(0.8*vol, loc, e, air_gap=air_gap_vol,\n new_tip='never')\n m300.drop_tip()\n\n \"\"\"\n ACTIONS\n \"\"\"\n # beads\n _pick_up(m300)\n # add beads\n m300.mix(10, 150, beads)\n for m in mag_samples_m:\n m300.transfer(bead_vol, beads, m, new_tip='never')\n m300.home()\n\n # prewash\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time, msg=f'Beads separating for \\\n{bead_settling_time} minutes.')\n remove_supernatant(bead_vol, drop=False)\n # keep tips for wash\n\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips, drop=False,\n change_tips_for_samples=False)\n\n # add sample and mix iteratively for ~30 minutes\n magdeck.disengage()\n for s, d, p in zip(starting_samples_m, mag_samples_m, parking_spots):\n if not m300.has_tip:\n _pick_up()\n m300.transfer(sample_vol, s, d, new_tip='never')\n m300.drop_tip(p)\n\n m300.default_speed = 200\n m300.flow_rate.aspirate = 46.43\n m300.flow_rate.dispense = 92.86\n mixes_per_min = 0.5\n num_mix_cycles = int(sample_mixing_time_minutes*mixes_per_min/num_cols)\n if TEST_MODE or not sample_incubation_mixing:\n num_mix_cycles = 5\n for i in range(num_mix_cycles):\n for j, (s, p) in enumerate(zip(mag_samples_m, parking_spots)):\n _pick_up(m300, p)\n side = 1 if j % 2 == 0 else -1\n loc = s.bottom().move(Point(x=side*radius*radial_offset,\n z=z_offset-1))\n for _ in range(mix_reps):\n m300.aspirate(sample_vol*mix_volume_percentage, loc)\n m300.dispense(sample_vol*mix_volume_percentage,\n s.bottom().move(Point(\n x=side*radius*radial_offset, z=7)))\n m300.blow_out(\n s.bottom(sample_mixing_blowout_height_from_bottom))\n m300.drop_tip(p)\n m300.default_speed = 400\n magdeck.engage(mag_height)\n ctx.delay(minutes=bead_settling_time)\n remove_supernatant(sample_vol, park=park_tips)\n\n # sample washes\n for w in range(2):\n wash(wash1_vol, wash1[w], park=park_tips)\n for w in range(3):\n wash(wash2_vol, wash2[w], park=park_tips)\n elute(elution_vol, park=park_tips)\n\n # track final used tip\n if tip_track and not ctx.is_simulating():\n if not os.path.isdir(folder_path):\n os.mkdir(folder_path)\n data = {pip.name: tip_log[pip]['count'] for pip in tip_log}\n with open(tip_file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/7062c9/normalization.ot2.apiv2.py.json b/protoBuilds/7062c9/normalization.ot2.apiv2.py.json index d095ada06f..932b560f94 100644 --- a/protoBuilds/7062c9/normalization.ot2.apiv2.py.json +++ b/protoBuilds/7062c9/normalization.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "metadata = {\n 'protocolName': 'Capping Assay: Steps 1-2',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n }\n\n\ndef run(ctx):\n [input_csv, p300_mount, p20_mount] = get_values( # noqa: F821\n 'input_csv', 'p300_mount', 'p20_mount')\n\n # labware\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '7',\n 'sample rack')\n final_plate = ctx.load_labware('neptune_96_aluminumblock_200ul',\n '5', 'normalized plate')\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '8',\n 'buffer + probe tuberack')\n tipracks20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '3')]\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # pipettes\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tipracks200])\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tipracks20)\n\n ctx._implementation._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.1)\n\n p300.flow_rate.dispense /= 5\n\n # reagents\n water = tuberack.wells()[0]\n buffer = tuberack.wells()[1]\n protease = tuberack.wells()[2]\n\n def drop_all_tips():\n for pipette in ctx.loaded_instruments.values():\n if pipette.has_tip:\n pipette.drop_tip()\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [tipracks200.rows()[0][::-1]]\n }\n }\n\n def pickup_p300(mode='single'):\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n # parse csv\n data = [\n [val for val in line.split(',')]\n for line in input_csv.splitlines()][1:]\n\n # prealocate water,\n for i, line in enumerate(data):\n water_vol = float(line[2])\n pip = p20 if water_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(water_vol, water)\n pip.dispense(water_vol, dest_well)\n drop_all_tips()\n\n # prealocate buffer\n for i, line in enumerate(data):\n buffer_vol = float(line[3])\n pip = p20 if buffer_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(buffer_vol, buffer)\n pip.dispense(buffer_vol, dest_well)\n drop_all_tips()\n\n last_probe = None\n for i, line in enumerate(data):\n probe_vol = float(line[4])\n probe = tuberack.wells_by_name()[line[5].upper().strip()]\n pip = p20 if probe_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not probe == last_probe:\n if pip.has_tip:\n pip.drop_tip()\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(probe_vol, probe)\n pip.dispense(probe_vol, dest_well)\n drop_all_tips()\n\n # transfer sample and mix\n for i, line in enumerate(data):\n sample_vol = float(line[1])\n total_vol = float(line[6])\n pip = p20 if sample_vol <= 20 else p300\n sample_well, dest_well = [\n sample_rack.wells()[i], final_plate.wells()[i]]\n if 0.8*total_vol < pip.max_volume:\n mix_vol = 0.8*total_vol\n else:\n mix_vol = 0.8*pip.max_volume\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(sample_vol, sample_well)\n pip.dispense(sample_vol, dest_well)\n pip.mix(3, mix_vol, dest_well)\n drop_all_tips()\n\n ctx.pause('Put sample plate in the thermal cycler for 30min')\n\n # transfer protease\n for i, line in enumerate(data):\n dest_well = final_plate.wells()[i]\n p20.transfer(5, protease, dest_well, mix_after=(3, 20))\n", + "content": "metadata = {\n 'protocolName': 'Capping Assay: Steps 1-2',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n }\n\n\ndef run(ctx):\n [input_csv, p300_mount, p20_mount] = get_values( # noqa: F821\n 'input_csv', 'p300_mount', 'p20_mount')\n\n # labware\n sample_rack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '7',\n 'sample rack')\n final_plate = ctx.load_labware('neptune_96_aluminumblock_200ul',\n '5', 'normalized plate')\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '8',\n 'buffer + probe tuberack')\n tipracks20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', '3')]\n tipracks200 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '9')\n\n # pipettes\n p300 = ctx.load_instrument('p300_multi_gen2', p300_mount,\n tip_racks=[tipracks200])\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount,\n tip_racks=tipracks20)\n\n ctx._hw_manager.hardware._attached_instruments[\n p300._implementation.get_mount()].update_config_item(\n 'pick_up_current', 0.1)\n\n p300.flow_rate.dispense /= 5\n\n # reagents\n water = tuberack.wells()[0]\n buffer = tuberack.wells()[1]\n protease = tuberack.wells()[2]\n\n def drop_all_tips():\n for pipette in ctx.loaded_instruments.values():\n if pipette.has_tip:\n pipette.drop_tip()\n\n tip_data = {\n 'single': {\n 'count': 0,\n 'tips': [\n well for col in tipracks200.columns()\n for well in col[::-1]]\n },\n 'multi': {\n 'count': 0,\n 'tips': [tipracks200.rows()[0][::-1]]\n }\n }\n\n def pickup_p300(mode='single'):\n p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n tip_data[mode]['count'] += 1\n\n # parse csv\n data = [\n [val for val in line.split(',')]\n for line in input_csv.splitlines()][1:]\n\n # prealocate water,\n for i, line in enumerate(data):\n water_vol = float(line[2])\n pip = p20 if water_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(water_vol, water)\n pip.dispense(water_vol, dest_well)\n drop_all_tips()\n\n # prealocate buffer\n for i, line in enumerate(data):\n buffer_vol = float(line[3])\n pip = p20 if buffer_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not pip.has_tip:\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(buffer_vol, buffer)\n pip.dispense(buffer_vol, dest_well)\n drop_all_tips()\n\n last_probe = None\n for i, line in enumerate(data):\n probe_vol = float(line[4])\n probe = tuberack.wells_by_name()[line[5].upper().strip()]\n pip = p20 if probe_vol <= 20 else p300\n dest_well = final_plate.wells()[i]\n if not probe == last_probe:\n if pip.has_tip:\n pip.drop_tip()\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(probe_vol, probe)\n pip.dispense(probe_vol, dest_well)\n drop_all_tips()\n\n # transfer sample and mix\n for i, line in enumerate(data):\n sample_vol = float(line[1])\n total_vol = float(line[6])\n pip = p20 if sample_vol <= 20 else p300\n sample_well, dest_well = [\n sample_rack.wells()[i], final_plate.wells()[i]]\n if 0.8*total_vol < pip.max_volume:\n mix_vol = 0.8*total_vol\n else:\n mix_vol = 0.8*pip.max_volume\n if pip == p20:\n pip.pick_up_tip()\n else:\n pickup_p300('single')\n pip.aspirate(sample_vol, sample_well)\n pip.dispense(sample_vol, dest_well)\n pip.mix(3, mix_vol, dest_well)\n drop_all_tips()\n\n ctx.pause('Put sample plate in the thermal cycler for 30min')\n\n # transfer protease\n for i, line in enumerate(data):\n dest_well = final_plate.wells()[i]\n p20.transfer(5, protease, dest_well, mix_after=(3, 20))\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/71381b/71381b.ot2.apiv2.py.json b/protoBuilds/71381b/71381b.ot2.apiv2.py.json index 22e371c474..5508f32eb9 100644 --- a/protoBuilds/71381b/71381b.ot2.apiv2.py.json +++ b/protoBuilds/71381b/71381b.ot2.apiv2.py.json @@ -147,5 +147,18 @@ "protocolName": "Zymo Quick DNA HMW + Labelling", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json b/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json index 4137c4bd19..dfb86c5a38 100644 --- a/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json +++ b/protoBuilds/747d99-assay-1/assay1.ot2.apiv2.py.json @@ -714,5 +714,18 @@ "author": "Opentrons ", "protocolName": "HP COVID-19 Assay 1 V1" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw deepwell plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw reaction tubeblock on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json b/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json index fd845d8c6e..3ef43deca7 100644 --- a/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json +++ b/protoBuilds/747d99-assay-2/assay2.ot2.apiv2.py.json @@ -693,5 +693,18 @@ "author": "Opentrons ", "protocolName": "HP COVID-19 Assay 2 V1" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 1 lw deepwell plate on Magnetic Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw reaction plate on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json b/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json index 668807087f..360d69e9eb 100644 --- a/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json +++ b/protoBuilds/74841a-2/extraction.ot2.apiv2.py.json @@ -191,5 +191,12 @@ "author": "Opentrons ", "protocolName": "Swift NormalaseTM Amplicon Panels (SNAP): Size Selection and Cleanup Part 2/2" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw PCR plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/74841a/extraction.ot2.apiv2.py.json b/protoBuilds/74841a/extraction.ot2.apiv2.py.json index 27e660cec3..34bee7f1fd 100644 --- a/protoBuilds/74841a/extraction.ot2.apiv2.py.json +++ b/protoBuilds/74841a/extraction.ot2.apiv2.py.json @@ -197,5 +197,12 @@ "author": "Opentrons ", "protocolName": "Swift NormalaseTM Amplicon Panels (SNAP): Size Selection and Cleanup Part 1/2" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw PCR plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/75cfa6/generic_station_C.ot2.apiv2.py.json b/protoBuilds/75cfa6/generic_station_C.ot2.apiv2.py.json deleted file mode 100644 index 7e1908240a..0000000000 --- a/protoBuilds/75cfa6/generic_station_C.ot2.apiv2.py.json +++ /dev/null @@ -1,1233 +0,0 @@ -{ - "content": "import math\n\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Nick ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n num_samples, p10_mount, m10_mount = get_values( # noqa: F821\n 'num_samples', 'p10_mount', 'm10_mount')\n\n tuberack = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap', '2',\n 'mastermix tuberack (column 1)')\n tiprack10s = [ctx.load_labware('opentrons_96_tiprack_10ul', '3')]\n tiprack10m = [ctx.load_labware('opentrons_96_tiprack_10ul', '6')]\n tempdeck1 = ctx.load_module('tempdeck', '4')\n pcr_plate = tempdeck1.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul', 'PCR plate')\n tempdeck2 = ctx.load_module('tempdeck', '7')\n sample_plate = tempdeck2.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul', 'sample plate')\n\n p10 = ctx.load_instrument('p10_single', p10_mount, tip_racks=tiprack10s)\n m10 = ctx.load_instrument('p10_single', m10_mount, tip_racks=tiprack10m)\n\n mms = tuberack.columns()[0]\n num_cols = math.ceil(num_samples/8)\n samples = sample_plate.rows()[0][:num_cols]\n\n # set temperature module temperature\n [tempdeck.set_temperature(6) for tempdeck in [tempdeck1, tempdeck2]]\n p10.home()\n ctx.pause(\"Temperature has reached 6\u00b0C. Place your reagents on the \\\n Temperature Module(s) before resuming.\")\n\n # transfer master mix\n wells_row_order = [well for row in pcr_plate.rows() for well in row]\n mm_sets = [wells_row_order[i::4] for i in range(4)]\n for mm, dest_set in zip(mms, mm_sets):\n p10.pick_up_tip()\n for d in dest_set:\n p10.transfer(8, mm, d, new_tip='never')\n p10.blow_out(d.bottom(5))\n p10.drop_tip()\n\n sample_sets = [pcr_plate.rows()[0][i*4:(i+1)*4] for i in range(num_cols)]\n for s, dest_set in zip(samples, sample_sets):\n for d in dest_set:\n m10.transfer(2, s, d, mix_after=(5, 5))\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "Applied Biosystems", - "brandId": [ - "4483354" - ] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.75, - "yDimension": 85.5, - "zDimension": 26.5 - }, - "groups": [ - { - "brand": { - "brand": "Applied Biosystems", - "brandId": [ - "4483354" - ] - }, - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Applied Biosystems 96 Aluminum Block 200 \u00b5L", - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "aluminumBlock", - "displayName": "Applied Biosystems 96 Aluminum Block 200 \u00b5L", - 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"share": false, - "slot": "7", - "type": "opentrons_96_aluminumblock_biorad_wellplate_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick ", - "protocolName": "PCR Prep", - "source": "Protocol Library" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json b/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json index 7e1908240a..cb777f1ee5 100644 --- a/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json +++ b/protoBuilds/75cfa6/pcr_prep.ot2.apiv2.py.json @@ -1229,5 +1229,18 @@ "protocolName": "PCR Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw PCR plate on Temperature Module GEN1 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 7 lw sample plate on Temperature Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json b/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json index b305006f4b..85abbbf699 100644 --- a/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json +++ b/protoBuilds/76ba23-bisulfite_conversion/76ba23-bisulfite_conversion.ot2.apiv2.py.json @@ -167,5 +167,12 @@ "protocolName": "Bisulfite Conversion", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 7 lw Collection Plate on Magnetic Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json b/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json index 1cde6430a5..79b1d91068 100644 --- a/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json +++ b/protoBuilds/76ba23-pcr1/76ba23-pcr1.ot2.apiv2.py.json @@ -104,5 +104,12 @@ "protocolName": "PCR 1", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json b/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json index e6ffa6d3f0..55ec38cdd1 100644 --- a/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json +++ b/protoBuilds/76ba23-pooling/76ba23-pooling.ot2.apiv2.py.json @@ -126,5 +126,12 @@ "protocolName": "Pooling and Clean Up", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json b/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json index 320d8e0417..7a1b7499a0 100644 --- a/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json +++ b/protoBuilds/76ba23/76ba23.ot2.apiv2.py.json @@ -137,5 +137,12 @@ "protocolName": "DNA extraction", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 7 lw USA Scientific 96 Deep Well Plate 2.4 mL on Magnetic Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json b/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json index 2e494261ac..83f237db84 100644 --- a/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json +++ b/protoBuilds/7805de-part-2/7805de-part-2.ot2.apiv2.py.json @@ -179,5 +179,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 2 -\n First and Second Strand cDNA Synthesis and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json b/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json index 693bd6b482..75ab874bae 100644 --- a/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json +++ b/protoBuilds/7805de-part-3/7805de-part-3.ot2.apiv2.py.json @@ -179,5 +179,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 3 -\n End Prep, Adapter Ligation and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json b/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json index 653fb1e911..28d8a3dc58 100644 --- a/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json +++ b/protoBuilds/7805de-part-4/7805de-part-4.ot2.apiv2.py.json @@ -173,5 +173,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 4 -\n PCR Enrichment and Bead Clean Up" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7805de/7805de.ot2.apiv2.py.json b/protoBuilds/7805de/7805de.ot2.apiv2.py.json index 79de28d20a..df0b0a30d4 100644 --- a/protoBuilds/7805de/7805de.ot2.apiv2.py.json +++ b/protoBuilds/7805de/7805de.ot2.apiv2.py.json @@ -161,5 +161,18 @@ "author": "Steve Plonk ", "protocolName": "NEBNext Ultra II Directional RNA Library Prep Kit\n for Illumina with poly(A) selection: part 1 -\n RNA Isolation, Fragmentation and Priming" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Mag Plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 3 lw 4 Degree Block on Temperature Module GEN2 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json b/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json index f467ed0977..d88f18f2cd 100644 --- a/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json +++ b/protoBuilds/7855ef-plate-part4/7855ef-plate-part4.ot2.apiv2.py.json @@ -261,868 +261,868 @@ "version": 1, "wells": { "A1": { - 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"z": 5.3 + "z": 4.8 }, "F12": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 113.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F2": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 23.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F3": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 32.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F4": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 41.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F5": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 50.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F6": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 59.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F7": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 68.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F8": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 77.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "F9": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 86.38, "y": 29.24, - "z": 5.3 + "z": 4.8 }, "G1": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 14.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G10": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 95.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G11": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 104.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G12": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 113.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G2": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 23.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G3": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 32.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G4": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 41.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G5": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 50.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G6": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 59.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G7": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 68.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G8": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 77.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "G9": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 86.38, "y": 20.24, - "z": 5.3 + "z": 4.8 }, "H1": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 14.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H10": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 95.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H11": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 104.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H12": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 113.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H2": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 23.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H3": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 32.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H4": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 41.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H5": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 50.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H6": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 59.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H7": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 68.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H8": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 77.38, "y": 11.24, - "z": 5.3 + "z": 4.8 }, "H9": { - "depth": 20.1, + "depth": 20.6, "diameter": 5.49, "shape": "circular", "totalLiquidVolume": 200, "x": 86.38, "y": 11.24, - "z": 5.3 + "z": 4.8 } } }, diff --git a/protoBuilds/796af8/796af8.ot2.apiv2.py.json b/protoBuilds/796af8/796af8.ot2.apiv2.py.json index 4d3a956176..a1993b64ff 100644 --- a/protoBuilds/796af8/796af8.ot2.apiv2.py.json +++ b/protoBuilds/796af8/796af8.ot2.apiv2.py.json @@ -156,5 +156,24 @@ "description": "Custom Protocol Request", "protocolName": "NEB Ultra II FS DNA Library Prep" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + }, + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 9 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 9", + "share": false, + "slot": "9", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json b/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json index 0382550609..987e577e66 100644 --- a/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json +++ b/protoBuilds/7a1ae8/7a1ae8.ot2.apiv2.py.json @@ -150,5 +150,18 @@ "protocolName": "Zymobiomics Magbead Nucleic Acid Purification", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw deepwell plate (on magdeck) on Magnetic Module GEN1 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 7 lw spot for drying mid-protocol on Temperature Module GEN1 on 7", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json b/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json index 99911453fb..a45d542987 100644 --- a/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json +++ b/protoBuilds/7aa3fd-library-pooling/lib_pooling.ot2.apiv2.py.json @@ -1201,7 +1201,7 @@ "type": "opentrons_96_filtertiprack_10ul" }, { - "name": "Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module GEN1 on 4", + "name": "Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module on 4", "share": false, "slot": "4", "type": "opentrons_24_aluminumblock_nest_2ml_snapcap" @@ -1231,5 +1231,18 @@ "protocolName": "NGS Prep Part 3/3: Library Pooling", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw None", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw Opentrons 24 Well Aluminum Block with NEST 2 mL Snapcap on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json b/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json index 88b666b44f..a9970224f0 100644 --- a/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json +++ b/protoBuilds/7aa3fd-library-quantification/lib_quant.ot2.apiv2.py.json @@ -1189,7 +1189,7 @@ "type": "opentrons_96_filtertiprack_10ul" }, { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module GEN1 on 4", + "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 4", "share": false, "slot": "4", "type": "eppendorftwin.tec_96_wellplate_150ul" @@ -1227,13 +1227,13 @@ }, "modules": [ { - "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw None", + "name": "MagneticModuleContext at Magnetic Module on 1 lw None", "share": false, "slot": "1", "type": "magdeck" }, { - "name": "TemperatureModuleContext at Temperature Module GEN1 on 4 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module GEN1 on 4", + "name": "TemperatureModuleContext at Temperature Module on 4 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Temperature Module on 4", "share": false, "slot": "4", "type": "tempdeck" diff --git a/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json b/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json index d4b6ba2fff..2a67c2460a 100644 --- a/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json +++ b/protoBuilds/7aa3fd-size-selection/size_selection.ot2.apiv2.py.json @@ -1210,7 +1210,7 @@ ], "labware": [ { - "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module GEN1 on 1", + "name": "Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module on 1", "share": false, "slot": "1", "type": "eppendorftwin.tec_96_wellplate_150ul" @@ -1258,5 +1258,12 @@ "protocolName": "NGS Prep Part 1/3: Size Selection", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Eppendorf Twin.tec 96 Well Plate 150 \u00b5L on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json b/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json index 9654913573..871c4cb8bf 100644 --- a/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json +++ b/protoBuilds/7cfbde/7cfbde.ot2.apiv2.py.json @@ -109,5 +109,12 @@ "author": "Chaz ", "protocolName": "3D Black Bio RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/925d07-v2/README.json b/protoBuilds/925d07-v2/README.json deleted file mode 100644 index e751d5bb0c..0000000000 --- a/protoBuilds/925d07-v2/README.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "PCR": [ - "PCR Prep" - ] - }, - "deck-setup": "\n", - "description": "This protocol performs a custom PCR prep from 4 source 96-well RNA plate to a single 384-well destination plate. The transfer scheme is shown below.\n", - "internal": "9250d7", - "labware": "\nOpentrons 20ul tips\nCorning 96 Well Plate 360 ul Flat\nCustom 384 Well Plate 100 ul\nGeneric PCR Strips in 96-well aluminum block\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* PCR\n\t* PCR Prep\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/925d07/deck.png)\n\n---\n\n", - "description": "\nThis protocol performs a custom PCR prep from 4 source 96-well RNA plate to a single 384-well destination plate. The transfer scheme is shown below.\n\n---\n\n", - "internal": "9250d7\n", - "labware": "* [Opentrons 20ul tips](https://shop.opentrons.com/collections/opentrons-tips)\n* Corning 96 Well Plate 360 ul Flat\n* Custom 384 Well Plate 100 ul\n* Generic PCR Strips in [96-well aluminum block](https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set)\n\n", - "modules": "* [Temperature Module GEN2](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n\n---\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "pipettes": "* [P20 Multi Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "title": "PCR Prep" - }, - "modules": [ - "Temperature Module GEN2" - ], - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "pipettes": "\nP20 Multi Channel Pipette\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "title": "PCR Prep" -} \ No newline at end of file diff --git a/protoBuilds/925d07-v2/metadata.json b/protoBuilds/925d07-v2/metadata.json deleted file mode 100644 index 0f18dc2cc9..0000000000 --- a/protoBuilds/925d07-v2/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "pcr_prep.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": false, - "skip-tests": false - }, - "path": "protocols/925d07-v2", - "slug": "925d07-v2", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/925d07-v2/pcr_prep.ot2.apiv2.py.json b/protoBuilds/925d07-v2/pcr_prep.ot2.apiv2.py.json deleted file mode 100644 index 5a6d872191..0000000000 --- a/protoBuilds/925d07-v2/pcr_prep.ot2.apiv2.py.json +++ /dev/null @@ -1,5604 +0,0 @@ -{ - "content": "from opentrons.types import Point\nimport math\n\nmetadata = {\n 'protocolName': 'PCR Prep',\n 'author': 'Nick Diehl ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n \"\"\"Protocol.\"\"\"\n [rna_plate_type, sample_vol, mm_vol, num_samples_1, num_samples_2,\n num_samples_3, num_samples_4, m20_mount] = get_values( # noqa: F821\n 'rna_plate_type', 'sample_vol', 'mm_vol', 'num_samples_1',\n 'num_samples_2', 'num_samples_3', 'num_samples_4', 'm20_mount')\n\n # load labware\n rna_source_plates = [\n ctx.load_labware(rna_plate_type, slot, f'RNA source plate {i+1}')\n for i, slot in enumerate(['2', '3', '5', '6'])]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n mm_strips = tempdeck.load_labware(\n 'opentrons_96_aluminumblock_generic_pcr_strip_200ul',\n 'mastermix strips (1-3)').rows()[0][:3]\n dest_plate = ctx.load_labware('custom_384_wellplate_100ul', '1',\n 'destination plate')\n tipracks = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['7', '8', '9', '10', '11']]\n\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tipracks)\n pick_up_current = 0.7\n ctx._implementation._hw_manager.hardware._attached_instruments[\n m20._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n\n num_cols_all = [\n math.ceil(num_samples/8)\n for num_samples in [\n num_samples_1, num_samples_2, num_samples_3, num_samples_4]]\n samples_sources_sets = [\n plate.rows()[0][:num_samples]\n for plate, num_samples in zip(rna_source_plates, num_cols_all)]\n destination_sets = [\n dest_plate.rows()[i][j*12:j*12+num_cols_all[i*2+j]]\n for i in range(2) for j in range(2)]\n mm_destinations = [\n well for set in destination_sets for well in set]\n\n # pre-add mastermix\n cols_per_mm_strip = 16\n m20.pick_up_tip()\n r_384 = dest_plate.wells()[0].diameter/2\n for i, d in enumerate(mm_destinations):\n mm_source = mm_strips[i//cols_per_mm_strip]\n m20.aspirate(2, mm_source.top()) # pre-air gap\n m20.aspirate(mm_vol, mm_source)\n m20.dispense(m20.current_volume, d.bottom(2))\n m20.move_to(d.bottom().move(Point(x=r_384*0.5, z=2)))\n m20.drop_tip()\n\n # add samples\n for i, (s_set, d_set) in enumerate(\n zip(samples_sources_sets, destination_sets)):\n ctx.pause(f'Ensure plate {i+1} is on deck before resuming.')\n for s, d in zip(s_set, d_set):\n m20.pick_up_tip()\n m20.aspirate(sample_vol, s.bottom(1))\n m20.aspirate(2, d.bottom(2))\n m20.dispense(m20.current_volume, d.bottom(2))\n m20.drop_tip()\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "custom", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.76, - "yDimension": 85.48, - "zDimension": 11 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "I1", - "J1", - "K1", - "L1", - "M1", - "N1", - "O1", - "P1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "I2", - "J2", - "K2", - "L2", - "M2", - "N2", - "O2", - "P2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "I3", - "J3", - "K3", - "L3", - "M3", - "N3", - "O3", - "P3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "I4", - "J4", - "K4", - "L4", - "M4", - "N4", - "O4", - "P4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "I5", - "J5", - "K5", - "L5", - "M5", - "N5", - "O5", - "P5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "I6", - "J6", - "K6", - "L6", - "M6", - "N6", - "O6", - "P6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "I7", - "J7", - "K7", - "L7", - "M7", - "N7", - "O7", - "P7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "I8", - "J8", - "K8", - "L8", - "M8", - "N8", - "O8", - "P8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "I9", - "J9", - "K9", - "L9", - "M9", - "N9", - "O9", - "P9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "I10", - "J10", - "K10", - "L10", - "M10", - "N10", - "O10", - "P10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "I11", - "J11", - "K11", - "L11", - "M11", - "N11", - "O11", - "P11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12", - "I12", - "J12", - "K12", - "L12", - "M12", - "N12", - "O12", - "P12", - "A13", - "B13", - "C13", - "D13", - "E13", - "F13", - "G13", - "H13", - "I13", - "J13", - "K13", - "L13", - 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"P22" - ], - [ - "A23", - "B23", - "C23", - "D23", - "E23", - "F23", - "G23", - "H23", - "I23", - "J23", - "K23", - "L23", - "M23", - "N23", - "O23", - "P23" - ], - [ - "A24", - "B24", - "C24", - "D24", - "E24", - "F24", - "G24", - "H24", - "I24", - "J24", - "K24", - "L24", - "M24", - "N24", - "O24", - "P24" - ] - ], - "parameters": { - "format": "384Standard", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "custom_384_wellplate_100ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 12.13, - "y": 76.48, - "z": 1.5 - }, - "A10": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 52.63, - "y": 76.48, - "z": 1.5 - }, - "A11": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 57.13, - "y": 76.48, - "z": 1.5 - }, - "A12": { - "depth": 9.5, - "diameter": 3.5, - 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"totalLiquidVolume": 100, - "x": 93.13, - "y": 76.48, - "z": 1.5 - }, - "A2": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 16.63, - "y": 76.48, - "z": 1.5 - }, - "A20": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 97.63, - "y": 76.48, - "z": 1.5 - }, - "A21": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 102.13, - "y": 76.48, - "z": 1.5 - }, - "A22": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 106.63, - "y": 76.48, - "z": 1.5 - }, - "A23": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 111.13, - "y": 76.48, - "z": 1.5 - }, - "A24": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - "x": 115.63, - "y": 76.48, - "z": 1.5 - }, - "A3": { - "depth": 9.5, - "diameter": 3.5, - "shape": "circular", - "totalLiquidVolume": 100, - 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"diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 32.4, - "y": 38.2, - "z": 1.7 - }, - "E4": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 41.4, - "y": 38.2, - "z": 1.7 - }, - "E5": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 50.4, - "y": 38.2, - "z": 1.7 - }, - "E6": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 59.4, - "y": 38.2, - "z": 1.7 - }, - "E7": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 68.4, - "y": 38.2, - "z": 1.7 - }, - "E8": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 77.4, - "y": 38.2, - "z": 1.7 - }, - "E9": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 86.4, - "y": 38.2, - "z": 1.7 - }, - "F1": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 14.4, - "y": 29.2, - "z": 1.7 - }, - "F10": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 95.4, - "y": 29.2, - "z": 1.7 - }, - "F11": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 104.4, - "y": 29.2, - "z": 1.7 - }, - "F12": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 113.4, - "y": 29.2, - "z": 1.7 - }, - "F2": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 23.4, - "y": 29.2, - "z": 1.7 - }, - "F3": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 32.4, - "y": 29.2, - "z": 1.7 - }, - "F4": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 41.4, - "y": 29.2, - "z": 1.7 - }, - "F5": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 50.4, - "y": 29.2, - "z": 1.7 - }, - "F6": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 59.4, - "y": 29.2, - "z": 1.7 - }, - "F7": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 68.4, - "y": 29.2, - "z": 1.7 - }, - "F8": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 77.4, - "y": 29.2, - "z": 1.7 - }, - "F9": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 86.4, - "y": 29.2, - "z": 1.7 - }, - "G1": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 14.4, - "y": 20.2, - "z": 1.7 - }, - "G10": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 95.4, - "y": 20.2, - "z": 1.7 - }, - "G11": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 104.4, - "y": 20.2, - "z": 1.7 - }, - "G12": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 113.4, - "y": 20.2, - "z": 1.7 - }, - "G2": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 23.4, - "y": 20.2, - "z": 1.7 - }, - "G3": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 32.4, - "y": 20.2, - "z": 1.7 - }, - "G4": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 41.4, - "y": 20.2, - "z": 1.7 - }, - "G5": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 50.4, - "y": 20.2, - "z": 1.7 - }, - "G6": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 59.4, - "y": 20.2, - "z": 1.7 - }, - "G7": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 68.4, - "y": 20.2, - "z": 1.7 - }, - "G8": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 77.4, - "y": 20.2, - "z": 1.7 - }, - "G9": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 86.4, - "y": 20.2, - "z": 1.7 - }, - "H1": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 14.4, - "y": 11.2, - "z": 1.7 - }, - "H10": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 95.4, - "y": 11.2, - "z": 1.7 - }, - "H11": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 104.4, - "y": 11.2, - "z": 1.7 - }, - "H12": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 113.4, - "y": 11.2, - "z": 1.7 - }, - "H2": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 23.4, - "y": 11.2, - "z": 1.7 - }, - "H3": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 32.4, - "y": 11.2, - "z": 1.7 - }, - "H4": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 41.4, - "y": 11.2, - "z": 1.7 - }, - "H5": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 50.4, - "y": 11.2, - "z": 1.7 - }, - "H6": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 59.4, - "y": 11.2, - "z": 1.7 - }, - "H7": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 68.4, - "y": 11.2, - "z": 1.7 - }, - "H8": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 77.4, - "y": 11.2, - "z": 1.7 - }, - "H9": { - "depth": 42.3, - "diameter": 8.3, - "shape": "circular", - "totalLiquidVolume": 2000, - "x": 86.4, - "y": 11.2, - "z": 1.7 - } - } - } - ], - "fields": [ - { - "label": "RNA source plate type", - "name": "rna_plate_type", - "options": [ - { - "label": "Corning plate", - "value": "corning_96_wellplate_360ul_flat" - }, - { - "label": "KingFisher 96 Deep Well Plate", - "value": "kingfisher_96_deepwell_plate_2ml" - } - ], - "type": "dropDown" - }, - { - "default": 1.0, - "label": "sample volume (ul)", - "name": "sample_vol", - "type": "float" - }, - { - "default": 9.0, - "label": "mastermix volume (ul)", - "name": "mm_vol", - "type": "float" - }, - { - "default": 96, - "label": "number of plate 1 samples (0-96)", - "name": "num_samples_1", - "type": "int" - }, - { - "default": 96, - "label": "number of plate 2 samples (0-96)", - "name": "num_samples_2", - "type": "int" - }, - { - "default": 96, - "label": "number of plate 3 samples (0-96)", - "name": "num_samples_3", - "type": "int" - }, - { - "default": 96, - "label": "number of plate 4 samples (0-96)", - "name": "num_samples_4", - "type": "int" - }, - { - "label": "P20 Multi GEN2 Mount", - "name": "m20_mount", - "options": [ - { - "label": "left", - "value": "left" - }, - { - "label": "right", - "value": "right" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "destination plate on 1", - "share": false, - "slot": "1", - "type": "custom_384_wellplate_100ul" - }, - { - "name": "RNA source plate 1 on 2", - "share": false, - "slot": "2", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "RNA source plate 2 on 3", - "share": false, - "slot": "3", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "mastermix strips (1-3) on Temperature Module GEN2 on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_aluminumblock_generic_pcr_strip_200ul" - }, - { - "name": "RNA source plate 3 on 5", - "share": false, - "slot": "5", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "RNA source plate 4 on 6", - "share": false, - "slot": "6", - "type": "corning_96_wellplate_360ul_flat" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons 96 Tip Rack 20 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_tiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Nick Diehl ", - "protocolName": "PCR Prep", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/9778eb_mass_norm/9778eb_mass_norm.ot2.apiv2.py.json b/protoBuilds/9778eb_mass_norm/9778eb_mass_norm.ot2.apiv2.py.json deleted file mode 100644 index 7579d82116..0000000000 --- a/protoBuilds/9778eb_mass_norm/9778eb_mass_norm.ot2.apiv2.py.json +++ /dev/null @@ -1,125 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\n\nmetadata = {\n 'protocolName': 'Normalization with CSV',\n 'author': 'Opentrons ',\n 'apiLevel': '2.12'\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [vol_water, src_plate, dst_plate,\n p20_mount, file_input] = get_values( # noqa: F821\n 'vol_water', 'src_plate', 'dst_plate', 'p20_mount', 'file_input')\n\n if p20_mount == 'right':\n p300_mount = 'left'\n else:\n p300_mount = 'right'\n source_plate = ctx.load_labware(src_plate, '1')\n dest_plate = ctx.load_labware(dst_plate, '2')\n reagent_tubes = ctx.load_labware('opentrons_6_tuberack_'\n 'falcon_50ml_conical', '4')\n\n # parse\n csv_rows = [val.strip() for val in file_input.split(',')]\n header_removed = csv_rows[6:]\n well_list = header_removed[::5]\n sample_mass = [eval(i) for i in header_removed[1::5]]\n sample_vol = [eval(i) for i in header_removed[2::5]]\n final_mass = [eval(i) for i in header_removed[3::5]]\n final_vol = [eval(i) for i in header_removed[4::5]]\n start_conc = []\n final_conc = []\n bad_wells = []\n\n for mass, vol in zip(sample_mass, sample_vol):\n start_conc.append(mass/vol)\n\n for mass, vol in zip(final_mass, final_vol):\n final_conc.append(mass/vol)\n\n transfer_vol = []\n nfw_vol = []\n for final, start, vol in zip(final_conc, start_conc, final_vol):\n transfer_vol.append(vol*round(final/start, 1))\n for s_vol, f_vol in zip(transfer_vol, final_vol):\n nfw_vol.append(f_vol-s_vol)\n lists = [well_list, sample_mass, sample_vol, final_mass, final_vol,\n start_conc, final_conc, transfer_vol, nfw_vol]\n # clean up bad wells from lists\n for i, (start, final) in enumerate(zip(start_conc, final_conc)):\n if start < final:\n bad_wells.append(well_list[i])\n for list in lists:\n del list[i]\n\n # Reagents and Well Lists\n\n nfw_source = reagent_tubes.wells()[0]\n\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['3', '6'][:math.ceil(len(well_list)/48)]]\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['5', '7'][:math.ceil(len(well_list)/48)]]\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips300)\n\n # liquid height tracking\n v_naught_dil = vol_water*1000\n radius = reagent_tubes.wells()[0].diameter/2\n h_naught_water = 0.85*v_naught_dil/(math.pi*radius**2)\n h = h_naught_water\n\n def adjust_height(vol):\n nonlocal h\n dh = vol/(math.pi*radius**2)\n h -= dh\n if h < 12:\n h = 1\n\n # do NFW addition first to save tips, mix after sample addition\n p20.pick_up_tip()\n p300.pick_up_tip()\n for nfw, d in zip(nfw_vol, well_list):\n if nfw >= 20:\n pip = p300\n else:\n pip = p20\n pip.transfer(nfw, nfw_source.bottom(h), dest_plate[d],\n new_tip='never')\n adjust_height(nfw)\n p20.drop_tip()\n p300.drop_tip()\n\n for t_vol, well in zip(transfer_vol, well_list):\n if t_vol >= 20:\n pip = p300\n else:\n pip = p20\n pip.pick_up_tip()\n pip.transfer(t_vol, source_plate.wells_by_name()[well],\n dest_plate.wells_by_name()[well], new_tip='never')\n pip.mix(4, f_vol/2, dest_plate.wells_by_name()[well])\n pip.drop_tip()\n\n # bad_list = [well.display_name.split(' ')[0] for well in bad_wells]\n # print(lists)\n\n if len(bad_wells) > 0:\n bad_msg = '\\n\\n'.join(bad_wells)\n ctx.comment(f'The following sample wells failed: \\n\\n{bad_msg}')\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 50, - "label": "Volume of Water in Falcon Tube (mL)", - "name": "vol_water", - "type": "int" - }, - { - "label": "Source Plate Type", - "name": "src_plate", - "options": [ - { - "label": "NEST 100uL 96 Well Plate", - "value": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "label": "NEST 96 Deepwell Plate 2mL", - "value": "nest_96_wellplate_2ml_deep" - }, - { - "label": "Thermofisher Semi-Skirted on Adapter 96 Well Plate", - "value": "customadapter_96_wellplate_200ul" - } - ], - "type": "dropDown" - }, - { - "label": "Destination Plate Type", - "name": "dst_plate", - "options": [ - { - "label": "NEST 100uL 96 Well Plate", - "value": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "label": "NEST 96 Deepwell Plate 2mL", - "value": "nest_96_wellplate_2ml_deep" - }, - { - "label": "Thermofisher Semi-Skirted on Adapter 96 Well Plate", - "value": "customadapter_96_wellplate_200ul" - } - ], - "type": "dropDown" - }, - { - "label": "P20 Single GEN2 Mount", - "name": "p20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "default": ",Well,nanograms,sample volume,goal concentration,normalized volume,A1,20,30,30,30,B1,6,30,5,30,C1,7,30,6,30", - "label": "Transfer .csv File", - "name": "file_input", - "type": "textFile" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_single_gen2" - }, - { - "mount": "right", - "name": "p20_single_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 6 Tube Rack with Falcon 50 mL Conical on 4", - "share": false, - "slot": "4", - "type": "opentrons_6_tuberack_falcon_50ml_conical" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.12", - "author": "Opentrons ", - "protocolName": "Normalization with CSV" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/9778eb_spri/spri_size.ot2.apiv2.py.json b/protoBuilds/9778eb_spri/spri_size.ot2.apiv2.py.json deleted file mode 100644 index 5dc6a38b9e..0000000000 --- a/protoBuilds/9778eb_spri/spri_size.ot2.apiv2.py.json +++ /dev/null @@ -1,1327 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\nimport threading\nfrom time import sleep\nfrom opentrons import types\nfrom opentrons import protocol_api\n\n\nmetadata = {\n 'protocolName': 'SPRI Bead Purification, Size Selection',\n 'author': 'Opentrons ',\n 'apiLevel': '2.11'\n}\n\n\n\"\"\"\nHere is where you can modify the magnetic module engage height:\n\"\"\"\nTEST_MODE = False\nflash = True\nmag_height = 10 # for custom labware sitting on mag modules\n# Definitions for deck light flashing\n\n\nclass CancellationToken:\n \"\"\"FLASH SETUP.\"\"\"\n\n def __init__(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n def set_true(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = True\n\n def set_false(self):\n \"\"\"FLASH SETUP.\"\"\"\n self.is_continued = False\n\n\ndef turn_on_blinking_notification(hardware, pause):\n \"\"\"FLASH SETUP.\"\"\"\n while pause.is_continued:\n hardware.set_lights(rails=True)\n sleep(1)\n hardware.set_lights(rails=False)\n sleep(1)\n\n\ndef create_thread(ctx, cancel_token):\n \"\"\"FLASH SETUP.\"\"\"\n t1 = threading.Thread(target=turn_on_blinking_notification,\n args=(ctx._hw_manager.hardware, cancel_token))\n t1.start()\n return t1\n\n\n# Start protocol\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n # Setup for flashing lights notification to empty trash\n cancellationToken = CancellationToken()\n\n [num_samples, vol_start, bead_ratio_1, bead_ratio_2,\n vol_trans, air_dry_time, incubation_delay_time, bead_delay_time,\n elution_vol, elution_time, vol_final_plate,\n flash, p300_mount, size_select] = get_values( # noqa: F821\n 'num_samples', 'vol_start', 'bead_ratio_1',\n 'bead_ratio_2', 'vol_trans', 'air_dry_time', 'incubation_delay_time',\n 'bead_delay_time', 'elution_vol', 'elution_time', 'vol_final_plate',\n 'flash', 'p300_mount', 'size_select')\n\n # Drop Down Variables for Testing\n # num_samples = 96\n # vol_start = 50 # volume of starting well\n # bead_ratio_1 = 0.6 # ratio of SPRI by volume\n # bead_ratio_2 = 0.8\n # vol_trans = 75\n # air_dry_time = 10\n # incubation_delay_time = 5\n # bead_delay_time = 5 # minutes real run, seconds for test run\n # elution_vol = 50\n # elution_time = 10\n # vol_final_plate = 50\n # flash = True\n # p300_mount = 'left'\n\n # Math and Calculations\n num_cols = math.ceil(num_samples/8)\n vol_bead_add_1 = vol_start*bead_ratio_1\n vol_post_add_1 = vol_bead_add_1+vol_start\n vol_bead_add_2 = (bead_ratio_2*vol_start*(vol_trans/vol_post_add_1))\\\n - vol_bead_add_1\n\n \"\"\"Above vol_bead_add_2 equation came from Illumina website. Source here:\n https://support.illumina.com/bulletins/2020/07/library-size-selection-\n using-sample-purification-beads.html\"\"\"\n\n # Deprecated calculations below\n # PEG_conc_correction = (vol_trans_post_SPRI_1/vol_total)*bead_ratio\n # PEG_vol_correction = round(PEG_conc_correction*vol_total, 1)\n\n supernatant_headspeed_modulator = 10\n flow_mod = 0.25\n if p300_mount == 'right':\n p20_mount = 'left'\n else:\n p20_mount = 'right'\n \"\"\"\n Here is where you can change the locations of your labware and modules\n (note that this is the recommended configuration)\n \"\"\"\n magdeck_1 = ctx.load_module('magnetic module gen2', '7')\n if size_select:\n magdeck_2 = ctx.load_module('magnetic module gen2', '6')\n magdeck_2.disengage()\n magplate_2 = magdeck_2.load_labware('customadapter_96_wellplate_200ul')\n magdeck_1.disengage()\n magplate_1 = magdeck_1.load_labware('customadapter_96_wellplate_200ul',\n 'sample plate')\n elutionplate = ctx.load_labware(\n 'customadapter_96_wellplate_200ul',\n '3')\n waste = ctx.load_labware('nest_1_reservoir_195ml', '4',\n 'Liquid Waste').wells()[0].top()\n res1 = ctx.load_labware('nest_12_reservoir_15ml', '5',\n 'reagent reservoir 1')\n tips300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot,\n '200\u00b5l filtertiprack')\n for slot in ['2', '9', '11']]\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot,\n '20\u00b5l filtertiprack')\n for slot in ['1', '8', '10']]\n\n parking_spots = [column for column in tips300[0].rows()[0][:num_cols]]\n parking_spots_2 = [column for column in tips300[0].rows()[0][:num_cols]]\n \"\"\"\n Above are the same location purely for clerical reasons to help track open\n tip rack parking spots\n \"\"\"\n\n sample_loc_1 = magplate_1.rows()[0][:num_cols]\n if size_select: # where samples start\n sample_dest_1 = magplate_2.rows()[0][:num_cols] # first super dest\n sample_dest_2 = elutionplate.rows()[0][:num_cols] # where final samples go\n\n bead_well = res1.wells()[0]\n # PEG = res1.wells()[1]\n etoh_1_wells = res1.wells()[1:3] # 10mL in each, 6 columns each\n etoh_2_wells = res1.wells()[3:5] # 10mL in each, 6 columns each\n elution_solution = res1.wells()[-1]\n # load pipettes\n m300 = ctx.load_instrument(\n 'p300_multi_gen2', p300_mount, tip_racks=tips300)\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount, tip_racks=tips20)\n\n # Custom Functions\n def bead_mixing(well, pip, mvol, asp_speed_mod, disp_speed_mod, reps=10):\n \"\"\"bead_mixing.\"\"\"\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the middle of the well & dispensing from the bottom to\n mix the beads with the other liquids as much as possible. Aspiration &\n dispensing will also be reversed to ensure proper mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n vol = mvol * .9\n\n pip.move_to(well.center())\n pip.flow_rate.aspirate *= asp_speed_mod\n pip.flow_rate.dispense *= disp_speed_mod\n for _ in range(reps):\n pip.aspirate(vol, well.bottom(1))\n pip.dispense(vol, well.bottom(5))\n pip.aspirate(vol, well.bottom(5))\n pip.dispense(vol, well.bottom(1))\n pip.flow_rate.aspirate /= asp_speed_mod\n pip.flow_rate.dispense /= disp_speed_mod\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE REPLACE TIPRACKS~~~~~~~~~~~~~~~\\n') # noqa: E501\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n pip.reset_tipracks()\n pick_up(pip)\n\n tips_dropped = 0\n\n def drop_tip(pip, home=True):\n nonlocal tips_dropped\n pip.drop_tip(home_after=home)\n if pip == m300:\n tips_dropped += 8\n else:\n tips_dropped += 4\n if tips_dropped >= 288:\n if flash:\n if not ctx._hw_manager.hardware.is_simulator:\n cancellationToken.set_true()\n thread = create_thread(ctx, cancellationToken)\n pip.home()\n ctx.pause('\\n\\n~~~~~~~~~~~~~~PLEASE EMPTY TRASH~~~~~~~~~~~~~~~\\n')\n ctx.home() # home before continuing with protocol\n if flash:\n cancellationToken.set_false() # stop light flashing after home\n thread.join()\n ctx.set_rail_lights(True)\n tips_dropped = 0\n\n # Default Values\n ctx.max_speeds['Z'] = 400\n ctx.max_speeds['A'] = 400\n m300.flow_rate.aspirate = 94\n m300.flow_rate.dispense = 94\n m20.flow_rate.aspirate = 7.6\n m20.flow_rate.dispense = 7.6\n\n # Begin Protocol\n if size_select:\n # bead addition 1\n ctx.comment('\\n\\n~~~~~~~~~~~~~~BEAD ADDITION 1~~~~~~~~~~~~~~~\\n')\n for i, dest in enumerate(sample_loc_1):\n if vol_bead_add_1 > 15:\n pip = m300\n speed_mod = 2.5\n else:\n pip = m20\n speed_mod = 2\n pick_up(pip)\n pip.flow_rate.aspirate *= flow_mod\n pip.flow_rate.dispense *= flow_mod\n if i == 0:\n bead_mixing(bead_well, pip, 20, flow_mod, flow_mod, reps=5)\n pip.aspirate(5, bead_well.top())\n pip.aspirate(vol_bead_add_1, bead_well)\n # pip.move_to(dest.top())\n pip.dispense(pip.current_volume, dest)\n pip.flow_rate.aspirate /= flow_mod\n pip.flow_rate.dispense /= flow_mod\n bead_mixing(dest, pip, vol_bead_add_1, speed_mod, speed_mod, reps=5)\n pip.aspirate(5, dest.top())\n drop_tip(pip)\n\n # 5 Minute Incubation\n ctx.comment('\\n\\n~~~~~~~~~~~~~~INCUBATING BEADS~~~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=incubation_delay_time)\n else:\n ctx.delay(minutes=incubation_delay_time)\n\n # Magnet engage\n ctx.comment('\\n\\n~~~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Move supernatant to new plate (this is everything under a certain size)\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING SUPERNATANT TO SLOT 6~~~~~~~~~~~~~\\n')\n for src, dest in zip(sample_loc_1, sample_dest_1):\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(10, src.top()) # extra air for full liquid dispense\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_trans, src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n m300.aspirate(10, src.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(10, dest.top())\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest.top()) # suck in droplets before drop_tip\n drop_tip(m300)\n\n magdeck_1.disengage()\n # samples are now in slot 6's mag plate, aka magdeck_2\n # Add second bead volume (this binds things above a certain size but\n # lower than the previous sizes selected!)\n # bead addition 2\n ctx.comment('\\n\\n~~~~~~~~~~~~~~BEAD ADDITION 2~~~~~~~~~~~~~~~\\n')\n for i, dest in enumerate(sample_dest_1):\n if vol_bead_add_2 > 15:\n pip = m300\n speed_mod = 2.5\n else:\n pip = m20\n speed_mod = 2\n pick_up(pip)\n pip.flow_rate.aspirate *= flow_mod\n pip.flow_rate.dispense *= flow_mod\n if i == 0:\n bead_mixing(bead_well, pip, 20, flow_mod, flow_mod, reps=5)\n pip.aspirate(5, bead_well.top(1))\n pip.aspirate(vol_bead_add_2, bead_well)\n pip.dispense(pip.current_volume, dest)\n pip.flow_rate.aspirate /= flow_mod\n pip.flow_rate.dispense /= flow_mod\n bead_mixing(dest, pip, vol_bead_add_2, speed_mod, speed_mod, reps=5)\n pip.aspirate(5, dest.top())\n drop_tip(pip)\n\n # 5 minute incubation for the new beads to help out\n ctx.comment('\\n\\n~~~~~~~~~~~~~~INCUBATING BEADS~~~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=incubation_delay_time)\n else:\n ctx.delay(minutes=incubation_delay_time)\n\n # Engage magnet 2\n ctx.comment('\\n\\n~~~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~~~\\n')\n magdeck_2.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Trash Super, leaves the bead-bound base pairs for specific size range\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING SUPERNATANT TO TRASH~~~~~~~~~~~~~\\n')\n for src in sample_dest_1:\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(10, src.top()) # extra air for full dispense\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_trans+vol_bead_add_2,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n m300.aspirate(10, src.top()) # air gap\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(10, waste)\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n drop_tip(m300)\n magdeck_2.disengage()\n\n # EtOH Wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 1~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_dest_1,\n parking_spots)):\n pick_up(m300)\n m300.aspirate(200, etoh_1_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n # Mag 2 Engage\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_2.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_dest_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n m300.drop_tip(park_loc)\n\n magdeck_2.disengage()\n\n # EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 2~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_dest_1,\n parking_spots)):\n m300.pick_up_tip(park_loc)\n m300.aspirate(200, etoh_2_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_2.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_dest_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n drop_tip(m300)\n\n magdeck_2.disengage()\n # Air dry\n ctx.comment('\\n\\n~~~~~~~~~~~~AIR DRYING BEADS~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=air_dry_time)\n else:\n ctx.delay(minutes=air_dry_time)\n\n # Elute from beads!\n ctx.comment('\\n\\n~~~~~~~~~~~~ADDING ELUTION SOLUTION~~~~~~~~~~~~~\\n')\n for dest, park_loc in zip(sample_dest_1, parking_spots_2):\n pick_up(m300)\n m300.aspirate(elution_vol, elution_solution)\n m300.dispense(m300.current_volume, dest)\n bead_mixing(dest, m300, 50, 2.5, 2.5, reps=5)\n m300.aspirate(20, dest.top())\n m300.drop_tip(park_loc)\n ctx.comment('\\n\\n~~~~~~~~~~INCUBATING WITH ELUTION SOLUTION~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=elution_time)\n else:\n ctx.delay(minutes=elution_time)\n\n # Mag deck 2 engage\n magdeck_2.engage(height_from_base=mag_height)\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # move elution solution to new, final plate\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING ELUTIONS TO SLOT 3~~~~~~~~~~~~~\\n')\n for src, dest, park_loc in zip(sample_dest_1, sample_dest_2,\n parking_spots_2):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_final_plate,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest) # suck in droplets before drop_tip\n drop_tip(m300)\n\n else:\n # single purification\n # bead addition\n ctx.comment('\\n\\n~~~~~~~~~~~~~~BEAD ADDITION~~~~~~~~~~~~~~~\\n')\n for i, dest in enumerate(sample_loc_1):\n if vol_bead_add_1 > 15:\n pip = m300\n speed_mod = 2.5\n else:\n pip = m20\n speed_mod = 2\n pick_up(pip)\n pip.flow_rate.aspirate *= flow_mod\n pip.flow_rate.dispense *= flow_mod\n if i == 0:\n bead_mixing(bead_well, pip, 20, flow_mod, flow_mod, reps=5)\n pip.aspirate(5, bead_well.top())\n pip.aspirate(vol_bead_add_1, bead_well)\n # pip.move_to(dest.top())\n pip.dispense(pip.current_volume, dest)\n pip.flow_rate.aspirate /= flow_mod\n pip.flow_rate.dispense /= flow_mod\n bead_mixing(dest, pip, vol_bead_add_1, speed_mod,\n speed_mod, reps=5)\n pip.aspirate(5, dest.top())\n drop_tip(pip)\n\n # 5 Minute Incubation\n ctx.comment('\\n\\n~~~~~~~~~~~~~~INCUBATING BEADS~~~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=incubation_delay_time)\n else:\n ctx.delay(minutes=incubation_delay_time)\n\n # Magnet engage\n ctx.comment('\\n\\n~~~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n # Move supernatant to trash\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING SUPERNATANT~~~~~~~~~~~~~\\n')\n for src in sample_loc_1:\n side = -1 if i % 2 == 0 else 1\n pick_up(m300)\n m300.aspirate(10, src.top()) # extra air for full liquid dispense\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_trans,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n m300.aspirate(10, src.top())\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(10, waste)\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest.top()) # suck in droplets before drop_tip\n drop_tip(m300)\n\n # EtOH Wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 1~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_loc_1,\n parking_spots)):\n pick_up(m300)\n m300.aspirate(200, etoh_1_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n # Mag 2 Engage\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 1\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_loc_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n m300.drop_tip(park_loc)\n\n magdeck_1.disengage()\n\n # EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~ETHANOL WASH 2~~~~~~~~~~~~~\\n')\n for i, (dest, park_loc) in enumerate(zip(sample_loc_1,\n parking_spots)):\n m300.pick_up_tip(park_loc)\n m300.aspirate(200, etoh_2_wells[i//6])\n m300.dispense(200, dest.top(-1))\n m300.drop_tip(park_loc)\n\n ctx.comment('\\n\\n~~~~~~~~~~~~SEPARATING BEADS~~~~~~~~~~~~~\\n')\n magdeck_1.engage(height_from_base=mag_height)\n if TEST_MODE:\n ctx.delay(seconds=bead_delay_time)\n else:\n ctx.delay(minutes=bead_delay_time)\n\n # Remove EtOH wash 2\n ctx.comment('\\n\\n~~~~~~~~~~~~REMOVING ETHANOL~~~~~~~~~~~~~\\n')\n for src, park_loc in zip(sample_loc_1, parking_spots):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(200,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(200, waste)\n m300.aspirate(20, waste) # suck in droplets before drop_tip\n drop_tip(m300)\n\n magdeck_1.disengage()\n # Air dry\n ctx.comment('\\n\\n~~~~~~~~~~~~AIR DRYING BEADS~~~~~~~~~~~~~\\n')\n if TEST_MODE:\n ctx.delay(seconds=air_dry_time)\n else:\n ctx.delay(minutes=air_dry_time)\n\n # move elution solution to new, final plate\n ctx.comment('\\n\\n~~~~~~~~~~~~MOVING ELUTIONS TO SLOT 3~~~~~~~~~~~~~\\n')\n for src, dest, park_loc in zip(sample_loc_1, sample_dest_2,\n parking_spots_2):\n side = -1 if i % 2 == 0 else 1\n m300.pick_up_tip(park_loc)\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(vol_final_plate,\n src.bottom().move(types.Point(x=side,\n y=0, z=0.2)))\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(m300.current_volume, dest)\n m300.aspirate(20, dest) # suck in droplets before drop_tip\n drop_tip(m300)\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "custom_adapter", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 128.21, - "yDimension": 85.85, - "zDimension": 22.05 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "Custom_adapter 96 Well Plate 200 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "customadapter_96_wellplate_200ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 74.36, - "z": 1.85 - }, - "A10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 74.36, - "z": 1.85 - }, - "A11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 74.36, - "z": 1.85 - }, - "A12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 74.36, - "z": 1.85 - }, - "A2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 74.36, - "z": 1.85 - }, - "A3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 74.36, - "z": 1.85 - }, - "A4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 74.36, - "z": 1.85 - }, - "A5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 74.36, - "z": 1.85 - }, - "A6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 74.36, - "z": 1.85 - }, - "A7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 74.36, - "z": 1.85 - }, - "A8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 74.36, - "z": 1.85 - }, - "A9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 74.36, - "z": 1.85 - }, - "B1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 65.36, - "z": 1.85 - }, - "B10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 65.36, - "z": 1.85 - }, - "B11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 65.36, - "z": 1.85 - }, - "B12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 65.36, - "z": 1.85 - }, - "B2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 65.36, - "z": 1.85 - }, - "B3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 65.36, - "z": 1.85 - }, - "B4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 65.36, - "z": 1.85 - }, - "B5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 65.36, - "z": 1.85 - }, - "B6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 65.36, - "z": 1.85 - }, - "B7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 65.36, - "z": 1.85 - }, - "B8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 65.36, - "z": 1.85 - }, - "B9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 65.36, - "z": 1.85 - }, - "C1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 56.36, - "z": 1.85 - }, - "C10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 56.36, - "z": 1.85 - }, - "C11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 56.36, - "z": 1.85 - }, - "C12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 56.36, - "z": 1.85 - }, - "C2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 56.36, - "z": 1.85 - }, - "C3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 56.36, - "z": 1.85 - }, - "C4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 56.36, - "z": 1.85 - }, - "C5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 56.36, - "z": 1.85 - }, - "C6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 56.36, - "z": 1.85 - }, - "C7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 56.36, - "z": 1.85 - }, - "C8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 56.36, - "z": 1.85 - }, - "C9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 56.36, - "z": 1.85 - }, - "D1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 47.36, - "z": 1.85 - }, - "D10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 47.36, - "z": 1.85 - }, - "D11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 47.36, - "z": 1.85 - }, - "D12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 47.36, - "z": 1.85 - }, - "D2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 47.36, - "z": 1.85 - }, - "D3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 47.36, - "z": 1.85 - }, - "D4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 47.36, - "z": 1.85 - }, - "D5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 47.36, - "z": 1.85 - }, - "D6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 47.36, - "z": 1.85 - }, - "D7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 47.36, - "z": 1.85 - }, - "D8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 47.36, - "z": 1.85 - }, - "D9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 47.36, - "z": 1.85 - }, - "E1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 38.36, - "z": 1.85 - }, - "E10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 38.36, - "z": 1.85 - }, - "E11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 38.36, - "z": 1.85 - }, - "E12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 38.36, - "z": 1.85 - }, - "E2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 38.36, - "z": 1.85 - }, - "E3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 38.36, - "z": 1.85 - }, - "E4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 38.36, - "z": 1.85 - }, - "E5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 38.36, - "z": 1.85 - }, - "E6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 38.36, - "z": 1.85 - }, - "E7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 38.36, - "z": 1.85 - }, - "E8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 38.36, - "z": 1.85 - }, - "E9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 38.36, - "z": 1.85 - }, - "F1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 29.36, - "z": 1.85 - }, - "F10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 29.36, - "z": 1.85 - }, - "F11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 29.36, - "z": 1.85 - }, - "F12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 29.36, - "z": 1.85 - }, - "F2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 29.36, - "z": 1.85 - }, - "F3": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 31.63, - "y": 29.36, - "z": 1.85 - }, - "F4": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 40.63, - "y": 29.36, - "z": 1.85 - }, - "F5": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 29.36, - "z": 1.85 - }, - "F6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 29.36, - "z": 1.85 - }, - "F7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 29.36, - "z": 1.85 - }, - "F8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 29.36, - "z": 1.85 - }, - "F9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 29.36, - "z": 1.85 - }, - "G1": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 13.63, - "y": 20.36, - "z": 1.85 - }, - "G10": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 94.63, - "y": 20.36, - "z": 1.85 - }, - "G11": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 103.63, - "y": 20.36, - "z": 1.85 - }, - "G12": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 112.63, - "y": 20.36, - "z": 1.85 - }, - "G2": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 22.63, - "y": 20.36, - "z": 1.85 - }, - "G3": { - "depth": 20.2, - 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"diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 49.63, - "y": 11.36, - "z": 1.85 - }, - "H6": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 58.63, - "y": 11.36, - "z": 1.85 - }, - "H7": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 67.63, - "y": 11.36, - "z": 1.85 - }, - "H8": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 76.63, - "y": 11.36, - "z": 1.85 - }, - "H9": { - "depth": 20.2, - "diameter": 5.5, - "shape": "circular", - "totalLiquidVolume": 200, - "x": 85.63, - "y": 11.36, - "z": 1.85 - } - } - } - ], - "fields": [ - { - "default": 96, - "label": "Number of Samples, 1-96", - "name": "num_samples", - "type": "int" - }, - { - "default": 50, - "label": "Initial Sample Volume (uL)", - "name": "vol_start", - "type": "int" - }, - { - "default": 0.6, - "label": "Bead Ratio 1", - "name": "bead_ratio_1", - "type": "float" - }, - { - "default": 0.8, - "label": "Bead Ratio 2", - "name": "bead_ratio_2", - "type": "float" - }, - { - "default": 75, - "label": "Transfer Volume Post-Bead Addition (uL)", - "name": "vol_trans", - "type": "int" - }, - { - "default": 10, - "label": "Bead Air Dry Time (Minutes)", - "name": "air_dry_time", - "type": "int" - }, - { - "default": 5, - "label": "Bead Incubation Time (Minutes)", - "name": "incubation_delay_time", - "type": "int" - }, - { - "default": 5, - "label": "Bead Separation Time (Minutes)", - "name": "bead_delay_time", - "type": "int" - }, - { - "default": 50, - "label": "Elution Solution Volume (uL)", - "name": "elution_vol", - "type": "int" - }, - { - "default": 10, - "label": "Elution Time (Minutes)", - "name": "elution_time", - "type": "int" - }, - { - "default": 50, - "label": "Final Plate Volume", - "name": "vol_final_plate", - "type": "int" - }, - { - "label": "Flash Robot on Pause", - "name": "flash", - "options": [ - { - "label": "yes", - "value": true - }, - { - "label": "no", - "value": false - } - ], - "type": "dropDown" - }, - { - "label": "P300 Multi Channel Pipette Mount", - "name": "p300_mount", - "options": [ - { - "label": "Left", - "value": "left" - }, - { - "label": "Right", - "value": "right" - } - ], - "type": "dropDown" - }, - { - "label": "Size Selection or Single Purification?", - "name": "size_select", - "options": [ - { - "label": "Size Selection", - "value": false - }, - { - "label": "Single Purification", - "value": false - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "20\u00b5l filtertiprack on 1", - "share": false, - "slot": "1", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "200\u00b5l filtertiprack on 2", - "share": false, - "slot": "2", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Custom_adapter 96 Well Plate 200 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "customadapter_96_wellplate_200ul" - }, - { - "name": "Liquid Waste on 4", - "share": false, - "slot": "4", - "type": "nest_1_reservoir_195ml" - }, - { - "name": "reagent reservoir 1 on 5", - "share": false, - "slot": "5", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "sample plate on Magnetic Module GEN2 on 7", - "share": false, - "slot": "7", - "type": "customadapter_96_wellplate_200ul" - }, - { - "name": "20\u00b5l filtertiprack on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "200\u00b5l filtertiprack on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "20\u00b5l filtertiprack on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "200\u00b5l filtertiprack on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "SPRI Bead Purification, Size Selection" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/979d28-pcr/normalization.ot2.apiv2.py.json b/protoBuilds/979d28-pcr/normalization.ot2.apiv2.py.json deleted file mode 100644 index 19b68005e2..0000000000 --- a/protoBuilds/979d28-pcr/normalization.ot2.apiv2.py.json +++ /dev/null @@ -1,2449 +0,0 @@ -{ - "content": "import math\nfrom opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'qPCR Prep',\n 'author': 'Opentrons ',\n 'apiLevel': '2.12'\n}\n\ndilution_factor = 10.0\ndilution_total_volume = 50.0\n\n\ndef run(ctx):\n\n num_samples, vol_mm, vol_dna, lw_384 = get_values( # noqa: F821\n 'num_samples', 'vol_mm', 'vol_dna', 'lw_384')\n\n source_plate = ctx.load_labware('vwr_96_aluminumblock_200ul', '11',\n 'source cDNA plate')\n dil_plate = ctx.load_labware('vwr_96_aluminumblock_200ul', '8',\n 'dilution plate')\n res = ctx.load_labware('nest_12_reservoir_15ml', '2')\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in ['7']]\n tips200 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in ['10']]\n plate384 = ctx.load_labware(lw_384, '5', '384-wellplate')\n\n water = res.wells()[0]\n mm = res.wells()[1]\n\n m20 = ctx.load_instrument('p20_multi_gen2', 'left', tip_racks=tips20)\n m300 = ctx.load_instrument('p300_multi_gen2', 'right', tip_racks=tips200)\n\n num_cols = math.ceil(num_samples/8)\n sources = source_plate.rows()[0][:num_cols]\n dil_locs = dil_plate.rows()[0][:num_cols]\n\n dest_sets_384 = [\n row[i*3:(i+1)*3]\n for row in plate384.rows()[:2] for i in range(8)][:num_cols+1]\n all_dests_384 = [well for set in dest_sets_384 for well in set]\n\n # add mastermix\n m20.pick_up_tip()\n for dest in all_dests_384:\n m20.aspirate(vol_mm, mm)\n m20.dispense(vol_mm, dest)\n m20.move_to(dest.bottom().move(Point(x=-1, z=5)))\n m20.drop_tip()\n\n # dilute and transfer to 384-well plate\n water_vol = dilution_total_volume*(dilution_factor-1)/dilution_factor\n vol_dna_dilution = dilution_total_volume/dilution_factor\n m300.pick_up_tip()\n for dest in dil_locs:\n m300.aspirate(water_vol, water)\n m300.dispense(water_vol, dest.bottom(1))\n m300.move_to(dest.bottom().move(Point(x=-2, z=5)))\n m300.drop_tip()\n\n for source, dest, dest_set in zip(sources, dil_locs,\n dest_sets_384[:num_cols]):\n if not m20.has_tip:\n m20.pick_up_tip()\n m20.aspirate(vol_dna_dilution, source)\n m20.dispense(vol_dna_dilution, dest)\n m20.mix(5, 10, dest)\n for final_well in dest_set:\n m20.aspirate(vol_dna, dest)\n m20.move_to(dest.bottom().move(Point(x=-1, z=5)))\n m20.dispense(vol_dna, final_well)\n m20.mix(5, 10, final_well)\n m20.move_to(final_well.bottom().move(Point(x=-1, z=5)))\n m20.drop_tip()\n\n # add blank\n for dest in dest_sets_384[-1]:\n m20.pick_up_tip()\n m20.aspirate(vol_dna, water)\n m20.dispense(vol_dna_dilution, dest)\n m20.mix(5, 10, dest)\n m20.move_to(dest.bottom().move(Point(x=-1, z=5)))\n m20.drop_tip()\n", - "custom_labware_defs": [ - { - "brand": { - "brand": "NEST Bioshake", - "brandId": [] - }, - "cornerOffsetFromSlot": { - "x": 0, - "y": 0, - "z": 0 - }, - "dimensions": { - "xDimension": 127.86, - "yDimension": 85.8, - "zDimension": 104.13 - }, - "groups": [ - { - "metadata": { - "wellBottomShape": "v" - }, - "wells": [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1", - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2", - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3", - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4", - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5", - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6", - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7", - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8", - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9", - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10", - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11", - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - } - ], - "metadata": { - "displayCategory": "wellPlate", - "displayName": "NEST Bioshake 96 Well Plate 2000 \u00b5L", - "displayVolumeUnits": "\u00b5L", - "tags": [] - }, - "namespace": "custom_beta", - "ordering": [ - [ - "A1", - "B1", - "C1", - "D1", - "E1", - "F1", - "G1", - "H1" - ], - [ - "A2", - "B2", - "C2", - "D2", - "E2", - "F2", - "G2", - "H2" - ], - [ - "A3", - "B3", - "C3", - "D3", - "E3", - "F3", - "G3", - "H3" - ], - [ - "A4", - "B4", - "C4", - "D4", - "E4", - "F4", - "G4", - "H4" - ], - [ - "A5", - "B5", - "C5", - "D5", - "E5", - "F5", - "G5", - "H5" - ], - [ - "A6", - "B6", - "C6", - "D6", - "E6", - "F6", - "G6", - "H6" - ], - [ - "A7", - "B7", - "C7", - "D7", - "E7", - "F7", - "G7", - "H7" - ], - [ - "A8", - "B8", - "C8", - "D8", - "E8", - "F8", - "G8", - "H8" - ], - [ - "A9", - "B9", - "C9", - "D9", - "E9", - "F9", - "G9", - "H9" - ], - [ - "A10", - "B10", - "C10", - "D10", - "E10", - "F10", - "G10", - "H10" - ], - [ - "A11", - "B11", - "C11", - "D11", - "E11", - "F11", - "G11", - "H11" - ], - [ - "A12", - "B12", - "C12", - "D12", - "E12", - "F12", - "G12", - "H12" - ] - ], - "parameters": { - "format": "irregular", - "isMagneticModuleCompatible": false, - "isTiprack": false, - "loadName": "nestbioshake_96_wellplate_2000ul", - "quirks": [] - }, - "schemaVersion": 2, - "version": 1, - "wells": { - "A1": { - "depth": 38, - "shape": "rectangular", - "totalLiquidVolume": 2000, - "x": 12.3, - "xDimension": 8.2, - "y": 76.65, - "yDimension": 8.2, - "z": 66.13 - }, - "A10": { - "depth": 38, - "shape": "rectangular", - "totalLiquidVolume": 2000, - "x": 93.3, - "xDimension": 8.2, - "y": 76.65, - "yDimension": 8.2, - "z": 66.13 - }, - 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"Opentrons 96 Filter Tip Rack 20 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "dilution plate on 8", - "share": false, - "slot": "8", - "type": "vwr_96_aluminumblock_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "source cDNA plate on 11", - "share": false, - "slot": "11", - "type": "vwr_96_aluminumblock_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.12", - "author": "Opentrons ", - "protocolName": "qPCR Prep" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json b/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json index a596dd8605..fe17d77541 100644 --- a/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json +++ b/protoBuilds/bc-rnadvance-viral-feat/beckman_viral.ot2.apiv2.py.json @@ -106,5 +106,18 @@ "author": "Opentrons ", "protocolName": "Beckman Coulter RNAdvance Viral RNA Isolation" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json b/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json index a596dd8605..fe17d77541 100644 --- a/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json +++ b/protoBuilds/bc-rnadvance-viral/beckman_viral.ot2.apiv2.py.json @@ -106,5 +106,18 @@ "author": "Opentrons ", "protocolName": "Beckman Coulter RNAdvance Viral RNA Isolation" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json b/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json index 34c821bf19..0276b5bdb0 100644 --- a/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json +++ b/protoBuilds/bpg-rna-extraction/bpg-rna-extraction.ot2.apiv2.py.json @@ -1216,7 +1216,7 @@ "type": "opentrons_96_tiprack_20ul" }, { - "name": "NEST 1mL Deep Well Plate on Magnetic Module GEN1 on 4", + "name": "NEST 1mL Deep Well Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "nest_96_wellplate_1000ul" @@ -1248,7 +1248,7 @@ }, "modules": [ { - "name": "MagneticModuleContext at Magnetic Module GEN1 on 4 lw NEST 1mL Deep Well Plate on Magnetic Module GEN1 on 4", + "name": "MagneticModuleContext at Magnetic Module on 4 lw NEST 1mL Deep Well Plate on Magnetic Module on 4", "share": false, "slot": "4", "type": "magdeck" diff --git a/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json b/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json index ead4d58367..5d09861027 100644 --- a/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json +++ b/protoBuilds/complete-pcr/complete_pcr.ot2.apiv2.py.json @@ -338,5 +338,12 @@ "protocolName": "Complete PCR Workflow with Thermocycler", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw thermocycler plate on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json b/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json index 1ca276603f..6ced651630 100644 --- a/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json +++ b/protoBuilds/covid19-rna-extraction/extraction.ot2.apiv2.py.json @@ -235,5 +235,18 @@ "author": "Opentrons ", "protocolName": "COVID-19 Station B RNA Extraction" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw deepwell plate on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/demo/test_drive.ot2.apiv2.py.json b/protoBuilds/demo/test_drive.ot2.apiv2.py.json index d99b3f2ff3..c5b6c97ff4 100644 --- a/protoBuilds/demo/test_drive.ot2.apiv2.py.json +++ b/protoBuilds/demo/test_drive.ot2.apiv2.py.json @@ -144,5 +144,12 @@ "protocolName": "OT-2 Demo", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw None", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json b/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json index fab6b1eb0f..c9e7de074a 100644 --- a/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json +++ b/protoBuilds/gna_octea/gna_octea.ot2.apiv2.py.json @@ -337,5 +337,18 @@ "protocolName": "Automated Sample Prep for GNA Octea", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 6 lw Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json b/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json index 2a2f14d2ab..e267441bcc 100644 --- a/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json +++ b/protoBuilds/gna_octea_v2/gna_octea_v2.ot2.apiv2.py.json @@ -369,5 +369,18 @@ "protocolName": "Automated Sample Prep for GNA Octea [v2]", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Snapcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json b/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json index 44fdc14478..3ff332f9e7 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part2/nexteraXT_dna_library_prep_part2.ot2.apiv2.py.json @@ -116,7 +116,7 @@ "type": "usascientific_12_reservoir_22ml" }, { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 4", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -158,5 +158,12 @@ "protocolName": "Illumina Nextera XT NGS Prep 2: Clean-Up Libraries", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json b/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json index ce0e8c8fe7..a47243d29e 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part3/nexteraXT_dna_library_prep_part3.ot2.apiv2.py.json @@ -86,7 +86,7 @@ "type": "usascientific_12_reservoir_22ml" }, { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 4", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", "share": false, "slot": "4", "type": "biorad_96_wellplate_200ul_pcr" @@ -128,5 +128,12 @@ "protocolName": "Illumina Nextera XT NGS Prep 3: Normalize Libraries", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json b/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json index 5a21453ed8..f0d0508759 100644 --- a/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json +++ b/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/nextera_flex_amplify_tagmented_dna.ot2.apiv2.py.json @@ -66,13 +66,13 @@ ], "labware": [ { - "name": "1 on Magnetic Module GEN1 on 1", + "name": "1 on Magnetic Module on 1", "share": false, "slot": "1", "type": "biorad_96_wellplate_200ul_pcr" }, { - "name": "4 on Temperature Module GEN1 on 4", + "name": "4 on Temperature Module on 4", "share": false, "slot": "4", "type": "opentrons_24_aluminumblock_nest_1.5ml_snapcap" @@ -120,5 +120,18 @@ "protocolName": "Nextera DNA Flex NGS Library Prep: Amplify Tagmented DNA", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw 1 on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 4 lw 4 on Temperature Module on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json b/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json index 56cd45900c..678b2be0f3 100644 --- a/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json +++ b/protoBuilds/nextera-flex-library-prep-cleanup-libraries/nextera_flex_cleanup_libraries.ot2.apiv2.py.json @@ -81,7 +81,7 @@ ], "labware": [ { - "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 1", + "name": "Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 1", "share": false, "slot": "1", "type": "biorad_96_wellplate_200ul_pcr" @@ -159,5 +159,12 @@ "protocolName": "Nextera DNA Flex NGS Library Prep: Cleanup Libraries", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json b/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json index 515d2edd1f..2090a10f54 100644 --- a/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json +++ b/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/nextera_flex_post_tag_cleanup.ot2.apiv2.py.json @@ -47,7 +47,7 @@ ], "labware": [ { - "name": "1 on Magnetic Module GEN1 on 1", + "name": "1 on Magnetic Module on 1", "share": false, "slot": "1", "type": "biorad_96_wellplate_200ul_pcr" @@ -107,5 +107,12 @@ "protocolName": "Nextera DNA Flex NGS Library Prep: Post Tagmentation Cleanup", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 1 lw 1 on Magnetic Module on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json b/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json index 015ea40727..f82e7b1617 100644 --- a/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json +++ b/protoBuilds/nucleic_acid_purification_with_magnetic_beads/dna_purification.ot2.apiv2.py.json @@ -180,5 +180,12 @@ "protocolName": "DNA Purification", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 1 lw Bio-Rad 96 Well Plate 200 \u00b5L PCR on Magnetic Module GEN1 on 1", + "share": false, + "slot": "1", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json b/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json index e270645f18..3d8d9af890 100644 --- a/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json +++ b/protoBuilds/omega-biotek-xpress/omega-biotek-xpress.ot2.apiv2.py.json @@ -179,5 +179,18 @@ "author": "Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [\n num_samples, m20_mount\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m20_mount\")\n\n # define all custom variables above here with descriptions:\n\n num_cols = math.ceil(num_samples/8)\n m20_speed_mod = 4\n airgap_library = 5\n # load modules\n mag_module = ctx.load_module('magnetic module gen2', '1')\n\n # load labware\n sample_plate = mag_module.load_labware('nest_96_wellplate'\n '_100ul_pcr_full_skirt')\n reagent_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2')\n # load tipracks\n tiprack20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul',\n str(slot))\n for slot in [3, 5, 6]]\n\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tiprack20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n # helper functions\n\n # reagents\n library_mix = reagent_plate.rows()[0][0]\n pcr_forward = reagent_plate.rows()[0][1]\n pcr_reverse = reagent_plate.rows()[0][2]\n # plate, tube rack maps\n sample_dest = sample_plate.rows()[0][:num_cols]\n # protocol\n\n # add library mix, 5 uL\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(5, library_mix)\n m20.move_to(library_mix.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(library_mix.top(-2))\n m20.aspirate(airgap_library, library_mix.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n # add forward, reverse primers, 2 uL each\n for reagent_source in [pcr_forward, pcr_reverse]:\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(2, reagent_source)\n m20.move_to(reagent_source.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(reagent_source.top(-2))\n m20.aspirate(airgap_library, reagent_source.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of Samples", - "name": "num_samples", - "type": "int" - }, - { - "label": "P20 Multi GEN2 mount", - "name": "m20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "rhAmpSeq Library Prep Part 1 - PCR 1", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/onsite-ganda-2/part2.ot2.apiv2.py.json b/protoBuilds/onsite-ganda-2/part2.ot2.apiv2.py.json deleted file mode 100644 index 45d3a72675..0000000000 --- a/protoBuilds/onsite-ganda-2/part2.ot2.apiv2.py.json +++ /dev/null @@ -1,124 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'rhAmpSeq Library Prep Part 1 - PCR 1',\n 'author': 'Opentrons ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [\n num_samples, m20_mount\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m20_mount\")\n\n # define all custom variables above here with descriptions:\n if m20_mount == 'right':\n m300_mount = 'left'\n else:\n m300_mount = 'right'\n num_cols = math.ceil(num_samples/8)\n num_etoh_wells = math.ceil((0.4*num_samples)/15)\n m20_speed_mod = 4\n airgap_library = 5\n etoh_res_vol = 15000\n # load modules\n mag_module = ctx.load_module('magnetic module gen2', '1')\n\n # load labware\n sample_plate = mag_module.load_labware('nest_96_wellplate'\n '_100ul_pcr_full_skirt')\n reagent_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2')\n reagent_resv = ctx.load_labware('nest_12_reservoir_15ml', '3')\n # load tipracks\n tiprack20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul',\n str(slot))\n for slot in [4, 5]]\n tiprack300 = [ctx.load_labware('opentrons_96_filtertiprack_200ul',\n str(slot))\n for slot in [6, 7, 8, 9, 10, 11]]\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tiprack20)\n m300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n tip_racks=tiprack300)\n # reagents\n sample_plate_dest = sample_plate.rows()[0][:num_cols]\n library_mix = reagent_plate.rows()[0][0]\n pcr_forward = reagent_plate.rows()[0][1]\n pcr_reverse = reagent_plate.rows()[0][2]\n beads_1 = reagent_plate.rows()[0][3]\n beads_2 = reagent_plate.rows()[0][4]\n idte = reagent_plate.rows()[0][5]\n # well volume tracking is better solution for this\n etoh_1 = reagent_resv.wells()[0]\n etoh_2 = reagent_resv.wells()[1]\n etoh_3 = reagent_resv.wells()[2]\n etoh_4 = reagent_resv.wells()[3]\n liquid_trash_1 = reagent_resv.wells()[8]\n liquid_trash_2 = reagent_resv.wells()[9]\n liquid_trash_3 = reagent_resv.wells()[10]\n liquid_trash_4 = reagent_resv.wells()[11]\n\n etoh_total = [etoh_1, etoh_2, etoh_3, etoh_4]\n trash_total = [liquid_trash_1, liquid_trash_2, liquid_trash_3,\n liquid_trash_4]\n # Volume and Height Tracking\n # class VolHeightTracker:\n # def __init__(self, labware, well_vol, start=0, end=12,\n # min_height=1, comp_coeff=0.9, msg='Reset Labware'):\n # try:\n # self.labware_wells = dict.fromkeys(\n # labware.wells()[start:end], 0)\n # except Exception:\n # self.labware_wells = dict.fromkeys(\n # labware, 0)\n # self.labware_wells_backup = self.labware_wells.copy()\n # self.well_vol = well_vol\n # self.start = start\n # self.end = end\n # self.min_height = min_height\n # self.comp_coeff = comp_coeff\n # self.width = labware.wells()[0].xDimension\n # self.length = labware.wells()[0].yDimension\n # self.area = self.width*self.length\n # self.msg = msg\n #\n # def tracker(self, vol):\n # '''tracker() will track how much liquid\n # was used up per well. If the volume of\n # a given well is greater than self.well_vol\n # it will remove it from the dictionary and iterate\n # to the next well which will act as the reservoir.'''\n # well = next(iter(self.labware_wells))\n # if self.labware_wells[well] + vol >= self.well_vol:\n # del self.labware_wells[well]\n # if len(self.labware_wells) < 1:\n # ctx.pause(self.msg)\n # self.labware_wells = self.labware_wells_backup.copy()\n # well = next(iter(self.labware_wells))\n # dh = (self.well_vol - self.labware_wells[well]) / self.area \\\n # * self.comp_coeff\n # height = self.min_height if dh < 1 else round(dh, 2)\n # self.labware_wells[well] = self.labware_wells[well] + vol\n # ctx.comment(f'''{int(self.labware_wells[well])} uL of liquid\n # used from {well}''')\n # ctx.comment(f'Current Liquid Height of {well}: {height}mm')\n # return well.bottom(height)\n #\n # def trash_tracker(self, vol):\n # '''WIP trash_tracker() will track how much liquid\n # was added per well. If the volume of\n # a given well is greater than self.well_vol\n # it will remove it from the dictionary and iterate\n # to the next well which will act as the new trash.'''\n # cutoff_vol = self.well_vol*0.75\n # well = next(iter(self.labware_wells))\n # if self.labware_wells[well] + vol >= cutoff_vol:\n # del self.labware_wells[well]\n # if len(self.labware_wells) < 1:\n # ctx.pause(self.msg)\n # self.labware_wells = self.labware_wells_backup.copy()\n # well = next(iter(self.labware_wells))\n # dh = (self.well_vol - self.labware_wells[well]) / self.area \\\n # * self.comp_coeff\n # height = self.min_height if dh < 1 else round(dh, 2)\n # self.labware_wells[well] = self.labware_wells[well] + vol\n # ctx.comment(f'''{int(self.labware_wells[well])} uL of liquid\n # used from {well}''')\n # ctx.comment(f'Current Liquid Height of {well}: {height}mm')\n # return well.bottom(height)\n\n # etohTrack = VolHeightTracker(etoh_total, well_vol=etoh_res_vol, start=0,\n # end=96)\n etoh_volumes = dict.fromkeys(reagent_resv.wells()[:4], 0)\n supernatant_headspeed_modulator = 5\n\n def liquid_tracker(vol):\n '''liquid_tracker() will track how much liquid\n was used up per well. If the volume of\n a given well is greater than 'liquid'_res_vol\n it will remove it from the dictionary and iterate\n to the next well which will act as the reservoir.'''\n well = next(iter(etoh_volumes))\n if etoh_volumes[well] > etoh_res_vol:\n del etoh_volumes[well]\n well = next(iter(etoh_volumes))\n etoh_volumes[well] = etoh_volumes[well] + vol\n ctx.comment(f'{int(etoh_volumes[well])} uL of water used from {well}')\n return well\n\n def bead_mixing(well, pip, mvol, reps=8):\n\n \"\"\"\n 'bead_mixing' will mix liquid that contains beads. This will be done by\n aspirating from the bottom of the well and dispensing from the top as to\n mix the beads with the other liquids as much as possible. Aspiration and\n dispensing will also be reversed for a short to to ensure maximal mixing.\n param well: The current well that the mixing will occur in.\n param pip: The pipet that is currently attached/ being used.\n param mvol: The volume that is transferred before the mixing steps.\n param reps: The number of mix repetitions that should occur. Note~\n During each mix rep, there are 2 cycles of aspirating from bottom,\n dispensing at the top and 2 cycles of aspirating from middle,\n dispensing at the bottom\n \"\"\"\n center = well.top().move(types.Point(x=0, y=0, z=5))\n aspbot = well.bottom(1)\n asptop = well.bottom(10)\n disbot = well.bottom(3)\n distop = well.top()\n\n vol = mvol * .9\n\n pip.move_to(center)\n for _ in range(reps):\n pip.aspirate(vol, aspbot)\n pip.dispense(vol, distop)\n pip.aspirate(vol, asptop)\n pip.dispense(vol, disbot)\n # PROTOCOL\n etoh_wash_vol = 200\n for dest in sample_plate_dest:\n m300.flow_rate.aspirate /= 4\n m300.flow_rate.dispense /= 4\n m300.pick_up_tip()\n m300.aspirate(30, beads_1)\n m300.dispense(30, dest)\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n bead_mixing(dest, m300, 30, reps=10)\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n m300.drop_tip()\n\n ctx.delay(minutes=10)\n mag_module.engage()\n ctx.delay(minutes=5)\n\n ctx.comment('''discarding supernatant''')\n ctx.max_speeds['Z'] = 50\n ctx.max_speeds['A'] = 50\n num_times = 1\n mag_module.engage()\n ctx.delay(minutes=3)\n for source in sample_plate_dest:\n side = 1 if num_times % 2 == 0 else -1\n m300.pick_up_tip()\n m300.flow_rate.aspirate /= 5\n m300.move_to(source.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(\n 50, source.bottom().move(types.Point(x=side,\n y=0, z=0.5)))\n m300.move_to(source.top())\n m300.flow_rate.aspirate *= 5\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, liquid_trash_1)\n m300.drop_tip()\n num_times += 1\n print(side)\n\n # etoh wash needs the multi-source well function to work!\n ctx.comment(\"Ethanol Wash\")\n for _ in range(2):\n for dest in sample_plate_dest:\n m300.pick_up_tip()\n m300.aspirate(200, etoh_1)\n m300.dispense(200, dest)\n m300.drop_tip()\n ctx.delay(minutes=1)\n for source in sample_plate_dest:\n side = 1 if num_times % 2 == 0 else -1\n m300.pick_up_tip()\n m300.flow_rate.aspirate /= 5\n m300.move_to(source.top())\n ctx.max_speeds['Z'] /= supernatant_headspeed_modulator\n ctx.max_speeds['A'] /= supernatant_headspeed_modulator\n m300.aspirate(\n 50, source.bottom().move(types.Point(x=side,\n y=0, z=0.5)))\n m300.move_to(source.top())\n m300.flow_rate.aspirate *= 5\n ctx.max_speeds['Z'] *= supernatant_headspeed_modulator\n ctx.max_speeds['A'] *= supernatant_headspeed_modulator\n m300.dispense(50, liquid_trash_1)\n m300.drop_tip()\n num_times += 1\n print(side)\n\n ctx.delay(minutes=3)\n mag_module.disengage()\n ctx.comment('Adding IDTE')\n for dest in sample_plate_dest:\n m20.pick_up_tip()\n m20.aspirate(15, idte)\n m20.dispense(15, idte)\n m20.drop_tip()\n\n ctx.pause(\"Please vortex and centrifuge sample plate, return to slot 1\")\n\n ctx.delay(minutes=3)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of Samples (max 288)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P20 Multi GEN2 mount", - "name": "m20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - }, - { - "default": 15, - "label": "Overage Percent", - "name": "overage_percent", - "type": "float" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 12 Well Reservoir 15 mL on 3", - "share": false, - "slot": "3", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 7", - "share": false, - "slot": "7", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 8", - "share": false, - "slot": "8", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 10", - "share": false, - "slot": "10", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 11", - "share": false, - "slot": "11", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "rhAmpSeq Library Prep Part 1 - PCR 1", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/onsite-ganda-3/part3.ot2.apiv2.py.json b/protoBuilds/onsite-ganda-3/part3.ot2.apiv2.py.json deleted file mode 100644 index a275a7ac85..0000000000 --- a/protoBuilds/onsite-ganda-3/part3.ot2.apiv2.py.json +++ /dev/null @@ -1,78 +0,0 @@ -{ - "content": "\"\"\"OPENTRONS.\"\"\"\nimport math\n\nmetadata = {\n 'protocolName': 'rhAmpSeq Library Prep Part 3 - PCR 2',\n 'author': 'Opentrons ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.11' # CHECK IF YOUR API LEVEL HERE IS UP TO DATE\n # IN SECTION 5.2 OF THE APIV2 \"VERSIONING\"\n}\n\n\ndef run(ctx):\n \"\"\"PROTOCOL.\"\"\"\n [\n num_samples, m20_mount\n ] = get_values( # noqa: F821 (<--- DO NOT REMOVE!)\n \"num_samples\", \"m20_mount\")\n\n # define all custom variables above here with descriptions:\n\n num_cols = math.ceil(num_samples/8)\n m20_speed_mod = 4\n airgap_library = 5\n # load modules\n mag_module = ctx.load_module('magnetic module gen2', '1')\n\n # load labware\n sample_plate = mag_module.load_labware('nest_96_wellplate'\n '_100ul_pcr_full_skirt')\n reagent_plate = ctx.load_labware('nest_96_wellplate_100ul_pcr_full_skirt',\n '2')\n # load tipracks\n tiprack20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul',\n str(slot))\n for slot in [3, 5, 6]]\n\n # load instrument\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=tiprack20)\n\n # pipette functions # INCLUDE ANY BINDING TO CLASS\n\n # helper functions\n\n # reagents\n library_mix = reagent_plate.rows()[0][3]\n index_i5 = reagent_plate.rows()[0][4]\n index_i7 = reagent_plate.rows()[0][5]\n # plate, tube rack maps\n sample_dest = sample_plate.rows()[0][:num_cols]\n # protocol\n\n # add library mix, 5 uL\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(5, library_mix)\n m20.move_to(library_mix.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(library_mix.top(-2))\n m20.aspirate(airgap_library, library_mix.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n # add indexing primers, 2 uL each\n for reagent_source in [index_i5, index_i7]:\n for dest in sample_dest:\n m20.flow_rate.aspirate /= m20_speed_mod\n m20.flow_rate.dispense /= m20_speed_mod\n m20.pick_up_tip()\n m20.aspirate(2, reagent_source)\n m20.move_to(reagent_source.top(-2))\n ctx.delay(seconds=2)\n m20.touch_tip(v_offset=-2)\n m20.move_to(reagent_source.top(-2))\n m20.aspirate(airgap_library, reagent_source.top())\n m20.dispense(airgap_library, dest.top())\n m20.dispense(5, dest)\n m20.drop_tip()\n m20.flow_rate.aspirate *= m20_speed_mod\n m20.flow_rate.dispense *= m20_speed_mod\n\n for c in ctx.commands():\n print(c)\n", - "custom_labware_defs": [], - "fields": [ - { - "default": 96, - "label": "Number of Samples (max 96)", - "name": "num_samples", - "type": "int" - }, - { - "label": "P20 Multi GEN2 mount", - "name": "m20_mount", - "options": [ - { - "label": "right", - "value": "right" - }, - { - "label": "left", - "value": "left" - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on 2", - "share": false, - "slot": "2", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.11", - "author": "Opentrons ", - "protocolName": "rhAmpSeq Library Prep Part 3 - PCR 2", - "source": "Custom Protocol Request" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json b/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json index d6b05f1a99..99390641bb 100644 --- a/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json +++ b/protoBuilds/pcr_test_plan/pcr_test_plan.ot2.apiv2.py.json @@ -108,5 +108,12 @@ "protocolName": "PCR Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json b/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json index 52b0cdc48f..b7ae7ed575 100644 --- a/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json +++ b/protoBuilds/promega-maxwell/promega-maxwell.ot2.apiv2.py.json @@ -136,5 +136,18 @@ "author": "Nick Diehl", "protocolName": "Promega Maxwell\u00ae HT Viral TNA Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/README.json b/protoBuilds/sci-illumina-dna-prep/README.json deleted file mode 100644 index 34007e21c1..0000000000 --- a/protoBuilds/sci-illumina-dna-prep/README.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "author": "Opentrons", - "categories": { - "NGS Library Prep": [ - "Illumina DNA Prep" - ] - }, - "deck-setup": "\nInital slot layout:\n1. Magnetic module for the sample plate (Nest 96 well plate full skirt).\n2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents\n3. Reagent plate 2: Temperature module with Bio-rad 200 \u00b5L plate on aluminum block. See Reagent Setup section for information about the location of the reagents\n4. 20 \u00b5L filter tiprack\n5. 200 \u00b5L filter tiprack\n6. 200 \u00b5L filter tiprack\n7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 \u00b5L\n8. Empty\n9. 200 \u00b5L filter tiprack\n10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots)\n11. Empty", - "description": "This protocol automates the Illumina DNA prep protocol. Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species\nThe protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 \u00b5L of 100 ng:s of sample DNA in each well. See the Illumina DNA Prep protocol for more information about sample input requirements.\n\n\nThe user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below.\nPlate Moving\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\nExplanation of parameters below:\n Number of samples: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above).\n Do a dry run?: Sets the Use modules? parameter to No (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes.\n Use modules?: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to Yes if the Do a dry run? parameter is set to Yes\n Tip reuse?: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run.\n Use tip offsets?: Whether to use specific offsets for each tip type\n Include tagmentation step in protocol run?: Run the tagmentation step or skip it.\n Run tagmentation incubation on the deck thermocycler?: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler.\n Run TSB step?: Run the TSB/adapter ligation step or not\n Run TSB incubation step on the deck thermocycler: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler\n Run tagmentation wash with TWB step: Run the bead washing steps with TWB\n Run PCR cycle step: Whether to run the PCR amplification step\n Run PCR step on deck thermocycler?: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler\n* Run post PCR cleanup step: Run or skip the post-PCR bead cleanup using AMPure beads\n", - "internal": "illumina-dna-prep", - "labware": "\nNest 96 well plate full skirt 100 \u00b5L\nNEST 2 mL 96-Well Deep Well Plate\nNEST 12-Well Reservoirs, 15 mL\nOpentrons aluminum block set\n", - "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n", - "categories": "* NGS Library Prep\n\t* Illumina DNA Prep\n\n", - "deck-setup": "![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/deck.jpg)\n\nInital slot layout:\n1. Magnetic module for the sample plate (Nest 96 well plate full skirt).\n2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents\n3. Reagent plate 2: Temperature module with Bio-rad 200 \u00b5L plate on aluminum block. See Reagent Setup section for information about the location of the reagents\n4. 20 \u00b5L filter tiprack\n5. 200 \u00b5L filter tiprack\n6. 200 \u00b5L filter tiprack\n7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 \u00b5L\n8. Empty\n9. 200 \u00b5L filter tiprack\n10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots)\n11. Empty\n\n", - "description": "This protocol automates the [Illumina DNA prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf). Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species\n\nThe protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 \u00b5L of 100 ng:s of sample DNA in each well. See the [Illumina DNA Prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf) for more information about sample input requirements.\n\n![Sample input and output columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/samples_output.jpg)\n\n![Sample columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/sample_setup.jpg)\n\nThe user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below.\n\n**Plate Moving**\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\n\nExplanation of parameters below:\n* `Number of samples`: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above).\n* `Do a dry run?`: Sets the `Use modules?` parameter to `No` (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes.\n* `Use modules?`: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to `Yes` if the `Do a dry run?` parameter is set to `Yes`\n* `Tip reuse?`: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run.\n* `Use tip offsets?`: Whether to use specific offsets for each tip type\n* `Include tagmentation step in protocol run?`: Run the tagmentation step or skip it.\n* `Run tagmentation incubation on the deck thermocycler?`: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler.\n* `Run TSB step?`: Run the TSB/adapter ligation step or not\n* `Run TSB incubation step on the deck thermocycler`: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler\n* `Run tagmentation wash with TWB step`: Run the bead washing steps with TWB\n* `Run PCR cycle step`: Whether to run the PCR amplification step\n* `Run PCR step on deck thermocycler?`: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler\n* `Run post PCR cleanup step`: Run or skip the post-PCR bead cleanup using AMPure beads\n---\n\n", - "internal": "illumina-dna-prep\n", - "labware": "* [Nest 96 well plate full skirt 100 \u00b5L](https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/)\n* [NEST 2 mL 96-Well Deep Well Plate](https://shop.opentrons.com/nest-2-ml-96-well-deep-well-plate-v-bottom/)\n* [NEST 12-Well Reservoirs, 15 mL](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/)\n* [Opentrons aluminum block set](https://shop.opentrons.com/aluminum-block-set/)\n\n", - "modules": "* [Temperature Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n* [Magnetic Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module)\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", - "partner": "[Illumina](https://www.illumina.com/)\n\n", - "pipettes": "* [P300 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [P20 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [P10 multi-Channel](https://shop.opentrons.com/8-channel-electronic-pipette/)\n**Tips**\n* [Opentrons 20 \u00b5L filter tiprack](https://shop.opentrons.com/opentrons-20ul-filter-tips/)\n* [Opentrons 200 \u00b5L filter tiprack](https://shop.opentrons.com/opentrons-200ul-filter-tips/)\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit 'Run'.\n\n", - "protocol-steps": "1. Prepare the thermocycler by setting the block temperature to 4 degrees, and the lid to 100 degrees.\n2. Add tagmentation mix to the samples\n3. User seals the plate and the protocol incubates the samples with the mix in the thermocycler, 55 degrees for 15 minutes.\n4. The thermocycler opens, and the user removes the seal.\n5. Add Tagmentation Stop Buffer to the samples.\n6. Seal and incubate the mix at 37 degrees for 15 minutes.\n7. User removes seal; remove the supernatant and wash the beads three times with Tagmentation Wash Buffer.\n8. Amplification of DNA: Addition of PCR mix and addition of barcodes.\n9. The protocol runs PCR protocol for 5 cycles. This takes 25 minutes to complete. The supernatant is transferred to columns 7, 9 and 11 depending on how many sample columns there are.\n10. Post-PCR cleanup using AMPure beads.\n11. The protocol performs two ethanol washes.\n12. RSB (resuspension buffer) is added to the bead wells and the supernatant is transferred to the output columns (8, 10, and 12).\n\n", - "reagent-setup": "* Reservoir, slot 2:\n![Reagent plate 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate1.jpg)\n* Reagent plate on temperature module, slot 3:\n![Reagent plate 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate2.jpg)\n\n---\n\n", - "reagents": "* [Illumina DNA Prep](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html)\n\n---\n\n", - "title": "Illumina DNA Prep - Opentrons v3" - }, - "modules": [ - "Temperature Module (GEN2)", - "Magnetic Module (GEN2)", - "Thermocycler Module" - ], - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Illumina", - "pipettes": "\nP300 multi-Channel (GEN2)\nP20 multi-Channel (GEN2)\nP10 multi-Channel\nTips\nOpentrons 20 \u00b5L filter tiprack\nOpentrons 200 \u00b5L filter tiprack\n", - "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "protocol-steps": "\nPrepare the thermocycler by setting the block temperature to 4 degrees, and the lid to 100 degrees.\nAdd tagmentation mix to the samples\nUser seals the plate and the protocol incubates the samples with the mix in the thermocycler, 55 degrees for 15 minutes.\nThe thermocycler opens, and the user removes the seal.\nAdd Tagmentation Stop Buffer to the samples.\nSeal and incubate the mix at 37 degrees for 15 minutes.\nUser removes seal; remove the supernatant and wash the beads three times with Tagmentation Wash Buffer.\nAmplification of DNA: Addition of PCR mix and addition of barcodes.\nThe protocol runs PCR protocol for 5 cycles. This takes 25 minutes to complete. The supernatant is transferred to columns 7, 9 and 11 depending on how many sample columns there are.\nPost-PCR cleanup using AMPure beads.\nThe protocol performs two ethanol washes.\nRSB (resuspension buffer) is added to the bead wells and the supernatant is transferred to the output columns (8, 10, and 12).\n", - "reagent-setup": "\nReservoir, slot 2:\n\nReagent plate on temperature module, slot 3:\n\n\n", - "reagents": [ - "Illumina DNA Prep" - ], - "title": "Illumina DNA Prep - Opentrons v3" -} \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/metadata.json b/protoBuilds/sci-illumina-dna-prep/metadata.json deleted file mode 100644 index d75df21c2f..0000000000 --- a/protoBuilds/sci-illumina-dna-prep/metadata.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "files": { - "OT 1 protocol": [], - "OT 2 protocol": [ - "sci-illumina-dna-prep.ot2.apiv2.py" - ], - "description": [ - "README.md" - ] - }, - "flags": { - "embedded-app": false, - "feature": false, - "hide-from-search": true, - "skip-tests": false - }, - "path": "protocols/sci-illumina-dna-prep", - "slug": "sci-illumina-dna-prep", - "status": "ok" -} \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py.json b/protoBuilds/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py.json deleted file mode 100644 index 3cca7dd7ef..0000000000 --- a/protoBuilds/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py.json +++ /dev/null @@ -1,278 +0,0 @@ -{ - "content": "from opentrons import protocol_api\n\nfrom opentrons import types\n\nimport inspect\n\nmetadata = {\n 'protocolName': 'Illumina DNA Prep',\n 'author': 'Opentrons ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.9'\n}\n# I removed the right() function because it is never used\n# settings\n# SAMPLES = '24x' # 8x, 16x, or 24x\n# YES or NO, DRYRUN = 'YES' will return tips, skip incubation times,\n# shorten mix, for testing purposes\n# DRYRUN = 'NO'\n# YES or NO, NOMODULES = 'YES' will not require modules on the deck and will\n# skip module steps, for testing purposes, if DRYRUN = 'YES', then NOMODULES\n# will automatically set itself to 'NO'\n# NOMODULES = 'NO'\n# TIPREUSE = 'NO'\n# YES or NO, Reusing tips on wash steps reduces tips needed, no tip refill\n# needed, suggested only for 24x run with all steps\n\n# YES or NO, Sets whether to use protocol specific z offsets for each tip and\n# labware or no offsets aside from defaults\n# OFFSET = 'YES'\n\n# sections\n# STEP_TAG = 1 # 1 is include, 0 is skip, steps with \"DECK\" are\n# for reaction\n# to take place with the on deck Thermocycler module\n# This arrangement makes it possibly to set up and run only the first\n# half, or to skips steps and resume if there is an Error.\n# STEP_TAGDECK = 1\n# If non \"DECK\" steps are skipped, then TIPREUSE will automatically set\n# itself to 'NO' in order to keep tip order correct.\n# STEP_TSB = 1\n# STEP_TSBDECK = 1\n# STEP_WASH = 1\n# STEP_PCR = 1\n# STEP_PCRDECK = 1\n# STEP_POSTPCR = 1\n\n\ndef run(protocol: protocol_api.ProtocolContext):\n\n global TIPREUSE\n\n [SAMPLES,\n DRYRUN,\n NOMODULES,\n TIPREUSE,\n OFFSET,\n STEP_TAG,\n STEP_TAGDECK,\n STEP_TSB,\n STEP_TSBDECK,\n STEP_WASH,\n STEP_PCR,\n STEP_PCRDECK,\n STEP_POSTPCR] = get_values( # noqa: F821\n \"SAMPLES\",\n \"DRYRUN\",\n \"NOMODULES\",\n \"TIPREUSE\",\n \"OFFSET\",\n \"STEP_TAG\",\n \"STEP_TAGDECK\",\n \"STEP_TSB\",\n \"STEP_TSBDECK\",\n \"STEP_WASH\",\n \"STEP_PCR\",\n \"STEP_PCRDECK\",\n \"STEP_POSTPCR\")\n\n STEPS = {STEP_TAG, STEP_TSB, STEP_WASH, STEP_PCR, STEP_POSTPCR}\n\n if DRYRUN == 'YES':\n protocol.comment(\"THIS IS A DRY RUN\")\n else:\n protocol.comment(\"THIS IS A REACTION RUN\")\n NOMODULES = 'NO'\n\n if all(STEPS) is True:\n if TIPREUSE == 'YES':\n TIPREUSE = 'YES'\n protocol.comment(\"TIP REUSING\")\n else:\n TIPREUSE = 'NO'\n protocol.comment(\"NO TIP REUSING\")\n\n # labware\n if NOMODULES == 'YES':\n protocol.comment(\"THIS IS A NO MODULE RUN\")\n # <--- Actually an Eppendorf 96 well, same dimensions\n sample_plate_mag = protocol.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '1')\n if TIPREUSE == 'NO':\n reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2')\n else:\n reservoir = protocol.load_labware(\n 'nest_96_wellplate_2ml_deep', '2')\n reagent_plate = protocol.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul', '3')\n tiprack_20 = protocol.load_labware(\n 'opentrons_96_filtertiprack_20ul', '4')\n tiprack_200_1 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '5')\n tiprack_200_2 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '6')\n sample_plate_thermo = protocol.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '7')\n tiprack_200_3 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '9')\n else:\n protocol.comment(\"THIS IS A MODULE RUN\")\n mag_block = protocol.load_module('magnetic module gen2', '1')\n # <--- Actually an Eppendorf 96 well, same dimensions\n sample_plate_mag = mag_block.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt')\n if TIPREUSE == 'NO':\n reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2')\n else:\n reservoir = protocol.load_labware(\n 'nest_96_wellplate_2ml_deep', '2')\n temp_block = protocol.load_module('temperature module gen2', '3')\n reagent_plate = temp_block.load_labware(\n 'opentrons_96_aluminumblock_biorad_wellplate_200ul')\n tiprack_20 = protocol.load_labware(\n 'opentrons_96_filtertiprack_20ul', '4')\n tiprack_200_1 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '5')\n tiprack_200_2 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '6')\n thermocycler = protocol.load_module('thermocycler module')\n sample_plate_thermo = thermocycler.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt')\n tiprack_200_3 = protocol.load_labware(\n 'opentrons_96_filtertiprack_200ul', '9')\n\n if TIPREUSE == 'YES':\n protocol.comment(\"THIS PROTOCOL WILL REUSE TIPS FOR WASHES\")\n\n # reagent - plate\n TAG = reagent_plate.wells_by_name()['A1']\n TSB = reagent_plate.wells_by_name()['A2']\n PCR = reagent_plate.wells_by_name()['A3']\n Barcodes1 = reagent_plate.wells_by_name()['A7']\n Barcodes2 = reagent_plate.wells_by_name()['A8']\n Barcodes3 = reagent_plate.wells_by_name()['A9']\n\n # reagent - deepwell\n if TIPREUSE == 'NO':\n AMPure = reservoir['A1']\n EtOH_1 = reservoir['A4']\n EtOH_2 = reservoir['A4']\n EtOH_3 = reservoir['A4']\n RSB = reservoir['A6']\n TWB_1 = reservoir['A8']\n TWB_2 = reservoir['A8']\n TWB_3 = reservoir['A8']\n Liquid_trash = reservoir['A12']\n else:\n AMPure = reservoir['A1']\n EtOH_1 = reservoir['A4']\n EtOH_2 = reservoir['A3']\n EtOH_3 = reservoir['A2']\n RSB = reservoir['A6']\n TWB_1 = reservoir['A8']\n TWB_2 = reservoir['A9']\n TWB_3 = reservoir['A10']\n Liquid_trash = reservoir['A12']\n\n # pipette\n if NOMODULES == 'NO':\n p300 = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[\n tiprack_200_1, tiprack_200_2,\n tiprack_200_3])\n p20 = protocol.load_instrument(\n 'p20_multi_gen2', 'right', tip_racks=[tiprack_20])\n else:\n p300 = protocol.load_instrument('p300_multi', 'left', tip_racks=[\n tiprack_200_1, tiprack_200_2,\n tiprack_200_3])\n p20 = protocol.load_instrument(\n 'p10_multi', 'right', tip_racks=[tiprack_20])\n\n # samples\n # FIXME: This does not seem to be used\n src_file_path = inspect.getfile(lambda: None)\n protocol.comment(src_file_path)\n\n # tip and sample tracking\n if SAMPLES == '8x':\n protocol.comment(\"There are 8 Samples\")\n samplecolumns = 1\n TWB_washtip_1 = tiprack_200_1['A3']\n TWB_removetip_1 = tiprack_200_1['A4']\n W1_ETOH_washtip_1 = tiprack_200_1['A10']\n W1_ETOH_removetip_1 = tiprack_200_1['A11']\n elif SAMPLES == '16x':\n protocol.comment(\"There are 16 Samples\")\n samplecolumns = 2\n TWB_washtip_1 = tiprack_200_1['A5']\n TWB_washtip_2 = tiprack_200_1['A6']\n TWB_removetip_1 = tiprack_200_1['A7']\n TWB_removetip_2 = tiprack_200_1['A8']\n W1_ETOH_washtip_1 = tiprack_200_2['A7']\n W1_ETOH_washtip_2 = tiprack_200_2['A8']\n W1_ETOH_removetip_1 = tiprack_200_2['A9']\n W1_ETOH_removetip_2 = tiprack_200_2['A10']\n elif SAMPLES == '24x':\n protocol.comment(\"There are 24 Samples\")\n samplecolumns = 3\n TWB_washtip_1 = tiprack_200_1['A7']\n TWB_washtip_2 = tiprack_200_1['A8']\n TWB_washtip_3 = tiprack_200_1['A9']\n TWB_removetip_1 = tiprack_200_1['A10']\n TWB_removetip_2 = tiprack_200_1['A11']\n TWB_removetip_3 = tiprack_200_1['A12']\n W1_ETOH_washtip_1 = tiprack_200_3['A4']\n W1_ETOH_washtip_2 = tiprack_200_3['A5']\n W1_ETOH_washtip_3 = tiprack_200_3['A6']\n W1_ETOH_removetip_1 = tiprack_200_3['A7']\n W1_ETOH_removetip_2 = tiprack_200_3['A8']\n W1_ETOH_removetip_3 = tiprack_200_3['A9']\n else:\n protocol.pause(\"ERROR?\")\n\n # FIXME: commented out variables are never used in the protocol\n p300_offset_Res = 0\n p300_offset_Thermo = 0\n p300_offset_Mag = 0\n # p300_offset_Deck = 0\n p300_offset_Temp = 0\n # p300_offset_Tube = 0\n # p20_offset_Res = 0\n p20_offset_Thermo = 0\n p20_offset_Mag = 0\n # p20_offset_Deck = 0\n p20_offset_Temp = 0\n # p20_offset_Tube = 0\n\n # offset\n if OFFSET == 'YES':\n if TIPREUSE == 'NO':\n p300_offset_Res = 2\n else:\n p300_offset_Res = 2\n p300_offset_Thermo = 1\n p300_offset_Mag = 0.70\n # p300_offset_Deck = 0.3\n p300_offset_Temp = 0.65\n # p300_offset_Tube = 0\n # if TIPREUSE == 'NO':\n # p20_offset_Res = 2\n # else:\n # p20_offset_Res = 2\n p20_offset_Thermo = 1\n p20_offset_Mag = 0.75\n # p20_offset_Deck = 0.3\n p20_offset_Temp = 0.85\n # p20_offset_Tube = 0\n\n # FIXME: Commented out variables are never used in the protocol\n # positions\n ##########################################################################\n # sample_plate_thermo on the Thermocycler\n # A1_p20_bead_side = sample_plate_thermo['A1'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right\n # A1_p20_bead_top = sample_plate_thermo['A1'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right\n # A1_p20_bead_mid = sample_plate_thermo['A1'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right\n A1_p300_bead_side = sample_plate_thermo['A1'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right\n A1_p300_bead_top = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right\n A1_p300_bead_mid = sample_plate_thermo['A1'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A1_p300_loc1 = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n A1_p300_loc2 = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A1_p300_loc3 = sample_plate_thermo['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n # A3_p20_bead_side = sample_plate_thermo['A3'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right\n # A3_p20_bead_top = sample_plate_thermo['A3'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right\n # A3_p20_bead_mid = sample_plate_thermo['A3'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right\n A3_p300_bead_side = sample_plate_thermo['A3'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right\n A3_p300_bead_top = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right\n A3_p300_bead_mid = sample_plate_thermo['A3'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A3_p300_loc1 = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n A3_p300_loc2 = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A3_p300_loc3 = sample_plate_thermo['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n # A5_p20_bead_side = sample_plate_thermo['A5'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right\n # A5_p20_bead_top = sample_plate_thermo['A5'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right\n # A5_p20_bead_mid = sample_plate_thermo['A5'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right\n A5_p300_bead_side = sample_plate_thermo['A5'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right\n A5_p300_bead_top = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right\n A5_p300_bead_mid = sample_plate_thermo['A5'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A5_p300_loc1 = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n A5_p300_loc2 = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right\n A5_p300_loc3 = sample_plate_thermo['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4))\n # Beads to the Right\n ##########################################################################\n\n bypass = protocol.deck.position_for(\n '11').move(types.Point(x=70, y=80, z=130))\n\n # commands\n if DRYRUN == 'NO':\n protocol.comment(\"SETTING THERMO and TEMP BLOCK Temperature\")\n thermocycler.set_block_temperature(4)\n thermocycler.set_lid_temperature(100)\n# temp_block.set_temperature(4)\n thermocycler.open_lid()\n protocol.pause(\"Ready\")\n\n if STEP_TAG == 1:\n protocol.comment('==============================================')\n protocol.comment('--> TAGMENTATION')\n protocol.comment('==============================================')\n\n protocol.comment('--> Adding Tagmentation Mix ')\n if DRYRUN == 'NO':\n TagVol = 20\n TagMixRep = 10\n TagMixVol = 40\n if DRYRUN == 'YES':\n TagVol = 20\n TagMixRep = 1\n TagMixVol = 40\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5)\n p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25)\n p300.dispense(TagVol, sample_plate_thermo[X].bottom(\n z=p300_offset_Thermo), rate=0.25)\n p300.mix(TagMixRep, TagMixVol)\n p300.blow_out(sample_plate_thermo[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5)\n p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25)\n p300.dispense(TagVol, sample_plate_thermo[X].bottom(\n z=p300_offset_Thermo), rate=0.25)\n p300.mix(TagMixRep, TagMixVol)\n p300.blow_out(sample_plate_thermo[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5)\n p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25)\n p300.dispense(TagVol, sample_plate_thermo[X].bottom(\n z=p300_offset_Thermo), rate=0.25)\n p300.mix(TagMixRep, TagMixVol)\n p300.blow_out(sample_plate_thermo[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if STEP_TAGDECK == 1:\n if DRYRUN == 'NO':\n ###################################################################\n protocol.pause('Seal, Run TAG (15min)')\n\n thermocycler.close_lid()\n profile_TAG = [\n {'temperature': 55, 'hold_time_minutes': 15}\n ]\n thermocycler.execute_profile(\n steps=profile_TAG, repetitions=1, block_max_volume=50)\n thermocycler.set_block_temperature(10)\n #######################################################################\n thermocycler.open_lid()\n protocol.pause(\"Remove Seal\")\n else:\n protocol.pause('Seal, Run ERAT (60min)')\n\n if STEP_TSB == 1:\n protocol.pause(\"Add TSB to Reagent Wells\")\n protocol.comment('==============================================')\n protocol.comment('--> Adapter Ligation')\n protocol.comment('==============================================')\n\n protocol.comment('--> Adding Tagmentation Stop Buffer')\n if DRYRUN == 'NO':\n if NOMODULES == 'NO':\n TSBVol = 10\n TSBMixRep = 10\n TSBMixVol = 20\n else:\n TSBVol = 10\n TSBMixRep = 10\n TSBMixVol = 10\n if DRYRUN == 'YES':\n if NOMODULES == 'NO':\n TSBVol = 10\n TSBMixRep = 1\n TSBMixVol = 20\n else:\n TSBVol = 10\n TSBMixRep = 1\n TSBMixVol = 10\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p20.pick_up_tip()\n p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp))\n p20.dispense(TSBVol, sample_plate_thermo[X].bottom(\n z=p20_offset_Thermo))\n p20.mix(TSBMixRep, TSBMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p20.pick_up_tip()\n p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp))\n p20.dispense(TSBVol, sample_plate_thermo[X].bottom(\n z=p20_offset_Thermo))\n p20.mix(TSBMixRep, TSBMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p20.pick_up_tip()\n p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp))\n p20.dispense(TSBVol, sample_plate_thermo[X].bottom(\n z=p20_offset_Thermo))\n p20.mix(TSBMixRep, TSBMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if STEP_TSBDECK == 1:\n if DRYRUN == 'NO':\n ###################################################################\n protocol.pause('Seal, Run PTC (15min)')\n\n thermocycler.close_lid()\n profile_PTC = [\n {'temperature': 37, 'hold_time_minutes': 15}\n ]\n thermocycler.execute_profile(\n steps=profile_PTC, repetitions=1, block_max_volume=60)\n thermocycler.set_block_temperature(10)\n ###################################################################\n thermocycler.open_lid()\n protocol.pause(\"Remove Seal\")\n else:\n protocol.pause('Seal, Run PTC (15min)')\n\n # FIXME: Commented out variables are never used in the protocol\n # positions\n ##########################################################################\n # sample_plate_mag on the Mag Block\n # A1_p20_bead_side = sample_plate_mag['A1'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A1_p20_bead_top = sample_plate_mag['A1'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A1_p20_bead_mid = sample_plate_mag['A1'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A1_p300_bead_side = sample_plate_mag['A1'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A1_p300_bead_top = sample_plate_mag['A1'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n A1_p300_bead_mid = sample_plate_mag['A1'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A1_p300_loc1 = sample_plate_mag['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A1_p300_loc2 = sample_plate_mag['A1'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A1_p300_loc3 = sample_plate_mag['A1'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A3_p20_bead_side = sample_plate_mag['A3'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A3_p20_bead_top = sample_plate_mag['A3'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A3_p20_bead_mid = sample_plate_mag['A3'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A3_p300_bead_side = sample_plate_mag['A3'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A3_p300_bead_top = sample_plate_mag['A3'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n A3_p300_bead_mid = sample_plate_mag['A3'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A3_p300_loc1 = sample_plate_mag['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A3_p300_loc2 = sample_plate_mag['A3'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A3_p300_loc3 = sample_plate_mag['A3'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A5_p20_bead_side = sample_plate_mag['A5'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A5_p20_bead_top = sample_plate_mag['A5'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A5_p20_bead_mid = sample_plate_mag['A5'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A5_p300_bead_side = sample_plate_mag['A5'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A5_p300_bead_top = sample_plate_mag['A5'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n A5_p300_bead_mid = sample_plate_mag['A5'].center().move(types.Point(\n x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A5_p300_loc1 = sample_plate_mag['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A5_p300_loc2 = sample_plate_mag['A5'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A5_p300_loc3 = sample_plate_mag['A5'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A7_p20_bead_side = sample_plate_mag['A7'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A7_p20_bead_top = sample_plate_mag['A7'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A7_p20_bead_mid = sample_plate_mag['A7'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A7_p300_bead_side = sample_plate_mag['A7'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A7_p300_bead_top = sample_plate_mag['A7'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n # A7_p300_bead_mid = sample_plate_mag['A7'].center().move(types.Point(\n # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A7_p300_loc1 = sample_plate_mag['A7'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A7_p300_loc2 = sample_plate_mag['A7'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A7_p300_loc3 = sample_plate_mag['A7'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A9_p20_bead_side = sample_plate_mag['A9'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A9_p20_bead_top = sample_plate_mag['A9'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A9_p20_bead_mid = sample_plate_mag['A9'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A9_p300_bead_side = sample_plate_mag['A9'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A9_p300_bead_top = sample_plate_mag['A9'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n # A9_p300_bead_mid = sample_plate_mag['A9'].center().move(types.Point(\n # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A9_p300_loc1 = sample_plate_mag['A9'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A9_p300_loc2 = sample_plate_mag['A9'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A9_p300_loc3 = sample_plate_mag['A9'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n # A11_p20_bead_side = sample_plate_mag['A11'].center().move(types.Point(\n # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right\n # A11_p20_bead_top = sample_plate_mag['A11'].center().move(types.Point(\n # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right\n # A11_p20_bead_mid = sample_plate_mag['A11'].center().move(types.Point(\n # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right\n A11_p300_bead_side = sample_plate_mag['A11'].center().move(types.Point(\n x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right\n A11_p300_bead_top = sample_plate_mag['A11'].center().move(types.Point(\n x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right\n # A11_p300_bead_mid = sample_plate_mag['A11'].center().move(types.Point(\n # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A11_p300_loc1 = sample_plate_mag['A11'].center().move(types.Point(\n x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right\n A11_p300_loc2 = sample_plate_mag['A11'].center().move(types.Point(\n x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right\n A11_p300_loc3 = sample_plate_mag['A11'].center().move(types.Point(\n x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4))\n # Beads to the Right\n ##########################################################################\n\n if STEP_WASH == 1:\n protocol.pause(\"PLACE sample_plate on MAGNET\")\n protocol.comment('==============================================')\n protocol.comment('--> TAGMENTATION WASH')\n protocol.comment('==============================================')\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n protocol.comment('--> Removing Supernatant')\n RemoveSup = 90\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n protocol.comment('--> Repeating 3 washes')\n washreps = 3\n for wash in range(washreps):\n protocol.comment('--> TWB Wash #' + str(wash + 1))\n if DRYRUN == 'NO':\n TWBMixRep = 15\n TWBMixVol = 70\n if DRYRUN == 'YES':\n TWBMixRep = 3\n TWBMixVol = 70\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_washtip_1)\n p300.aspirate(100, TWB_1.bottom(z=p300_offset_Res))\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n p300.default_speed = 5\n reps = 4\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(100)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_bead_mid)\n if X == 'A3':\n p300.move_to(A3_p300_bead_mid)\n if X == 'A5':\n p300.move_to(A5_p300_bead_mid)\n p300.mix(TWBMixRep, TWBMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(TWBMixRep, TWBMixVol)\n p300.default_speed = 400\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_washtip_2)\n p300.aspirate(100, TWB_2.bottom(z=p300_offset_Res))\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n p300.default_speed = 5\n reps = 4\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(100)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_bead_mid)\n if X == 'A3':\n p300.move_to(A3_p300_bead_mid)\n if X == 'A5':\n p300.move_to(A5_p300_bead_mid)\n p300.mix(TWBMixRep, TWBMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(TWBMixRep, TWBMixVol)\n p300.default_speed = 400\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_washtip_3)\n p300.aspirate(100, TWB_3.bottom(z=p300_offset_Res))\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n p300.default_speed = 5\n reps = 4\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(100)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(100, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_bead_mid)\n if X == 'A3':\n p300.move_to(A3_p300_bead_mid)\n if X == 'A5':\n p300.move_to(A5_p300_bead_mid)\n p300.mix(TWBMixRep, TWBMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(TWBMixRep, TWBMixVol)\n p300.default_speed = 400\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n protocol.comment('--> Remove TWB Wash #' + str(wash + 1))\n RemoveSup = 110\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_removetip_1)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_removetip_2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()if TIPREUSE == 'NO' else \\\n p300.pick_up_tip(TWB_removetip_3)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_bead_side)\n if X == 'A3':\n p300.move_to(A3_p300_bead_side)\n if X == 'A5':\n p300.move_to(A5_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.2)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n wash += 1\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=5)\n\n protocol.comment('--> Removing Residual Supernatant')\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3))\n p300.aspirate(50, rate=0.25)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3))\n p300.aspirate(50, rate=0.25)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3))\n p300.aspirate(50, rate=0.25)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n mag_block.engage(height_from_base=3)\n protocol.delay(minutes=0.5)\n\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n if STEP_PCR == 1:\n protocol.comment('==============================================')\n protocol.comment('--> AMPLIFICATION')\n protocol.comment('==============================================')\n\n protocol.comment('ADDING PCR')\n if DRYRUN == 'NO':\n PCRVol = 40\n PCRMixRep = 5\n PCRMixVol = 30\n if DRYRUN == 'YES':\n PCRVol = 40\n PCRMixRep = 1\n PCRMixVol = 30\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p300.pick_up_tip()\n p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp))\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(PCRVol, rate=0.5)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(PCRVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p300.pick_up_tip()\n p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp))\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(PCRVol, rate=0.5)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(PCRVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p300.pick_up_tip()\n p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp))\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.dispense(PCRVol / 5, rate=0.75)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.dispense(PCRVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(PCRVol, rate=0.5)\n if X == 'A1':\n p300.move_to(A1_p300_bead_top)\n if X == 'A3':\n p300.move_to(A3_p300_bead_top)\n if X == 'A5':\n p300.move_to(A5_p300_bead_top)\n p300.dispense(PCRVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc1)\n if X == 'A3':\n p300.move_to(A3_p300_loc1)\n if X == 'A5':\n p300.move_to(A5_p300_loc1)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc2)\n if X == 'A3':\n p300.move_to(A3_p300_loc2)\n if X == 'A5':\n p300.move_to(A5_p300_loc2)\n p300.mix(PCRMixRep, PCRMixVol)\n if X == 'A1':\n p300.move_to(A1_p300_loc3)\n if X == 'A3':\n p300.move_to(A3_p300_loc3)\n if X == 'A5':\n p300.move_to(A5_p300_loc3)\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(PCRMixRep, PCRMixVol)\n p300.move_to(sample_plate_mag[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n protocol.comment('--> Adding Barcodes')\n BarcodeVol = 10\n BarcodeMixRep = 10\n BarcodeMixVol = 10\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n p20.pick_up_tip()\n p20.aspirate(BarcodeVol, Barcodes1.bottom(\n z=p20_offset_Temp), rate=0.25)\n p20.dispense(\n BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.mix(BarcodeMixRep, BarcodeMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n p20.pick_up_tip()\n p20.aspirate(BarcodeVol, Barcodes2.bottom(\n z=p20_offset_Temp), rate=0.25)\n p20.dispense(\n BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.mix(BarcodeMixRep, BarcodeMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n p20.pick_up_tip()\n p20.aspirate(BarcodeVol, Barcodes3.bottom(\n z=p20_offset_Temp), rate=0.25)\n p20.dispense(\n BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.mix(BarcodeMixRep, BarcodeMixVol)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if DRYRUN == 'NO':\n protocol.pause(\"PLACE sample_plate on THERMO\")\n\n if STEP_PCRDECK == 1:\n #######################################################################\n protocol.pause('Seal, Run PCR (25min)')\n\n thermocycler.close_lid()\n profile_PCR_1 = [\n {'temperature': 68, 'hold_time_minutes': 3},\n {'temperature': 98, 'hold_time_minutes': 3}\n ]\n thermocycler.execute_profile(\n steps=profile_PCR_1, repetitions=1, block_max_volume=50)\n profile_PCR_2 = [\n {'temperature': 98, 'hold_time_seconds': 45},\n {'temperature': 62, 'hold_time_seconds': 30},\n {'temperature': 68, 'hold_time_minutes': 2}\n ]\n thermocycler.execute_profile(\n steps=profile_PCR_2, repetitions=5, block_max_volume=50)\n profile_PCR_3 = [\n {'temperature': 68, 'hold_time_minutes': 1}\n ]\n thermocycler.execute_profile(\n steps=profile_PCR_3, repetitions=1, block_max_volume=50)\n thermocycler.set_block_temperature(4)\n #######################################################################\n thermocycler.open_lid()\n protocol.pause(\"Remove Seal\")\n else:\n protocol.pause('Seal, Run PCR (60min)')\n\n Liquid_trash = reservoir['A11']\n\n if STEP_POSTPCR == 1:\n protocol.pause(\"PLACE sample_plate on MAGNET\")\n protocol.comment('==============================================')\n protocol.comment('--> CLEANUP')\n protocol.comment('==============================================')\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n protocol.comment('--> Transferring Supernatant')\n TransferSup = 45\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A1'\n Y = 'A7'\n p300.pick_up_tip()\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag + 1), rate=0.5)\n protocol.delay(seconds=0.1)\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag), rate=0.5)\n p300.dispense(\n TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag))\n protocol.delay(seconds=0.1)\n p300.blow_out(sample_plate_mag[Y].top(z=-2))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A3'\n Y = 'A9'\n p300.pick_up_tip()\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag + 1), rate=0.5)\n protocol.delay(seconds=0.1)\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag), rate=0.5)\n p300.dispense(\n TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag))\n protocol.delay(seconds=0.1)\n p300.blow_out(sample_plate_mag[Y].top(z=-2))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A5'\n Y = 'A11'\n p300.pick_up_tip()\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].\n bottom(z=p300_offset_Mag + 1), rate=0.5)\n protocol.delay(seconds=0.1)\n p300.aspirate(\n TransferSup / 2, sample_plate_mag[X].bottom(z=p300_offset_Mag),\n rate=0.5)\n p300.dispense(\n TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag))\n protocol.delay(seconds=0.1)\n p300.blow_out(sample_plate_mag[Y].top(z=-2))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n protocol.comment('--> ADDING AMPure (0.8x)')\n AMPureVol = 40\n AMPureMixRep = 50\n AMPureMixVol = 80\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p300.pick_up_tip()\n p300.mix(10, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res))\n p300.aspirate(AMPureVol, AMPure.bottom(\n z=p300_offset_Res), rate=0.25)\n p300.dispense(AMPureVol, sample_plate_mag[X].bottom(\n z=p300_offset_Mag), rate=0.25)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(AMPureMixRep, AMPureMixVol)\n p300.blow_out(sample_plate_mag[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p300.pick_up_tip()\n p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res))\n p300.aspirate(AMPureVol, AMPure.bottom(\n z=p300_offset_Res), rate=0.25)\n p300.dispense(AMPureVol, sample_plate_mag[X].bottom(\n z=p300_offset_Mag), rate=0.25)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(AMPureMixRep, AMPureMixVol)\n p300.blow_out(sample_plate_mag[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p300.pick_up_tip()\n p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res))\n p300.aspirate(AMPureVol, AMPure.bottom(\n z=p300_offset_Res), rate=0.25)\n p300.dispense(AMPureVol, sample_plate_mag[X].bottom(\n z=p300_offset_Mag), rate=0.25)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.mix(AMPureMixRep, AMPureMixVol)\n p300.blow_out(sample_plate_mag[X].top(z=-5))\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.delay(minutes=5)\n\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=8.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7.5)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=7)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=6)\n protocol.delay(minutes=1)\n mag_block.engage(height_from_base=5)\n protocol.delay(minutes=1)\n\n if TIPREUSE == 'NO':\n if all(STEPS) is True:\n protocol.pause('RESET TIPS')\n p300.reset_tipracks()\n p20.reset_tipracks()\n\n protocol.comment('--> Removing Supernatant')\n RemoveSup = 100\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.1)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.1)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p300.pick_up_tip()\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(RemoveSup - 30, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(20, rate=0.2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n protocol.delay(minutes=0.1)\n p300.aspirate(10, rate=0.1)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(bypass)\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n\n protocol.comment('--> Repeating 2 washes')\n washreps = 2\n for wash in range(washreps):\n protocol.comment('--> ETOH Wash #' + str(wash + 1))\n ETOHMaxVol = 150\n WASHNUM = 1\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_washtip_1)\n elif WASHNUM == 2:\n pass # # FIXME: W2_ETOH_washtip_1 is never defined\n # p300.pick_up_tip(W2_ETOH_washtip_1)\n p300.aspirate(ETOHMaxVol, EtOH_1.bottom(z=p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n p300.dispense(ETOHMaxVol - 50, rate=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.dispense(50, rate=0.5)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 5\n p300.move_to(sample_plate_mag[X].top(z=-2))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_washtip_2)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_washtip_2 is never defined\n # p300.pick_up_tip(W2_ETOH_washtip_2)\n p300.aspirate(ETOHMaxVol, EtOH_2.bottom(z=p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n p300.dispense(ETOHMaxVol - 50, rate=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.dispense(50, rate=0.5)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 5\n p300.move_to(sample_plate_mag[X].top(z=-2))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_washtip_3)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_washtip_3 is undefined\n # p300.pick_up_tip(W2_ETOH_washtip_3)\n p300.aspirate(ETOHMaxVol, EtOH_3.bottom(z=p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n p300.dispense(ETOHMaxVol - 50, rate=0.5)\n p300.move_to(sample_plate_mag[X].center())\n p300.dispense(50, rate=0.5)\n p300.move_to(sample_plate_mag[X].top(z=2))\n p300.default_speed = 5\n p300.move_to(sample_plate_mag[X].top(z=-2))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.default_speed = 400\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n protocol.delay(minutes=0.5)\n\n protocol.comment('--> Remove ETOH Wash #' + str(wash + 1))\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_removetip_1)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_removetip_1 is never defined\n # p300.pick_up_tip(W2_ETOH_removetip_1)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(ETOHMaxVol, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(200 - ETOHMaxVol, rate=0.25)\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(Liquid_trash.top(z=5))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_removetip_2)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_removetip_2 is never defined\n # p300.pick_up_tip(W2_ETOH_removetip_2)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(ETOHMaxVol, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(200 - ETOHMaxVol, rate=0.25)\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(Liquid_trash.top(z=5))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n if TIPREUSE == 'NO':\n p300.pick_up_tip()\n elif WASHNUM == 1:\n p300.pick_up_tip(W1_ETOH_removetip_3)\n elif WASHNUM == 2:\n pass\n # FIXME: W2_ETOH_removetip_3 is never defined\n # p300.pick_up_tip(W2_ETOH_removetip_3)\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4))\n p300.aspirate(ETOHMaxVol, rate=0.25)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_bead_side)\n if X == 'A9':\n p300.move_to(A9_p300_bead_side)\n if X == 'A11':\n p300.move_to(A11_p300_bead_side)\n protocol.delay(minutes=0.1)\n p300.aspirate(200 - ETOHMaxVol, rate=0.25)\n p300.default_speed = 400\n p300.dispense(200, Liquid_trash)\n p300.move_to(Liquid_trash.top(z=5))\n protocol.delay(minutes=0.1)\n p300.blow_out()\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n wash += 1\n\n if DRYRUN == 'NO':\n protocol.delay(minutes=2)\n\n protocol.comment('--> Removing Residual ETOH')\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate(\n 10, rate=0.25)\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate(\n 10, rate=0.25)\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate(\n 10, rate=0.25)\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if DRYRUN == 'NO':\n mag_block.engage(height_from_base=6)\n protocol.comment('AIR DRY')\n protocol.delay(minutes=0.5)\n\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n\n protocol.comment('--> Adding RSB')\n RSBVol = 32\n RSBMixRep = 5\n RSBMixVol = 25\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n p300.pick_up_tip()\n p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(RSBVol, rate=0.5)\n if X == 'A7':\n p300.move_to(A7_p300_bead_top)\n if X == 'A9':\n p300.move_to(A9_p300_bead_top)\n if X == 'A11':\n p300.move_to(A11_p300_bead_top)\n p300.dispense(RSBVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()\n [X].bottom(z=p300_offset_Mag))\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag.wells_by_name()[X].center())\n p300.default_speed = 400\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n p300.pick_up_tip()\n p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(RSBVol, rate=0.5)\n if X == 'A7':\n p300.move_to(A7_p300_bead_top)\n if X == 'A9':\n p300.move_to(A9_p300_bead_top)\n if X == 'A11':\n p300.move_to(A11_p300_bead_top)\n p300.dispense(RSBVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()\n [X].bottom(z=p300_offset_Mag))\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag.wells_by_name()[X].center())\n p300.default_speed = 400\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n p300.pick_up_tip()\n p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res))\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n p300.default_speed = 5\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.dispense(RSBVol / 5, rate=0.75)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.dispense(RSBVol / 5, rate=0.75)\n reps = 5\n for x in range(reps):\n p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag))\n p300.aspirate(RSBVol, rate=0.5)\n if X == 'A7':\n p300.move_to(A7_p300_bead_top)\n if X == 'A9':\n p300.move_to(A9_p300_bead_top)\n if X == 'A11':\n p300.move_to(A11_p300_bead_top)\n p300.dispense(RSBVol, rate=1)\n reps = 3\n for x in range(reps):\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc1)\n if X == 'A9':\n p300.move_to(A9_p300_loc1)\n if X == 'A11':\n p300.move_to(A11_p300_loc1)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc2)\n if X == 'A9':\n p300.move_to(A9_p300_loc2)\n if X == 'A11':\n p300.move_to(A11_p300_loc2)\n p300.mix(RSBMixRep, RSBMixVol)\n if X == 'A7':\n p300.move_to(A7_p300_loc3)\n if X == 'A9':\n p300.move_to(A9_p300_loc3)\n if X == 'A11':\n p300.move_to(A11_p300_loc3)\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()\n [X].bottom(z=p300_offset_Mag))\n p300.mix(RSBMixRep, RSBMixVol)\n p300.move_to(sample_plate_mag.wells_by_name()[X].top())\n protocol.delay(seconds=0.5)\n p300.move_to(sample_plate_mag.wells_by_name()[X].center())\n p300.default_speed = 400\n if TIPREUSE == 'NO':\n p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip()\n else:\n p300.return_tip()\n\n if DRYRUN == 'NO':\n protocol.delay(minutes=2)\n\n protocol.comment('MAGNET ENGAGE')\n mag_block.engage(height_from_base=5)\n\n protocol.delay(minutes=4)\n\n protocol.comment('--> Transferring Supernatant')\n\n if NOMODULES == 'NO':\n TransferSup = 30\n else:\n TransferSup = 20\n if samplecolumns >= 1: # ----------------------------------------\n X = 'A7'\n Y = 'A8'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 2: # ----------------------------------------\n X = 'A9'\n Y = 'A10'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n if samplecolumns >= 3: # ----------------------------------------\n X = 'A11'\n Y = 'A12'\n p20.pick_up_tip()\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag))\n p20.aspirate(TransferSup / 2, rate=0.25)\n p20.dispense(\n TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag))\n p20.move_to(bypass)\n p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip()\n\n if DRYRUN == 'NO':\n protocol.comment('MAGNET DISENGAGE')\n mag_block.disengage()\n", - "custom_labware_defs": [], - "fields": [ - { - "label": "Number of samples", - "name": "SAMPLES", - "options": [ - { - "label": "24 samples", - "value": "24x" - }, - { - "label": "16 samples", - "value": "16x" - }, - { - "label": "8 samples", - "value": "8x" - } - ], - "type": "dropDown" - }, - { - "label": "Do a dry run?", - "name": "DRYRUN", - "options": [ - { - "label": "No", - "value": "NO" - }, - { - "label": "Yes", - "value": "YES" - } - ], - "type": "dropDown" - }, - { - "label": "Use modules?", - "name": "NOMODULES", - "options": [ - { - "label": "No", - "value": "NO" - }, - { - "label": "Yes", - "value": "YES" - } - ], - "type": "dropDown" - }, - { - "label": "Tip reuse?", - "name": "TIPREUSE", - "options": [ - { - "label": "No", - "value": "NO" - }, - { - "label": "Yes", - "value": "YES" - } - ], - "type": "dropDown" - }, - { - "label": "Offset?", - "name": "OFFSET", - "options": [ - { - "label": "Yes", - "value": "YES" - }, - { - "label": "No", - "value": "NO" - } - ], - "type": "dropDown" - }, - { - "label": "Include tagmentation step in protocol run?", - "name": "STEP_TAG", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run tagmentation incubation on the deck thermocycler?", - "name": "STEP_TAGDECK", - "options": [ - { - "label": "Yes", - "value": 1 - }, - { - "label": "No", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run TSB step?", - "name": "STEP_TSB", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run TSB incubation step on the deck thermocycler", - "name": "STEP_TSBDECK", - "options": [ - { - "label": "Yes", - "value": 1 - }, - { - "label": "No", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run tagmentation wash with TWB step", - "name": "STEP_WASH", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run PCR cycle step", - "name": "STEP_PCR", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run PCR step on deck thermocycler?", - "name": "STEP_PCRDECK", - "options": [ - { - "label": "Yes", - "value": 1 - }, - { - "label": "No", - "value": 0 - } - ], - "type": "dropDown" - }, - { - "label": "Run post PCR cleanup step", - "name": "STEP_POSTPCR", - "options": [ - { - "label": "Include", - "value": 1 - }, - { - "label": "Skip", - "value": 0 - } - ], - "type": "dropDown" - } - ], - "instruments": [ - { - "mount": "left", - "name": "p300_multi_gen2" - }, - { - "mount": "right", - "name": "p20_multi_gen2" - } - ], - "labware": [ - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 1", - "share": false, - "slot": "1", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "NEST 12 Well Reservoir 15 mL on 2", - "share": false, - "slot": "2", - "type": "nest_12_reservoir_15ml" - }, - { - "name": "Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L on Temperature Module GEN2 on 3", - "share": false, - "slot": "3", - "type": "opentrons_96_aluminumblock_biorad_wellplate_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 20 \u00b5L on 4", - "share": false, - "slot": "4", - "type": "opentrons_96_filtertiprack_20ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 5", - "share": false, - "slot": "5", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 6", - "share": false, - "slot": "6", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", - "share": false, - "slot": "7", - "type": "nest_96_wellplate_100ul_pcr_full_skirt" - }, - { - "name": "Opentrons 96 Filter Tip Rack 200 \u00b5L on 9", - "share": false, - "slot": "9", - "type": "opentrons_96_filtertiprack_200ul" - }, - { - "name": "Opentrons Fixed Trash on 12", - "share": false, - "slot": "12", - "type": "opentrons_1_trash_1100ml_fixed" - } - ], - "metadata": { - "apiLevel": "2.9", - "author": "Opentrons ", - "protocolName": "Illumina DNA Prep", - "source": "Protocol Library" - }, - "modules": [] -} \ No newline at end of file diff --git a/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json b/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json index b6325090fb..06173c2267 100644 --- a/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json +++ b/protoBuilds/sci-macherey-nagel-nucleomag/sci-macherey-nagel-nucleomag.ot2.apiv2.py.json @@ -250,5 +250,12 @@ "author": "Opentrons ", "protocolName": "NucleoMag\u00ae Virus Viral DNA/RNA Isolation" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json b/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json index a86f16694e..fe463c1273 100644 --- a/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json +++ b/protoBuilds/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.ot2.apiv2.py.json @@ -232,5 +232,12 @@ "author": "Opentrons ", "protocolName": "Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json b/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json index 6b2855a5d7..ec63555526 100644 --- a/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json +++ b/protoBuilds/sci-mgi-mgieasy-nucleic-acid-extraction-kit/sci-mgi-mgieasy-nucleic-acid-extraction-kit.ot2.apiv2.py.json @@ -187,5 +187,18 @@ "author": "Opentrons ", "protocolName": "MGIEasy Nucleic Acid Extraction Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json b/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json index 881903d579..64664fd678 100644 --- a/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json +++ b/protoBuilds/sci-omegabiotek-extraction/sci-omegabiotek-extraction.ot2.apiv2.py.json @@ -182,5 +182,12 @@ "protocolName": "Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json b/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json index 1ef7ae2ede..ecf6f8a47f 100644 --- a/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json +++ b/protoBuilds/sci-omegabiotek-magbind/sci-omegabiotek-magbind.ot2.apiv2.py.json @@ -151,5 +151,18 @@ "author": "Opentrons ", "protocolName": "Mag-Bind\u00ae Viral DNA/RNA 96 Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 3 lw deepwell plate on Magnetic Module GEN1 on 3", + "share": false, + "slot": "3", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json index 00345b692a..0a9e19bdd2 100644 --- a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json +++ b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/sci-promega-magazorb-dna-mini-prep-kit.ot2.apiv2.py.json @@ -232,5 +232,12 @@ "author": "Opentrons ", "protocolName": "MagaZorb\u00ae DNA Mini-Prep Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json b/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json index 10d6782c81..6646742bc7 100644 --- a/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json +++ b/protoBuilds/sci-thermofisher-magmax/extraction.ot2.apiv2.py.json @@ -214,5 +214,18 @@ "author": "Opentrons ", "protocolName": "Thermofisher MagMAX Viral/Pathogen Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw deepwell plate on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw elution plate on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json b/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json index 8aa6db59b0..42a9760d81 100644 --- a/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json +++ b/protoBuilds/sci-zymo-directzol-magbead/sci-zymo-directzol-magbead.ot2.apiv2.py.json @@ -181,5 +181,18 @@ "author": "Opentrons ", "protocolName": "Zymo Research Direct-zol\u2122-96 MagBead RNA Kit" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN1 on 6 lw deepwell plate on Magnetic Module GEN1 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 1 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN2 on 1", + "share": false, + "slot": "1", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json b/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json index 801f13ee7e..94cd12d789 100644 --- a/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json +++ b/protoBuilds/swift-2s-turbo-pt1/swift-2s-turbo-pt1.ot2.apiv2.py.json @@ -87,5 +87,12 @@ "protocolName": "Swift 2S Turbo DNA Library Kit Protocol: Part 1/3 - Enzymatic Prep & Ligation", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "TemperatureModuleContext at Temperature Module GEN1 on 3 lw Opentrons 24-Well Aluminum Block on Temperature Module GEN1 on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json b/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json index d3a64c665b..fb4803c4a2 100644 --- a/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json +++ b/protoBuilds/thermocycler/thermocycler.ot2.apiv2.py.json @@ -102,5 +102,12 @@ "protocolName": "Thermocycler Example Protocol", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw None", + "share": false, + "slot": "7", + "type": "thermocycler" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json b/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json index 6e478c31e7..7c49c5d4d9 100644 --- a/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json +++ b/protoBuilds/zymo-quick-96/zymo-quick-96.ot2.apiv2.py.json @@ -1268,5 +1268,12 @@ "protocolName": "Zymo Quick-DNA/RNA Viral Kit [Custom]", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 7 lw VWR 96 Well Plate 1000 \u00b5L on Magnetic Module GEN2 on 7", + "share": false, + "slot": "7", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json b/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json index d1e5fc31d0..a7c6457f4f 100644 --- a/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json +++ b/protoBuilds/zymo-quick-custom/zymo-quick-custom.ot2.apiv2.py.json @@ -154,5 +154,12 @@ "protocolName": "Zymo Quick-DNA/RNA Viral Kit with PCR Prep", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json b/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json index 2566963ab0..140d0242fc 100644 --- a/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json +++ b/protoBuilds/zymo-quick/zymo-quick.ot2.apiv2.py.json @@ -169,5 +169,12 @@ "protocolName": "Zymo Quick-DNA/RNA Viral Kit", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 4 lw NEST 96 Deepwell Plate 2mL on Magnetic Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "magdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json index 74d449a8f6..92c6bd231b 100644 --- a/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\nimport os\nfrom opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Select-a-Size \\\nMagBead Clean-up (robot 2)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, cleanup_stage, p20_mount,\n p300_mount] = get_values( # noqa: F821\n 'number_of_samples', 'cleanup_stage', 'p20_mount', 'p300_mount')\n\n # load modules and labware\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '4']\n ]\n elution_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '2', 'elution PCR plate')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '3', 'reagent reservoir')\n magdeck = ctx.load_module('magnetic module gen2', '6')\n mag_plate = magdeck.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['5', '8', '10', '11']\n ]\n waste = ctx.load_labware(\n 'agilent_1_reservoir_290ml', '9', 'waste reservoir').wells()[0].top()\n\n # pipettes\n if p20_mount == p300_mount:\n raise Exception('Pipette mounts cannot match.')\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount)\n m300 = ctx.load_instrument('p300_multi_gen2', p300_mount)\n\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n if 'tips300' in data:\n tip300_count = data['tips300']\n else:\n tip300_count = 0\n else:\n tip20_count = 0\n tip300_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.rows()[0]]\n all_tips300 = [tip for rack in racks300 for tip in rack.rows()[0]]\n tip20_max = len(all_tips20)\n tip300_max = len(all_tips300)\n\n def pick_up(pip):\n nonlocal tip20_count\n nonlocal tip300_count\n if pip == m20:\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n else:\n if tip300_count == tip300_max:\n ctx.pause('Replace tipracks before resuming.')\n tip300_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips300[tip300_count])\n tip300_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n mag_samples = mag_plate.rows()[0][:math.ceil(number_of_samples/8)]\n elution_samples = elution_plate.rows()[0][:math.ceil(number_of_samples/8)]\n beads = reagent_res.wells()[0]\n wash_buffer = reagent_res.wells()[1:4]\n dna_eb = reagent_res.wells()[4]\n # waste = [chan.top() for chan in reagent_res.wells()[6:]]\n\n # setup cleanup parameters\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n start_vol = 75\n bead_vol = 150\n elution_vol = 10\n tempdeck = ctx.load_module('temperature module gen2', '7')\n # tempplate = tempdeck.load_labware(\n # 'opentrons_96_aluminumblock_nest_wellplate_100ul')\n inc_temp = 95\n inc_time = 5\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P7 adapter ligation':\n start_vol = 40\n bead_vol = 60\n elution_vol = 10\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P5 adapter ligation':\n start_vol = 100\n bead_vol = 100\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-library index PCR':\n start_vol = 100\n bead_vol = 85\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'The eluate is your final RNA-Seq library 3. Libraries may be \\\nstored at \u2264 4\u00b0C overnight or \u2264 -20\u00b0C for long-term storage.'\n\n \"\"\" Appendix A: Select-a-Size MagBead Clean-up Protocol \"\"\"\n # mix and transfer beads\n pick_up(m300)\n for _ in range(10):\n m300.aspirate(250, beads.bottom(2))\n m300.dispense(250, beads.bottom(20))\n for m in mag_samples:\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n m300.transfer(\n bead_vol,\n beads,\n m,\n air_gap=20,\n mix_after=(5, bead_vol),\n new_tip='never'\n )\n m300.drop_tip()\n\n ctx.delay(minutes=5, msg='Incubating at room temperature for 5 minutes')\n\n # separate beads and remove supernatant\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n supernatant_vol = start_vol + bead_vol\n for i, m in enumerate(mag_samples):\n pick_up(m300)\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n # m300.transfer(\n # supernatant_vol*1.1, m, waste[i//6], air_gap=30, new_tip='never')\n m300.drop_tip()\n\n # 2x washes\n for wash in range(2):\n pick_up(m300)\n for i, m in enumerate(mag_samples):\n chan = (i+wash*12)//8\n m300.transfer(\n 200,\n wash_buffer[chan],\n m.top(),\n air_gap=20,\n new_tip='never'\n )\n for i, m in enumerate(mag_samples):\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n chan = (i+wash*12)//8\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m300.move_to(m.center())\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n m300.drop_tip()\n\n magdeck.disengage()\n ctx.delay(minutes=3, msg='Airdrying beads for 3 minutes.')\n\n # resuspend in elution buffer\n for i, m in enumerate(mag_samples):\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, y=0, z=0.5))\n pick_up(m20)\n if elution_vol > 10:\n pre_vol = elution_vol - 10\n m20.transfer(pre_vol, dna_eb, m.top(), new_tip='never')\n m20.blow_out(m.top())\n m20.aspirate(10, dna_eb)\n m20.move_to(m.center())\n m20.dispense(10, loc)\n m20.mix(10, 9, m)\n m20.blow_out(m.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n if inc_temp and inc_time:\n tempdeck.set_temperature(inc_temp)\n # m20.move_to(tempplate.wells()[0].top(10))\n m20.home()\n ctx.pause('Transfer plate from magnetic module to aluminum block on \\\ntemperature module. Once you resume, the plate will incubate for \\\n' + str(inc_temp) + ' minutes.')\n ctx.delay(minutes=inc_time)\n ctx.pause('Transfer plate back to magnetic module from aluminum block \\\non temperature module.')\n\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n\n # transfer elution to new plate\n for m, e in zip(mag_samples, elution_samples):\n pick_up(m20)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m20.move_to(m.center())\n m20.transfer(elution_vol, loc, e, new_tip='never')\n m20.blow_out(e.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n magdeck.disengage()\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n tempdeck.deactivate()\n ctx.comment(end_msg)\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n if cleanup_stage == 'post-library index PCR':\n data = {\n 'tips20': 0,\n 'tips300': 0\n }\n else:\n data = {\n 'tips20': tip20_count,\n 'tips300': tip300_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import math\nimport json\nimport os\nfrom opentrons.types import Point\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Select-a-Size \\\nMagBead Clean-up (robot 2)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, cleanup_stage, p20_mount,\n p300_mount] = get_values( # noqa: F821\n 'number_of_samples', 'cleanup_stage', 'p20_mount', 'p300_mount')\n\n # load modules and labware\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '4']\n ]\n elution_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '2', 'elution PCR plate')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '3', 'reagent reservoir')\n magdeck = ctx.load_module('magnetic module gen2', '6')\n mag_plate = magdeck.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks300 = [\n ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['5', '8', '10', '11']\n ]\n waste = ctx.load_labware(\n 'agilent_1_reservoir_290ml', '9', 'waste reservoir').wells()[0].top()\n\n # pipettes\n if p20_mount == p300_mount:\n raise Exception('Pipette mounts cannot match.')\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount)\n m300 = ctx.load_instrument('p300_multi_gen2', p300_mount)\n\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n if 'tips300' in data:\n tip300_count = data['tips300']\n else:\n tip300_count = 0\n else:\n tip20_count = 0\n tip300_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.rows()[0]]\n all_tips300 = [tip for rack in racks300 for tip in rack.rows()[0]]\n tip20_max = len(all_tips20)\n tip300_max = len(all_tips300)\n\n def pick_up(pip):\n nonlocal tip20_count\n nonlocal tip300_count\n if pip == m20:\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n else:\n if tip300_count == tip300_max:\n ctx.pause('Replace tipracks before resuming.')\n tip300_count = 0\n [rack.reset() for rack in racks300]\n pip.pick_up_tip(all_tips300[tip300_count])\n tip300_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n mag_samples = mag_plate.rows()[0][:math.ceil(number_of_samples/8)]\n elution_samples = elution_plate.rows()[0][:math.ceil(number_of_samples/8)]\n beads = reagent_res.wells()[0]\n wash_buffer = reagent_res.wells()[1:4]\n dna_eb = reagent_res.wells()[4]\n # waste = [chan.top() for chan in reagent_res.wells()[6:]]\n\n # setup cleanup parameters\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n start_vol = 75\n bead_vol = 150\n elution_vol = 10\n tempdeck = ctx.load_module('temperature module gen2', '7')\n # tempplate = tempdeck.load_labware(\n # 'opentrons_96_aluminumblock_nest_wellplate_100ul')\n inc_temp = 95\n inc_time = 5\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P7 adapter ligation':\n start_vol = 40\n bead_vol = 60\n elution_vol = 10\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-P5 adapter ligation':\n start_vol = 100\n bead_vol = 100\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'This is a safe stopping point. Cleaned-up DNA can be safely \\\nstored at \u2264 4\u00b0C overnight or \u2264 \u221220\u00b0C for up to one week.'\n elif cleanup_stage == 'post-library index PCR':\n start_vol = 100\n bead_vol = 85\n elution_vol = 20\n inc_temp = None\n inc_time = None\n end_msg = 'The eluate is your final RNA-Seq library 3. Libraries may be \\\nstored at \u2264 4\u00b0C overnight or \u2264 -20\u00b0C for long-term storage.'\n\n \"\"\" Appendix A: Select-a-Size MagBead Clean-up Protocol \"\"\"\n # mix and transfer beads\n pick_up(m300)\n for _ in range(10):\n m300.aspirate(250, beads.bottom(2))\n m300.dispense(250, beads.bottom(20))\n for m in mag_samples:\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n m300.transfer(\n bead_vol,\n beads,\n m,\n air_gap=20,\n mix_after=(5, bead_vol),\n new_tip='never'\n )\n m300.drop_tip()\n\n ctx.delay(minutes=5, msg='Incubating at room temperature for 5 minutes')\n\n # separate beads and remove supernatant\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n supernatant_vol = start_vol + bead_vol\n for i, m in enumerate(mag_samples):\n pick_up(m300)\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n # m300.transfer(\n # supernatant_vol*1.1, m, waste[i//6], air_gap=30, new_tip='never')\n m300.drop_tip()\n\n # 2x washes\n for wash in range(2):\n pick_up(m300)\n for i, m in enumerate(mag_samples):\n chan = (i+wash*12)//8\n m300.transfer(\n 200,\n wash_buffer[chan],\n m.top(),\n air_gap=20,\n new_tip='never'\n )\n for i, m in enumerate(mag_samples):\n if not m300.hw_pipette['has_tip']:\n pick_up(m300)\n chan = (i+wash*12)//8\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m300.move_to(m.center())\n m300.aspirate(supernatant_vol*1.1, m)\n m300.air_gap(20)\n m300.dispense(supernatant_vol*1.1+30, waste)\n m300.air_gap(20)\n m300.drop_tip()\n\n magdeck.disengage()\n ctx.delay(minutes=3, msg='Airdrying beads for 3 minutes.')\n\n # resuspend in elution buffer\n for i, m in enumerate(mag_samples):\n side = 1 if i % 2 == 0 else -1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, y=0, z=0.5))\n pick_up(m20)\n if elution_vol > 10:\n pre_vol = elution_vol - 10\n m20.transfer(pre_vol, dna_eb, m.top(), new_tip='never')\n m20.blow_out(m.top())\n m20.aspirate(10, dna_eb)\n m20.move_to(m.center())\n m20.dispense(10, loc)\n m20.mix(10, 9, m)\n m20.blow_out(m.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n if inc_temp and inc_time:\n tempdeck.set_temperature(inc_temp)\n # m20.move_to(tempplate.wells()[0].top(10))\n m20.home()\n ctx.pause('Transfer plate from magnetic module to aluminum block on \\\ntemperature module. Once you resume, the plate will incubate for \\\n' + str(inc_temp) + ' minutes.')\n ctx.delay(minutes=inc_time)\n ctx.pause('Transfer plate back to magnetic module from aluminum block \\\non temperature module.')\n\n magdeck.engage()\n ctx.delay(minutes=3, msg='Incubating on magnet for 3 minutes.')\n\n # transfer elution to new plate\n for m, e in zip(mag_samples, elution_samples):\n pick_up(m20)\n side = -1 if i % 2 == 0 else 1\n loc = m.bottom().move(Point(x=side*m.diameter/2*0.9, z=0.5))\n m20.move_to(m.center())\n m20.transfer(elution_vol, loc, e, new_tip='never')\n m20.blow_out(e.top(-2))\n m20.air_gap(5)\n m20.drop_tip()\n\n magdeck.disengage()\n if cleanup_stage == 'post-first-strand synthesis and universal depletion':\n tempdeck.deactivate()\n ctx.comment(end_msg)\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n if cleanup_stage == 'post-library index PCR':\n data = {\n 'tips20': 0,\n 'tips300': 0\n }\n else:\n data = {\n 'tips20': tip20_count,\n 'tips300': tip300_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -141,10 +141,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep Select-a-Size MagBead Clean-up (robot 2)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module GEN2 on 6 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Magnetic Module GEN2 on 6", + "share": false, + "slot": "6", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 7 lw None", + "share": false, + "slot": "7", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json index 8ca7e5b62e..8638d51748 100644 --- a/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep First-Strand \\\ncDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, starting_vol, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'starting_vol', 'rna_input', 'p20_mount',\n 'm20_mount')\n # [number_of_samples, starting_vol, rna_input, p20_mount, p50_mount] = [\n # 96, 5, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '6')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n r1, r2, h2o = tempblock.rows()[0][:3]\n d1, d2, d3 = tempblock.rows()[1][:3]\n etoh = reagent_res.wells()[0]\n\n tip20s_count = 0\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20m_count = 0\n tip20m_max = len(racks20m*12)\n tip20s_max = len(racks20s*96)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n \"\"\" Section 1.1: First-Strand cDNA Synthesis (Yellow Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # bring samples up to 8\u00b5l with H2O if necessary\n vol_h2o = 9 - starting_vol if rna_input != '< 100ng' else 8 - starting_vol\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_h2o, h2o, s, new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # transfer R1\n vol_r1 = 1 if rna_input != '< 100ng' else 2\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_r1, r1, s, mix_after=(3, 5), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute primer annealing\n profile_1_1 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_1, repetitions=1, block_max_volume=10)\n tc.open_lid()\n\n # transfer R2\n for s in samples:\n pick_up(p20)\n p20.transfer(10, r2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # execute reverse transcription\n profile_1_2 = [\n {'temperature': 25, 'hold_time_minutes': 5},\n {'temperature': 48, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_2, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n \"\"\" Section 1.2: RiboFreeTM Universal Depletion (Red Caps) \"\"\"\n\n # distribute D reagents to predispesing plate\n if number_of_samples > 24:\n predispense_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '9',\n 'plate to predispense D reagent')\n vol_per_well = 11*math.ceil(number_of_samples/8)\n for d_reagent, col in zip(\n [d1, d2, d3], predispense_plate.columns()[:3]):\n pick_up(p20)\n for well in col:\n p20.transfer(\n vol_per_well, d_reagent, well, air_gap=1, new_tip='never')\n p20.blow_out(well.top(-5))\n p20.touch_tip(well)\n p20.drop_tip()\n d1, d2, d3 = predispense_plate.rows()[0][:3]\n d_pip = m20\n d_samples = samples_multi\n else:\n d_pip = p20\n d_samples = samples\n\n # transfer D1\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d1, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute pre-depletion incubation\n profile_1_3 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 68, 'hold_time_minutes': 5}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_3, repetitions=1, block_max_volume=30)\n tc.open_lid()\n\n # transfer D2\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d2, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # exeute depletion reaction\n if rna_input == '> 1\u00b5g':\n inc_time = 30\n elif rna_input == '250ng-1\u00b5g':\n inc_time = 60\n else:\n inc_time = 120\n profile_1_4 = [\n {'temperature': 68, 'hold_time_minutes': inc_time}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_4, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n # transfer D3\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d3, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # execute stop depletion\n profile_1_5 = [\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 25, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_5, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer EtOH\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 25, etoh, m.top(-2), air_gap=2, new_tip='never')\n m20.mix(5, 20, m),\n m20.blow_out(m.top(-2))\n m20.air_gap(2)\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import math\nimport json\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep First-Strand \\\ncDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, starting_vol, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'starting_vol', 'rna_input', 'p20_mount',\n 'm20_mount')\n # [number_of_samples, starting_vol, rna_input, p20_mount, p50_mount] = [\n # 96, 5, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '6')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n r1, r2, h2o = tempblock.rows()[0][:3]\n d1, d2, d3 = tempblock.rows()[1][:3]\n etoh = reagent_res.wells()[0]\n\n tip20s_count = 0\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20m_count = 0\n tip20m_max = len(racks20m*12)\n tip20s_max = len(racks20s*96)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n \"\"\" Section 1.1: First-Strand cDNA Synthesis (Yellow Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # bring samples up to 8\u00b5l with H2O if necessary\n vol_h2o = 9 - starting_vol if rna_input != '< 100ng' else 8 - starting_vol\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_h2o, h2o, s, new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # transfer R1\n vol_r1 = 1 if rna_input != '< 100ng' else 2\n for s in samples:\n pick_up(p20)\n p20.transfer(vol_r1, r1, s, mix_after=(3, 5), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute primer annealing\n profile_1_1 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_1, repetitions=1, block_max_volume=10)\n tc.open_lid()\n\n # transfer R2\n for s in samples:\n pick_up(p20)\n p20.transfer(10, r2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n\n # execute reverse transcription\n profile_1_2 = [\n {'temperature': 25, 'hold_time_minutes': 5},\n {'temperature': 48, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_2, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n \"\"\" Section 1.2: RiboFreeTM Universal Depletion (Red Caps) \"\"\"\n\n # distribute D reagents to predispesing plate\n if number_of_samples > 24:\n predispense_plate = ctx.load_labware(\n 'nest_96_wellplate_100ul_pcr_full_skirt', '9',\n 'plate to predispense D reagent')\n vol_per_well = 11*math.ceil(number_of_samples/8)\n for d_reagent, col in zip(\n [d1, d2, d3], predispense_plate.columns()[:3]):\n pick_up(p20)\n for well in col:\n p20.transfer(\n vol_per_well, d_reagent, well, air_gap=1, new_tip='never')\n p20.blow_out(well.top(-5))\n p20.touch_tip(well)\n p20.drop_tip()\n d1, d2, d3 = predispense_plate.rows()[0][:3]\n d_pip = m20\n d_samples = samples_multi\n else:\n d_pip = p20\n d_samples = samples\n\n # transfer D1\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d1, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute pre-depletion incubation\n profile_1_3 = [\n {'temperature': 98, 'hold_time_minutes': 3},\n {'temperature': 68, 'hold_time_minutes': 5}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_3, repetitions=1, block_max_volume=30)\n tc.open_lid()\n\n # transfer D2\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d2, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # exeute depletion reaction\n if rna_input == '> 1\u00b5g':\n inc_time = 30\n elif rna_input == '250ng-1\u00b5g':\n inc_time = 60\n else:\n inc_time = 120\n profile_1_4 = [\n {'temperature': 68, 'hold_time_minutes': inc_time}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_4, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n # transfer D3\n for s in d_samples:\n pick_up(d_pip)\n d_pip.transfer(10, d3, s, mix_after=(3, 15), new_tip='never')\n d_pip.blow_out(s.top(-2))\n d_pip.drop_tip()\n\n # execute stop depletion\n profile_1_5 = [\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 25, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_1_5, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer EtOH\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 25, etoh, m.top(-2), air_gap=2, new_tip='never')\n m20.mix(5, 20, m),\n m20.blow_out(m.top(-2))\n m20.air_gap(2)\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = '/protocols/tip_track.json'\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -135,10 +135,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep First-Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json index d29328c137..f92abdd225 100644 --- a/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Library Index \\\nPCR (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'rna_input', 'p20_mount', 'm20_mount')\n # [number_of_samples, rna_input, p20_mount, m20_mount] = [\n # 96, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n index_plate = ctx.load_labware(\n 'opentrons_96_aluminumblock_nest_wellplate_100ul',\n '9', 'UDI primer plate')\n racks20m = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['3', '6']\n ]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s'] % 96\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m'] % 12\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n udi_primers = index_plate.rows()[0][:math.ceil(number_of_samples/8)]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n taq_premix = tempblock.rows()[3][0]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.3: Library Index PCR (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer UDI primers\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 5, udi_primers, m, mix_after=(3, 15), air_gap=1, new_tip='never')\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n # transfer taq premix\n for s in samples:\n for i, vol in enumerate([15, 10]):\n pick_up(p20)\n p20.transfer(vol, taq_premix, s.bottom(1), new_tip='never')\n if i == 0:\n p20.drop_tip()\n p20.mix(3, 15, s)\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down sample plate and replace on thermoycler.')\n\n # run first part of profile 1\n tc.close_lid()\n if rna_input == '> 1\u00b5g':\n cycles = 10\n elif rna_input == '250ng-1\u00b5g':\n cycles = 11\n elif rna_input == '100ng-250ng':\n cycles = 12\n elif rna_input == '< 100ng':\n cycles = 13\n profile_2_4 = [{'temperature': 95, 'hold_time_minutes': 10}]\n profile_2_5 = [\n {'temperature': 95, 'hold_time_seconds': 30},\n {'temperature': 60, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 1}\n ]\n profile_2_6 = [\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.execute_profile(steps=profile_2_4, repetitions=1, block_max_volume=50)\n tc.execute_profile(\n steps=profile_2_5, repetitions=cycles, block_max_volume=50)\n tc.execute_profile(steps=profile_2_6, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer elution buffer\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(50, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n", + "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep Library Index \\\nPCR (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, rna_input, p20_mount,\n m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'rna_input', 'p20_mount', 'm20_mount')\n # [number_of_samples, rna_input, p20_mount, m20_mount] = [\n # 96, '> 1\u00b5g', 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n index_plate = ctx.load_labware(\n 'opentrons_96_aluminumblock_nest_wellplate_100ul',\n '9', 'UDI primer plate')\n racks20m = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['3', '6']\n ]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s'] % 96\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m'] % 12\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n udi_primers = index_plate.rows()[0][:math.ceil(number_of_samples/8)]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n taq_premix = tempblock.rows()[3][0]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.3: Library Index PCR (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer UDI primers\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(\n 5, udi_primers, m, mix_after=(3, 15), air_gap=1, new_tip='never')\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n # transfer taq premix\n for s in samples:\n for i, vol in enumerate([15, 10]):\n pick_up(p20)\n p20.transfer(vol, taq_premix, s.bottom(1), new_tip='never')\n if i == 0:\n p20.drop_tip()\n p20.mix(3, 15, s)\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down sample plate and replace on thermoycler.')\n\n # run first part of profile 1\n tc.close_lid()\n if rna_input == '> 1\u00b5g':\n cycles = 10\n elif rna_input == '250ng-1\u00b5g':\n cycles = 11\n elif rna_input == '100ng-250ng':\n cycles = 12\n elif rna_input == '< 100ng':\n cycles = 13\n profile_2_4 = [{'temperature': 95, 'hold_time_minutes': 10}]\n profile_2_5 = [\n {'temperature': 95, 'hold_time_seconds': 30},\n {'temperature': 60, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 1}\n ]\n profile_2_6 = [\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.execute_profile(steps=profile_2_4, repetitions=1, block_max_volume=50)\n tc.execute_profile(\n steps=profile_2_5, repetitions=cycles, block_max_volume=50)\n tc.execute_profile(steps=profile_2_6, repetitions=1, block_max_volume=50)\n tc.open_lid()\n\n # transfer elution buffer\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(50, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n", "custom_labware_defs": [], "fields": [ { @@ -129,10 +129,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep Library Index PCR (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json index cec4ece473..bf04c5e19a 100644 --- a/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P5 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount, m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount', 'm20_mount')\n # [number_of_samples, p20_mount, m20_mount] = [96, 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '9')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s']\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m']\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n l3 = tempblock.rows()[2][2]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.2: P5 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L3\n for s in samples:\n pick_up(p20)\n p20.transfer(10, l3, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P5 ligation reaction\n profile_2_3 = [\n {'temperature': 25, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_3, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transer DNA elution buffer\n ctx.pause('Briefly spin down plate before resuming.')\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(80, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import math\nimport json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P5 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount, m20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount', 'm20_mount')\n # [number_of_samples, p20_mount, m20_mount] = [96, 'right', 'left']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20s = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n reagent_res = ctx.load_labware(\n 'nest_12_reservoir_15ml', '5', 'reagent reservoir')\n racks20m = [ctx.load_labware('opentrons_96_tiprack_20ul', '9')]\n\n # pipettes\n if p20_mount == m20_mount:\n raise Exception('Pipette mounts cannot match.')\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20s)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n m20 = ctx.load_instrument('p20_multi_gen2', m20_mount, tip_racks=racks20m)\n\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n # file_path = 'protocols/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20s' in data:\n tip20s_count = data['tips20s']\n else:\n tip20s_count = 0\n if 'tips20m' in data:\n tip20m_count = data['tips20m']\n else:\n tip20m_count = 0\n else:\n tip20s_count = 0\n tip20m_count = 0\n\n all_tips20s = [tip for rack in racks20s for tip in rack.wells()]\n all_tips20m = [tip for rack in racks20m for tip in rack.rows()[0]]\n tip20s_max = len(all_tips20s)\n tip20m_max = len(all_tips20m)\n\n def pick_up(pip):\n nonlocal tip20s_count\n nonlocal tip20m_count\n if pip == p20:\n if tip20s_count == tip20s_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20s_count = 0\n [rack.reset() for rack in racks20s]\n pip.pick_up_tip(all_tips20s[tip20s_count])\n tip20s_count += 1\n else:\n if tip20m_count == tip20m_max:\n ctx.pause('Replace tipracks before resuming.')\n tip20m_count = 0\n [rack.reset() for rack in racks20m]\n pip.pick_up_tip(all_tips20m[tip20m_count])\n tip20m_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n samples_multi = tc_plate.rows()[0][:math.ceil(number_of_samples/8)]\n l3 = tempblock.rows()[2][2]\n dna_eb = reagent_res.wells()[1]\n\n \"\"\" Section 2.2: P5 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L3\n for s in samples:\n pick_up(p20)\n p20.transfer(10, l3, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P5 ligation reaction\n profile_2_3 = [\n {'temperature': 25, 'hold_time_minutes': 15},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_3, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transer DNA elution buffer\n ctx.pause('Briefly spin down plate before resuming.')\n for m in samples_multi:\n pick_up(m20)\n m20.transfer(80, dna_eb, m.top(-2), new_tip='never')\n m20.mix(5, 15, m)\n m20.blow_out(m.top(-2))\n m20.drop_tip()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20s': tip20s_count,\n 'tips20m': tip20m_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -106,10 +106,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep P5 Adapter Ligation (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json b/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json index 03c6da2e8a..944173eaa8 100644 --- a/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json +++ b/protoBuilds/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P7 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.0'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount')\n # [number_of_samples, p20_mount] = [96, 'right']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n else:\n tip20_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.wells()]\n tip20_max = len(all_tips20)\n\n def pick_up():\n nonlocal tip20_count\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks20]\n p20.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n l1, l2 = tempblock.rows()[2][:2]\n\n \"\"\" Section 2.1: P7 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L1\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(10, l1, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P7 ligation reaction\n profile_2_1 = [\n {'temperature': 37, 'hold_time_minutes': 15},\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_1, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transfer L2\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(20, l2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute second strand synthesis\n profile_2_2 = [\n {'temperature': 95, 'hold_time_minutes': 10},\n {'temperature': 63, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_2, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20': tip20_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", + "content": "import json\nimport os\n\nmetadata = {\n 'protocolName': 'Zymo-Seq RiboFree\u2122 Total RNA Library Prep P7 Adapter \\\nLigation (robot 1)',\n 'author': 'Nick ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.3'\n}\n\n\ndef run(ctx):\n\n [number_of_samples, p20_mount] = get_values( # noqa: F821\n 'number_of_samples', 'p20_mount')\n # [number_of_samples, p20_mount] = [96, 'right']\n\n # load modules and labware\n tc = ctx.load_module('thermocycler')\n tc.set_lid_temperature(100)\n tc.set_block_temperature(4)\n tc_plate = tc.load_labware('nest_96_wellplate_100ul_pcr_full_skirt')\n racks20 = [\n ctx.load_labware('opentrons_96_tiprack_20ul', slot)\n for slot in ['1', '2', '3', '6']\n ]\n tempdeck = ctx.load_module('temperature module gen2', '4')\n tempdeck.set_temperature(4)\n tempblock = tempdeck.load_labware(\n 'opentrons_24_aluminumblock_nest_1.5ml_screwcap')\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=racks20)\n p20.flow_rate.aspirate = 10\n p20.flow_rate.dispense = 20\n p20.flow_rate.blow_out = 30\n\n # file_path = 'protocols/tip_track.json'\n if not ctx.is_simulating():\n file_path = '/data/csv/tip_track.json'\n if os.path.isfile(file_path):\n with open(file_path) as json_file:\n data = json.load(json_file)\n if 'tips20' in data:\n tip20_count = data['tips20']\n else:\n tip20_count = 0\n else:\n tip20_count = 0\n\n all_tips20 = [tip for rack in racks20 for tip in rack.wells()]\n tip20_max = len(all_tips20)\n\n def pick_up():\n nonlocal tip20_count\n if tip20_count == tip20_max:\n ctx.pause('Replace 20\u00b5l tipracks before resuming.')\n tip20_count = 0\n [rack.reset() for rack in racks20]\n p20.pick_up_tip(all_tips20[tip20_count])\n tip20_count += 1\n\n # reagents and sample setup\n if number_of_samples > 96 or number_of_samples < 1:\n raise Exception('Invalid number of samples (must be 1-96).')\n samples = tc_plate.wells()[:number_of_samples]\n l1, l2 = tempblock.rows()[2][:2]\n\n \"\"\" Section 2.1: P7 Adapter Ligation (Green Caps) \"\"\"\n if tc.lid_position == 'closed':\n tc.open_lid()\n\n # transfer L1\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(10, l1, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute P7 ligation reaction\n profile_2_1 = [\n {'temperature': 37, 'hold_time_minutes': 15},\n {'temperature': 98, 'hold_time_minutes': 2},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_1, repetitions=1, block_max_volume=20)\n tc.open_lid()\n\n # transfer L2\n for s in samples:\n p20.pick_up_tip()\n p20.transfer(20, l2, s, mix_after=(3, 15), new_tip='never')\n p20.blow_out(s.top(-2))\n p20.drop_tip()\n ctx.pause('Briefly spin down plate before resuming.')\n\n # execute second strand synthesis\n profile_2_2 = [\n {'temperature': 95, 'hold_time_minutes': 10},\n {'temperature': 63, 'hold_time_seconds': 30},\n {'temperature': 72, 'hold_time_minutes': 7},\n {'temperature': 4, 'hold_time_seconds': 10}\n ]\n tc.close_lid()\n tc.execute_profile(steps=profile_2_2, repetitions=1, block_max_volume=40)\n tc.open_lid()\n\n ctx.comment('Carefully remove sample plate from thermocycler and proceed \\\nwith cleanup.')\n\n # track final used tip\n # file_path = '/data/csv/tip_track.json'\n if not ctx.is_simulating():\n data = {\n 'tips20': tip20_count\n }\n with open(file_path, 'w') as outfile:\n json.dump(data, outfile)\n", "custom_labware_defs": [], "fields": [ { @@ -75,10 +75,23 @@ } ], "metadata": { - "apiLevel": "2.0", + "apiLevel": "2.3", "author": "Nick ", "protocolName": "Zymo-Seq RiboFree\u2122 Total RNA Library Prep P7 Adapter Ligation (robot 1)", "source": "Custom Protocol Request" }, - "modules": [] + "modules": [ + { + "name": "ThermocyclerContext at Thermocycler Module on 7 lw NEST 96 Well Plate 100 \u00b5L PCR Full Skirt on Thermocycler Module on 7", + "share": false, + "slot": "7", + "type": "thermocycler" + }, + { + "name": "TemperatureModuleContext at Temperature Module GEN2 on 4 lw Opentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap on Temperature Module GEN2 on 4", + "share": false, + "slot": "4", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json b/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json index d276be662c..6f26d9f12e 100644 --- a/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json +++ b/protoBuilds/zymo-rna-extraction/zymo-rna-extraction.ot2.apiv2.py.json @@ -79,13 +79,13 @@ "type": "nest_12_reservoir_15ml" }, { - "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module GEN1 on 3", + "name": "Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 3", "share": false, "slot": "3", "type": "opentrons_96_aluminumblock_nest_wellplate_100ul" }, { - "name": "NEST 96 Deepwell Plate 2mL on Magnetic Module GEN1 on 4", + "name": "NEST 96 Deepwell Plate 2mL on Magnetic Module on 4", "share": false, "slot": "4", "type": "nest_96_wellplate_2ml_deep" @@ -145,5 +145,18 @@ "protocolName": "Zymo Quick-DNA/RNA MagBead Station B", "source": "Protocol Library" }, - "modules": [] + "modules": [ + { + "name": "MagneticModuleContext at Magnetic Module on 4 lw NEST 96 Deepwell Plate 2mL on Magnetic Module on 4", + "share": false, + "slot": "4", + "type": "magdeck" + }, + { + "name": "TemperatureModuleContext at Temperature Module on 3 lw Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L on Temperature Module on 3", + "share": false, + "slot": "3", + "type": "tempdeck" + } + ] } \ No newline at end of file diff --git a/protocols/118e8c/118e8c.ot2.apiv2.py b/protocols/118e8c/118e8c.ot2.apiv2.py index 8dc8a65792..29f4a9c2eb 100644 --- a/protocols/118e8c/118e8c.ot2.apiv2.py +++ b/protocols/118e8c/118e8c.ot2.apiv2.py @@ -145,7 +145,7 @@ def height_dec(self, vol): self.current_volume = self.current_volume - vol else: self.current_volume = 0 - return(self.well.bottom(self.height)) + return (self.well.bottom(self.height)) def height_inc(self, vol, top=False): if self.diameter is not None: @@ -161,9 +161,9 @@ def height_inc(self, vol, top=False): self.height = self.depth self.current_volume += vol if top is False: - return(self.well.bottom(self.height)) + return (self.well.bottom(self.height)) else: - return(self.well.top()) + return (self.well.top()) # to track liquid height water = WellH(w, min_height=1, current_volume=water_volume) @@ -194,14 +194,14 @@ def pick_up(pip): p20m.flow_rate.dispense = 3.8 # capture and report original value for p20m pick_up_current - default_current = ctx._implementation._hw_manager.hardware.\ + default_current = ctx._hw_manager.hardware.\ _attached_instruments[p20m._implementation.get_mount()].\ config.pick_up_current ctx.comment("""Tip pick-up current for the p20 multi-channel pipette initially configured to {} mAmp.""".format(str(default_current))) # temporarily reduce p20m pick_up_current for one-channel tip pickup - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p20m._implementation.get_mount()].update_config_item( 'pick_up_current', reduced_pick_up_current) ctx.comment("""Tip pick-up current configuration for the p20 multi-channel @@ -212,12 +212,12 @@ def pick_up(pip): pick_up(p20m) # reset p20m pick_up_current to original value - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p20m._implementation.get_mount()].update_config_item( 'pick_up_current', default_current) ctx.comment("""Tip pick-up current for the p20 multi-channel pipette restored to initial value of {} mAmp for standard 8-tip pickup.""".format( - str(ctx._implementation._hw_manager.hardware._attached_instruments[ + str(ctx._hw_manager.hardware._attached_instruments[ p20m._implementation.get_mount()].config.pick_up_current))) # water then fluomix to last well of 1st col each tray diff --git a/protocols/121d15-4/manual_cleave.ot2.apiv2.py b/protocols/121d15-4/manual_cleave.ot2.apiv2.py index 8a49aa010f..cff627f949 100644 --- a/protocols/121d15-4/manual_cleave.ot2.apiv2.py +++ b/protocols/121d15-4/manual_cleave.ot2.apiv2.py @@ -119,7 +119,7 @@ def pick_up(num_tips, reagent_type): if num_tips > 1: pip = m300 pick_up_current = num_tips*per_tip_pickup_current - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ pip._implementation.get_mount()].update_config_item( 'pick_up_current', pick_up_current) else: @@ -227,6 +227,6 @@ def return_tip(pip, tip_loc, chunk_len, reagent_type): with open(tip_file_path, 'w') as outfile: json.dump(tip_data, outfile) - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ m300._implementation.get_mount()].update_config_item( 'pick_up_current', 1.0) diff --git a/protocols/1bcd67/normalization.ot2.apiv2.py b/protocols/1bcd67/normalization.ot2.apiv2.py index a1c3f41e3e..d03c77b004 100644 --- a/protocols/1bcd67/normalization.ot2.apiv2.py +++ b/protocols/1bcd67/normalization.ot2.apiv2.py @@ -56,7 +56,7 @@ def run(ctx): def pickup_p300(mode='single'): current = 0.1 if mode == 'single' else 0.5 - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', current) diff --git a/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py b/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py index c727ddec00..1f0f852f3a 100644 --- a/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py +++ b/protocols/2ed4de-2/fluribogreen.ot2.apiv2.py @@ -58,7 +58,7 @@ def run(ctx): def pickup_p300(mode='single'): current = 0.1 if mode == 'single' else 0.5 - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', current) diff --git a/protocols/2ed4de/fluribogreen.ot2.apiv2.py b/protocols/2ed4de/fluribogreen.ot2.apiv2.py index bc5b28b0c5..ba87d1737d 100644 --- a/protocols/2ed4de/fluribogreen.ot2.apiv2.py +++ b/protocols/2ed4de/fluribogreen.ot2.apiv2.py @@ -57,7 +57,7 @@ def run(ctx): def pickup_p300(mode='single'): current = 0.1 if mode == 'single' else 0.5 - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', current) diff --git a/protocols/7062c9-2/extraction.ot2.apiv2.py b/protocols/7062c9-2/extraction.ot2.apiv2.py index d1a205b1f2..ba37ff1ad3 100644 --- a/protocols/7062c9-2/extraction.ot2.apiv2.py +++ b/protocols/7062c9-2/extraction.ot2.apiv2.py @@ -98,7 +98,7 @@ def run(ctx): magdeck.disengage() # just in case tempdeck.set_temperature(85) - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ m300._implementation.get_mount()].update_config_item( 'pick_up_current', 0.5) diff --git a/protocols/7062c9/normalization.ot2.apiv2.py b/protocols/7062c9/normalization.ot2.apiv2.py index 5f812d7682..e0e894f4ff 100644 --- a/protocols/7062c9/normalization.ot2.apiv2.py +++ b/protocols/7062c9/normalization.ot2.apiv2.py @@ -28,7 +28,7 @@ def run(ctx): p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tipracks20) - ctx._implementation._hw_manager.hardware._attached_instruments[ + ctx._hw_manager.hardware._attached_instruments[ p300._implementation.get_mount()].update_config_item( 'pick_up_current', 0.1) diff --git a/protocols/sci-illumina-dna-prep/.hide-from-search b/protocols/sci-illumina-dna-prep/.hide-from-search deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/protocols/sci-illumina-dna-prep/.ignore b/protocols/sci-illumina-dna-prep/.ignore deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/protocols/sci-illumina-dna-prep/README.md b/protocols/sci-illumina-dna-prep/README.md deleted file mode 100644 index a4c486e434..0000000000 --- a/protocols/sci-illumina-dna-prep/README.md +++ /dev/null @@ -1,117 +0,0 @@ -# Illumina DNA Prep - Opentrons v3 -### Author -[Opentrons](https://opentrons.com/) - -### Partner -[Illumina](https://www.illumina.com/) - -## Categories -* NGS Library Prep - * Illumina DNA Prep - -## Description -This protocol automates the [Illumina DNA prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf). Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species - -The protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 µL of 100 ng:s of sample DNA in each well. See the [Illumina DNA Prep protocol](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/illumina_prep/illumina-dna-prep-reference-guide-1000000025416-09.pdf) for more information about sample input requirements. - -![Sample input and output columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/samples_output.jpg) - -![Sample columns](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/sample_setup.jpg) - -The user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below. - -**Plate Moving** -The Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration. - -Explanation of parameters below: -* `Number of samples`: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above). -* `Do a dry run?`: Sets the `Use modules?` parameter to `No` (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes. -* `Use modules?`: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to `Yes` if the `Do a dry run?` parameter is set to `Yes` -* `Tip reuse?`: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run. -* `Use tip offsets?`: Whether to use specific offsets for each tip type -* `Include tagmentation step in protocol run?`: Run the tagmentation step or skip it. -* `Run tagmentation incubation on the deck thermocycler?`: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler. -* `Run TSB step?`: Run the TSB/adapter ligation step or not -* `Run TSB incubation step on the deck thermocycler`: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler -* `Run tagmentation wash with TWB step`: Run the bead washing steps with TWB -* `Run PCR cycle step`: Whether to run the PCR amplification step -* `Run PCR step on deck thermocycler?`: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler -* `Run post PCR cleanup step`: Run or skip the post-PCR bead cleanup using AMPure beads ---- - -### Modules -* [Temperature Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck) -* [Magnetic Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) -* [Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module) - -### Labware -* [Nest 96 well plate full skirt 100 µL](https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/) -* [NEST 2 mL 96-Well Deep Well Plate](https://shop.opentrons.com/nest-2-ml-96-well-deep-well-plate-v-bottom/) -* [NEST 12-Well Reservoirs, 15 mL](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/) -* [Opentrons aluminum block set](https://shop.opentrons.com/aluminum-block-set/) - -### Pipettes -* [P300 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) -* [P20 multi-Channel (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) -* [P10 multi-Channel](https://shop.opentrons.com/8-channel-electronic-pipette/) -**Tips** -* [Opentrons 20 µL filter tiprack](https://shop.opentrons.com/opentrons-20ul-filter-tips/) -* [Opentrons 200 µL filter tiprack](https://shop.opentrons.com/opentrons-200ul-filter-tips/) - -### Reagents -* [Illumina DNA Prep](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-dna-flex.html) - ---- - -### Deck Setup -![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/deck.jpg) - -Inital slot layout: -1. Magnetic module for the sample plate (Nest 96 well plate full skirt). -2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents -3. Reagent plate 2: Temperature module with Bio-rad 200 µL plate on aluminum block. See Reagent Setup section for information about the location of the reagents -4. 20 µL filter tiprack -5. 200 µL filter tiprack -6. 200 µL filter tiprack -7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 µL -8. Empty -9. 200 µL filter tiprack -10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots) -11. Empty - -### Reagent Setup -* Reservoir, slot 2: -![Reagent plate 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate1.jpg) -* Reagent plate on temperature module, slot 3: -![Reagent plate 2](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-illumina-dna-prep/v3/reagent_plate2.jpg) - ---- - -### Protocol Steps -1. Prepare the thermocycler by setting the block temperature to 4 degrees, and the lid to 100 degrees. -2. Add tagmentation mix to the samples -3. User seals the plate and the protocol incubates the samples with the mix in the thermocycler, 55 degrees for 15 minutes. -4. The thermocycler opens, and the user removes the seal. -5. Add Tagmentation Stop Buffer to the samples. -6. Seal and incubate the mix at 37 degrees for 15 minutes. -7. User removes seal; remove the supernatant and wash the beads three times with Tagmentation Wash Buffer. -8. Amplification of DNA: Addition of PCR mix and addition of barcodes. -9. The protocol runs PCR protocol for 5 cycles. This takes 25 minutes to complete. The supernatant is transferred to columns 7, 9 and 11 depending on how many sample columns there are. -10. Post-PCR cleanup using AMPure beads. -11. The protocol performs two ethanol washes. -12. RSB (resuspension buffer) is added to the bead wells and the supernatant is transferred to the output columns (8, 10, and 12). - -### Process -1. Input your protocol parameters above. -2. Download your protocol and unzip if needed. -3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed. -4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab. -5. Set up your deck according to the deck map. -6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2). -7. Hit 'Run'. - -### Additional Notes -If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/). - -###### Internal -illumina-dna-prep diff --git a/protocols/sci-illumina-dna-prep/fields.json b/protocols/sci-illumina-dna-prep/fields.json deleted file mode 100644 index 75e33c7e4c..0000000000 --- a/protocols/sci-illumina-dna-prep/fields.json +++ /dev/null @@ -1,120 +0,0 @@ -[ - { - "type": "dropDown", - "label": "Number of samples", - "name": "SAMPLES", - "options": [ - {"label": "24 samples", "value": "24x"}, - {"label": "16 samples", "value": "16x"}, - {"label": "8 samples", "value": "8x"} - ] - }, - { - "type": "dropDown", - "label": "Do a dry run?", - "name": "DRYRUN", - "options": [ - {"label": "No", "value": "NO"}, - {"label": "Yes", "value": "YES"} - ] - }, - { - "type": "dropDown", - "label": "Use modules?", - "name": "NOMODULES", - "options": [ - {"label": "No", "value": "NO"}, - {"label": "Yes", "value": "YES"} - ] - }, - { - "type": "dropDown", - "label": "Tip reuse?", - "name": "TIPREUSE", - "options": [ - { "label": "No", "value": "NO"}, - {"label": "Yes", "value": "YES"} - ] - }, - { - "type": "dropDown", - "label": "Offset?", - "name": "OFFSET", - "options": [ - { "label": "Yes", "value": "YES"}, - { "label": "No", "value": "NO"} - ] - }, - { - "type": "dropDown", - "label": "Include tagmentation step in protocol run?", - "name": "STEP_TAG", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run tagmentation incubation on the deck thermocycler?", - "name": "STEP_TAGDECK", - "options": [ - { "label": "Yes", "value": 1}, - { "label": "No", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run TSB step?", - "name": "STEP_TSB", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run TSB incubation step on the deck thermocycler", - "name": "STEP_TSBDECK", - "options": [ - { "label": "Yes", "value": 1}, - { "label": "No", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run tagmentation wash with TWB step", - "name": "STEP_WASH", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run PCR cycle step", - "name": "STEP_PCR", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run PCR step on deck thermocycler?", - "name": "STEP_PCRDECK", - "options": [ - { "label": "Yes", "value": 1}, - { "label": "No", "value": 0} - ] - }, - { - "type": "dropDown", - "label": "Run post PCR cleanup step", - "name": "STEP_POSTPCR", - "options": [ - { "label": "Include", "value": 1}, - { "label": "Skip", "value": 0} - ] - } -] diff --git a/protocols/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py b/protocols/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py deleted file mode 100644 index c12857b90e..0000000000 --- a/protocols/sci-illumina-dna-prep/sci-illumina-dna-prep.ot2.apiv2.py +++ /dev/null @@ -1,2048 +0,0 @@ -from opentrons import protocol_api - -from opentrons import types - -import inspect - -metadata = { - 'protocolName': 'Illumina DNA Prep', - 'author': 'Opentrons ', - 'source': 'Protocol Library', - 'apiLevel': '2.9' -} -# I removed the right() function because it is never used -# settings -# SAMPLES = '24x' # 8x, 16x, or 24x -# YES or NO, DRYRUN = 'YES' will return tips, skip incubation times, -# shorten mix, for testing purposes -# DRYRUN = 'NO' -# YES or NO, NOMODULES = 'YES' will not require modules on the deck and will -# skip module steps, for testing purposes, if DRYRUN = 'YES', then NOMODULES -# will automatically set itself to 'NO' -# NOMODULES = 'NO' -# TIPREUSE = 'NO' -# YES or NO, Reusing tips on wash steps reduces tips needed, no tip refill -# needed, suggested only for 24x run with all steps - -# YES or NO, Sets whether to use protocol specific z offsets for each tip and -# labware or no offsets aside from defaults -# OFFSET = 'YES' - -# sections -# STEP_TAG = 1 # 1 is include, 0 is skip, steps with "DECK" are -# for reaction -# to take place with the on deck Thermocycler module -# This arrangement makes it possibly to set up and run only the first -# half, or to skips steps and resume if there is an Error. -# STEP_TAGDECK = 1 -# If non "DECK" steps are skipped, then TIPREUSE will automatically set -# itself to 'NO' in order to keep tip order correct. -# STEP_TSB = 1 -# STEP_TSBDECK = 1 -# STEP_WASH = 1 -# STEP_PCR = 1 -# STEP_PCRDECK = 1 -# STEP_POSTPCR = 1 - - -def run(protocol: protocol_api.ProtocolContext): - - global TIPREUSE - - [SAMPLES, - DRYRUN, - NOMODULES, - TIPREUSE, - OFFSET, - STEP_TAG, - STEP_TAGDECK, - STEP_TSB, - STEP_TSBDECK, - STEP_WASH, - STEP_PCR, - STEP_PCRDECK, - STEP_POSTPCR] = get_values( # noqa: F821 - "SAMPLES", - "DRYRUN", - "NOMODULES", - "TIPREUSE", - "OFFSET", - "STEP_TAG", - "STEP_TAGDECK", - "STEP_TSB", - "STEP_TSBDECK", - "STEP_WASH", - "STEP_PCR", - "STEP_PCRDECK", - "STEP_POSTPCR") - - STEPS = {STEP_TAG, STEP_TSB, STEP_WASH, STEP_PCR, STEP_POSTPCR} - - if DRYRUN == 'YES': - protocol.comment("THIS IS A DRY RUN") - else: - protocol.comment("THIS IS A REACTION RUN") - NOMODULES = 'NO' - - if all(STEPS) is True: - if TIPREUSE == 'YES': - TIPREUSE = 'YES' - protocol.comment("TIP REUSING") - else: - TIPREUSE = 'NO' - protocol.comment("NO TIP REUSING") - - # labware - if NOMODULES == 'YES': - protocol.comment("THIS IS A NO MODULE RUN") - # <--- Actually an Eppendorf 96 well, same dimensions - sample_plate_mag = protocol.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt', '1') - if TIPREUSE == 'NO': - reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2') - else: - reservoir = protocol.load_labware( - 'nest_96_wellplate_2ml_deep', '2') - reagent_plate = protocol.load_labware( - 'opentrons_96_aluminumblock_biorad_wellplate_200ul', '3') - tiprack_20 = protocol.load_labware( - 'opentrons_96_filtertiprack_20ul', '4') - tiprack_200_1 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '5') - tiprack_200_2 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '6') - sample_plate_thermo = protocol.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt', '7') - tiprack_200_3 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '9') - else: - protocol.comment("THIS IS A MODULE RUN") - mag_block = protocol.load_module('magnetic module gen2', '1') - # <--- Actually an Eppendorf 96 well, same dimensions - sample_plate_mag = mag_block.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt') - if TIPREUSE == 'NO': - reservoir = protocol.load_labware('nest_12_reservoir_15ml', '2') - else: - reservoir = protocol.load_labware( - 'nest_96_wellplate_2ml_deep', '2') - temp_block = protocol.load_module('temperature module gen2', '3') - reagent_plate = temp_block.load_labware( - 'opentrons_96_aluminumblock_biorad_wellplate_200ul') - tiprack_20 = protocol.load_labware( - 'opentrons_96_filtertiprack_20ul', '4') - tiprack_200_1 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '5') - tiprack_200_2 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '6') - thermocycler = protocol.load_module('thermocycler module') - sample_plate_thermo = thermocycler.load_labware( - 'nest_96_wellplate_100ul_pcr_full_skirt') - tiprack_200_3 = protocol.load_labware( - 'opentrons_96_filtertiprack_200ul', '9') - - if TIPREUSE == 'YES': - protocol.comment("THIS PROTOCOL WILL REUSE TIPS FOR WASHES") - - # reagent - plate - TAG = reagent_plate.wells_by_name()['A1'] - TSB = reagent_plate.wells_by_name()['A2'] - PCR = reagent_plate.wells_by_name()['A3'] - Barcodes1 = reagent_plate.wells_by_name()['A7'] - Barcodes2 = reagent_plate.wells_by_name()['A8'] - Barcodes3 = reagent_plate.wells_by_name()['A9'] - - # reagent - deepwell - if TIPREUSE == 'NO': - AMPure = reservoir['A1'] - EtOH_1 = reservoir['A4'] - EtOH_2 = reservoir['A4'] - EtOH_3 = reservoir['A4'] - RSB = reservoir['A6'] - TWB_1 = reservoir['A8'] - TWB_2 = reservoir['A8'] - TWB_3 = reservoir['A8'] - Liquid_trash = reservoir['A12'] - else: - AMPure = reservoir['A1'] - EtOH_1 = reservoir['A4'] - EtOH_2 = reservoir['A3'] - EtOH_3 = reservoir['A2'] - RSB = reservoir['A6'] - TWB_1 = reservoir['A8'] - TWB_2 = reservoir['A9'] - TWB_3 = reservoir['A10'] - Liquid_trash = reservoir['A12'] - - # pipette - if NOMODULES == 'NO': - p300 = protocol.load_instrument('p300_multi_gen2', 'left', tip_racks=[ - tiprack_200_1, tiprack_200_2, - tiprack_200_3]) - p20 = protocol.load_instrument( - 'p20_multi_gen2', 'right', tip_racks=[tiprack_20]) - else: - p300 = protocol.load_instrument('p300_multi', 'left', tip_racks=[ - tiprack_200_1, tiprack_200_2, - tiprack_200_3]) - p20 = protocol.load_instrument( - 'p10_multi', 'right', tip_racks=[tiprack_20]) - - # samples - # FIXME: This does not seem to be used - src_file_path = inspect.getfile(lambda: None) - protocol.comment(src_file_path) - - # tip and sample tracking - if SAMPLES == '8x': - protocol.comment("There are 8 Samples") - samplecolumns = 1 - TWB_washtip_1 = tiprack_200_1['A3'] - TWB_removetip_1 = tiprack_200_1['A4'] - W1_ETOH_washtip_1 = tiprack_200_1['A10'] - W1_ETOH_removetip_1 = tiprack_200_1['A11'] - elif SAMPLES == '16x': - protocol.comment("There are 16 Samples") - samplecolumns = 2 - TWB_washtip_1 = tiprack_200_1['A5'] - TWB_washtip_2 = tiprack_200_1['A6'] - TWB_removetip_1 = tiprack_200_1['A7'] - TWB_removetip_2 = tiprack_200_1['A8'] - W1_ETOH_washtip_1 = tiprack_200_2['A7'] - W1_ETOH_washtip_2 = tiprack_200_2['A8'] - W1_ETOH_removetip_1 = tiprack_200_2['A9'] - W1_ETOH_removetip_2 = tiprack_200_2['A10'] - elif SAMPLES == '24x': - protocol.comment("There are 24 Samples") - samplecolumns = 3 - TWB_washtip_1 = tiprack_200_1['A7'] - TWB_washtip_2 = tiprack_200_1['A8'] - TWB_washtip_3 = tiprack_200_1['A9'] - TWB_removetip_1 = tiprack_200_1['A10'] - TWB_removetip_2 = tiprack_200_1['A11'] - TWB_removetip_3 = tiprack_200_1['A12'] - W1_ETOH_washtip_1 = tiprack_200_3['A4'] - W1_ETOH_washtip_2 = tiprack_200_3['A5'] - W1_ETOH_washtip_3 = tiprack_200_3['A6'] - W1_ETOH_removetip_1 = tiprack_200_3['A7'] - W1_ETOH_removetip_2 = tiprack_200_3['A8'] - W1_ETOH_removetip_3 = tiprack_200_3['A9'] - else: - protocol.pause("ERROR?") - - # FIXME: commented out variables are never used in the protocol - p300_offset_Res = 0 - p300_offset_Thermo = 0 - p300_offset_Mag = 0 - # p300_offset_Deck = 0 - p300_offset_Temp = 0 - # p300_offset_Tube = 0 - # p20_offset_Res = 0 - p20_offset_Thermo = 0 - p20_offset_Mag = 0 - # p20_offset_Deck = 0 - p20_offset_Temp = 0 - # p20_offset_Tube = 0 - - # offset - if OFFSET == 'YES': - if TIPREUSE == 'NO': - p300_offset_Res = 2 - else: - p300_offset_Res = 2 - p300_offset_Thermo = 1 - p300_offset_Mag = 0.70 - # p300_offset_Deck = 0.3 - p300_offset_Temp = 0.65 - # p300_offset_Tube = 0 - # if TIPREUSE == 'NO': - # p20_offset_Res = 2 - # else: - # p20_offset_Res = 2 - p20_offset_Thermo = 1 - p20_offset_Mag = 0.75 - # p20_offset_Deck = 0.3 - p20_offset_Temp = 0.85 - # p20_offset_Tube = 0 - - # FIXME: Commented out variables are never used in the protocol - # positions - ########################################################################## - # sample_plate_thermo on the Thermocycler - # A1_p20_bead_side = sample_plate_thermo['A1'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right - # A1_p20_bead_top = sample_plate_thermo['A1'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right - # A1_p20_bead_mid = sample_plate_thermo['A1'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right - A1_p300_bead_side = sample_plate_thermo['A1'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right - A1_p300_bead_top = sample_plate_thermo['A1'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right - A1_p300_bead_mid = sample_plate_thermo['A1'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A1_p300_loc1 = sample_plate_thermo['A1'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - A1_p300_loc2 = sample_plate_thermo['A1'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A1_p300_loc3 = sample_plate_thermo['A1'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - # A3_p20_bead_side = sample_plate_thermo['A3'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right - # A3_p20_bead_top = sample_plate_thermo['A3'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right - # A3_p20_bead_mid = sample_plate_thermo['A3'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right - A3_p300_bead_side = sample_plate_thermo['A3'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right - A3_p300_bead_top = sample_plate_thermo['A3'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right - A3_p300_bead_mid = sample_plate_thermo['A3'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A3_p300_loc1 = sample_plate_thermo['A3'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - A3_p300_loc2 = sample_plate_thermo['A3'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A3_p300_loc3 = sample_plate_thermo['A3'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - # A5_p20_bead_side = sample_plate_thermo['A5'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Thermo - 5)) # Beads to the Right - # A5_p20_bead_top = sample_plate_thermo['A5'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Thermo + 2)) # Beads to the Right - # A5_p20_bead_mid = sample_plate_thermo['A5'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Thermo - 2)) # Beads to the Right - A5_p300_bead_side = sample_plate_thermo['A5'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Thermo - 7.2)) # Beads to the Right - A5_p300_bead_top = sample_plate_thermo['A5'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Thermo - 1)) # Beads to the Right - A5_p300_bead_mid = sample_plate_thermo['A5'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A5_p300_loc1 = sample_plate_thermo['A5'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - A5_p300_loc2 = sample_plate_thermo['A5'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Thermo - 4)) # Beads to the Right - A5_p300_loc3 = sample_plate_thermo['A5'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Thermo - 4)) - # Beads to the Right - ########################################################################## - - bypass = protocol.deck.position_for( - '11').move(types.Point(x=70, y=80, z=130)) - - # commands - if DRYRUN == 'NO': - protocol.comment("SETTING THERMO and TEMP BLOCK Temperature") - thermocycler.set_block_temperature(4) - thermocycler.set_lid_temperature(100) -# temp_block.set_temperature(4) - thermocycler.open_lid() - protocol.pause("Ready") - - if STEP_TAG == 1: - protocol.comment('==============================================') - protocol.comment('--> TAGMENTATION') - protocol.comment('==============================================') - - protocol.comment('--> Adding Tagmentation Mix ') - if DRYRUN == 'NO': - TagVol = 20 - TagMixRep = 10 - TagMixVol = 40 - if DRYRUN == 'YES': - TagVol = 20 - TagMixRep = 1 - TagMixVol = 40 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5) - p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25) - p300.dispense(TagVol, sample_plate_thermo[X].bottom( - z=p300_offset_Thermo), rate=0.25) - p300.mix(TagMixRep, TagMixVol) - p300.blow_out(sample_plate_thermo[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5) - p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25) - p300.dispense(TagVol, sample_plate_thermo[X].bottom( - z=p300_offset_Thermo), rate=0.25) - p300.mix(TagMixRep, TagMixVol) - p300.blow_out(sample_plate_thermo[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.mix(3, 20, TAG.bottom(z=p300_offset_Temp), rate=0.5) - p300.aspirate(TagVol, TAG.bottom(z=p300_offset_Temp), rate=0.25) - p300.dispense(TagVol, sample_plate_thermo[X].bottom( - z=p300_offset_Thermo), rate=0.25) - p300.mix(TagMixRep, TagMixVol) - p300.blow_out(sample_plate_thermo[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if STEP_TAGDECK == 1: - if DRYRUN == 'NO': - ################################################################### - protocol.pause('Seal, Run TAG (15min)') - - thermocycler.close_lid() - profile_TAG = [ - {'temperature': 55, 'hold_time_minutes': 15} - ] - thermocycler.execute_profile( - steps=profile_TAG, repetitions=1, block_max_volume=50) - thermocycler.set_block_temperature(10) - ####################################################################### - thermocycler.open_lid() - protocol.pause("Remove Seal") - else: - protocol.pause('Seal, Run ERAT (60min)') - - if STEP_TSB == 1: - protocol.pause("Add TSB to Reagent Wells") - protocol.comment('==============================================') - protocol.comment('--> Adapter Ligation') - protocol.comment('==============================================') - - protocol.comment('--> Adding Tagmentation Stop Buffer') - if DRYRUN == 'NO': - if NOMODULES == 'NO': - TSBVol = 10 - TSBMixRep = 10 - TSBMixVol = 20 - else: - TSBVol = 10 - TSBMixRep = 10 - TSBMixVol = 10 - if DRYRUN == 'YES': - if NOMODULES == 'NO': - TSBVol = 10 - TSBMixRep = 1 - TSBMixVol = 20 - else: - TSBVol = 10 - TSBMixRep = 1 - TSBMixVol = 10 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p20.pick_up_tip() - p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp)) - p20.dispense(TSBVol, sample_plate_thermo[X].bottom( - z=p20_offset_Thermo)) - p20.mix(TSBMixRep, TSBMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p20.pick_up_tip() - p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp)) - p20.dispense(TSBVol, sample_plate_thermo[X].bottom( - z=p20_offset_Thermo)) - p20.mix(TSBMixRep, TSBMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p20.pick_up_tip() - p20.aspirate(TSBVol, TSB.bottom(z=p20_offset_Temp)) - p20.dispense(TSBVol, sample_plate_thermo[X].bottom( - z=p20_offset_Thermo)) - p20.mix(TSBMixRep, TSBMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if STEP_TSBDECK == 1: - if DRYRUN == 'NO': - ################################################################### - protocol.pause('Seal, Run PTC (15min)') - - thermocycler.close_lid() - profile_PTC = [ - {'temperature': 37, 'hold_time_minutes': 15} - ] - thermocycler.execute_profile( - steps=profile_PTC, repetitions=1, block_max_volume=60) - thermocycler.set_block_temperature(10) - ################################################################### - thermocycler.open_lid() - protocol.pause("Remove Seal") - else: - protocol.pause('Seal, Run PTC (15min)') - - # FIXME: Commented out variables are never used in the protocol - # positions - ########################################################################## - # sample_plate_mag on the Mag Block - # A1_p20_bead_side = sample_plate_mag['A1'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A1_p20_bead_top = sample_plate_mag['A1'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A1_p20_bead_mid = sample_plate_mag['A1'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A1_p300_bead_side = sample_plate_mag['A1'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A1_p300_bead_top = sample_plate_mag['A1'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - A1_p300_bead_mid = sample_plate_mag['A1'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A1_p300_loc1 = sample_plate_mag['A1'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A1_p300_loc2 = sample_plate_mag['A1'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A1_p300_loc3 = sample_plate_mag['A1'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A3_p20_bead_side = sample_plate_mag['A3'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A3_p20_bead_top = sample_plate_mag['A3'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A3_p20_bead_mid = sample_plate_mag['A3'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A3_p300_bead_side = sample_plate_mag['A3'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A3_p300_bead_top = sample_plate_mag['A3'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - A3_p300_bead_mid = sample_plate_mag['A3'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A3_p300_loc1 = sample_plate_mag['A3'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A3_p300_loc2 = sample_plate_mag['A3'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A3_p300_loc3 = sample_plate_mag['A3'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A5_p20_bead_side = sample_plate_mag['A5'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A5_p20_bead_top = sample_plate_mag['A5'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A5_p20_bead_mid = sample_plate_mag['A5'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A5_p300_bead_side = sample_plate_mag['A5'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A5_p300_bead_top = sample_plate_mag['A5'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - A5_p300_bead_mid = sample_plate_mag['A5'].center().move(types.Point( - x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A5_p300_loc1 = sample_plate_mag['A5'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A5_p300_loc2 = sample_plate_mag['A5'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A5_p300_loc3 = sample_plate_mag['A5'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A7_p20_bead_side = sample_plate_mag['A7'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A7_p20_bead_top = sample_plate_mag['A7'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A7_p20_bead_mid = sample_plate_mag['A7'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A7_p300_bead_side = sample_plate_mag['A7'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A7_p300_bead_top = sample_plate_mag['A7'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - # A7_p300_bead_mid = sample_plate_mag['A7'].center().move(types.Point( - # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A7_p300_loc1 = sample_plate_mag['A7'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A7_p300_loc2 = sample_plate_mag['A7'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A7_p300_loc3 = sample_plate_mag['A7'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A9_p20_bead_side = sample_plate_mag['A9'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A9_p20_bead_top = sample_plate_mag['A9'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A9_p20_bead_mid = sample_plate_mag['A9'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A9_p300_bead_side = sample_plate_mag['A9'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A9_p300_bead_top = sample_plate_mag['A9'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - # A9_p300_bead_mid = sample_plate_mag['A9'].center().move(types.Point( - # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A9_p300_loc1 = sample_plate_mag['A9'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A9_p300_loc2 = sample_plate_mag['A9'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A9_p300_loc3 = sample_plate_mag['A9'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - # A11_p20_bead_side = sample_plate_mag['A11'].center().move(types.Point( - # x=-1.8 * 0.50, y=0, z=p20_offset_Mag - 5)) # Beads to the Right - # A11_p20_bead_top = sample_plate_mag['A11'].center().move(types.Point( - # x=1.5, y=0, z=p20_offset_Mag + 2)) # Beads to the Right - # A11_p20_bead_mid = sample_plate_mag['A11'].center().move(types.Point( - # x=1, y=0, z=p20_offset_Mag - 2)) # Beads to the Right - A11_p300_bead_side = sample_plate_mag['A11'].center().move(types.Point( - x=-0.50, y=0, z=p300_offset_Mag - 7.6)) # Beads to the Right - A11_p300_bead_top = sample_plate_mag['A11'].center().move(types.Point( - x=1.30, y=0, z=p300_offset_Mag - 1)) # Beads to the Right - # A11_p300_bead_mid = sample_plate_mag['A11'].center().move(types.Point( - # x=0.80, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A11_p300_loc1 = sample_plate_mag['A11'].center().move(types.Point( - x=1.3 * 0.8, y=1.3 * 0.8, z=p300_offset_Mag - 4)) # Beads to the Right - A11_p300_loc2 = sample_plate_mag['A11'].center().move(types.Point( - x=1.3, y=0, z=p300_offset_Mag - 4)) # Beads to the Right - A11_p300_loc3 = sample_plate_mag['A11'].center().move(types.Point( - x=1.3 * 0.8, y=-1.3 * 0.8, z=p300_offset_Mag - 4)) - # Beads to the Right - ########################################################################## - - if STEP_WASH == 1: - protocol.pause("PLACE sample_plate on MAGNET") - protocol.comment('==============================================') - protocol.comment('--> TAGMENTATION WASH') - protocol.comment('==============================================') - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - protocol.comment('--> Removing Supernatant') - RemoveSup = 90 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - protocol.comment('--> Repeating 3 washes') - washreps = 3 - for wash in range(washreps): - protocol.comment('--> TWB Wash #' + str(wash + 1)) - if DRYRUN == 'NO': - TWBMixRep = 15 - TWBMixVol = 70 - if DRYRUN == 'YES': - TWBMixRep = 3 - TWBMixVol = 70 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_washtip_1) - p300.aspirate(100, TWB_1.bottom(z=p300_offset_Res)) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - p300.default_speed = 5 - reps = 4 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(100) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_bead_mid) - if X == 'A3': - p300.move_to(A3_p300_bead_mid) - if X == 'A5': - p300.move_to(A5_p300_bead_mid) - p300.mix(TWBMixRep, TWBMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(TWBMixRep, TWBMixVol) - p300.default_speed = 400 - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_washtip_2) - p300.aspirate(100, TWB_2.bottom(z=p300_offset_Res)) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - p300.default_speed = 5 - reps = 4 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(100) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_bead_mid) - if X == 'A3': - p300.move_to(A3_p300_bead_mid) - if X == 'A5': - p300.move_to(A5_p300_bead_mid) - p300.mix(TWBMixRep, TWBMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(TWBMixRep, TWBMixVol) - p300.default_speed = 400 - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_washtip_3) - p300.aspirate(100, TWB_3.bottom(z=p300_offset_Res)) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - p300.default_speed = 5 - reps = 4 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(100) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(100, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_bead_mid) - if X == 'A3': - p300.move_to(A3_p300_bead_mid) - if X == 'A5': - p300.move_to(A5_p300_bead_mid) - p300.mix(TWBMixRep, TWBMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(TWBMixRep, TWBMixVol) - p300.default_speed = 400 - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - protocol.comment('--> Remove TWB Wash #' + str(wash + 1)) - RemoveSup = 110 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_removetip_1) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_removetip_2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip()if TIPREUSE == 'NO' else \ - p300.pick_up_tip(TWB_removetip_3) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_bead_side) - if X == 'A3': - p300.move_to(A3_p300_bead_side) - if X == 'A5': - p300.move_to(A5_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.2) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - wash += 1 - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=5) - - protocol.comment('--> Removing Residual Supernatant') - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3)) - p300.aspirate(50, rate=0.25) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3)) - p300.aspirate(50, rate=0.25) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 3)) - p300.aspirate(50, rate=0.25) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - mag_block.engage(height_from_base=3) - protocol.delay(minutes=0.5) - - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - if STEP_PCR == 1: - protocol.comment('==============================================') - protocol.comment('--> AMPLIFICATION') - protocol.comment('==============================================') - - protocol.comment('ADDING PCR') - if DRYRUN == 'NO': - PCRVol = 40 - PCRMixRep = 5 - PCRMixVol = 30 - if DRYRUN == 'YES': - PCRVol = 40 - PCRMixRep = 1 - PCRMixVol = 30 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p300.pick_up_tip() - p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp)) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(PCRVol, rate=0.5) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(PCRVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p300.pick_up_tip() - p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp)) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(PCRVol, rate=0.5) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(PCRVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p300.pick_up_tip() - p300.aspirate(PCRVol, PCR.bottom(p300_offset_Temp)) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.dispense(PCRVol / 5, rate=0.75) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.dispense(PCRVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(PCRVol, rate=0.5) - if X == 'A1': - p300.move_to(A1_p300_bead_top) - if X == 'A3': - p300.move_to(A3_p300_bead_top) - if X == 'A5': - p300.move_to(A5_p300_bead_top) - p300.dispense(PCRVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc1) - if X == 'A3': - p300.move_to(A3_p300_loc1) - if X == 'A5': - p300.move_to(A5_p300_loc1) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc2) - if X == 'A3': - p300.move_to(A3_p300_loc2) - if X == 'A5': - p300.move_to(A5_p300_loc2) - p300.mix(PCRMixRep, PCRMixVol) - if X == 'A1': - p300.move_to(A1_p300_loc3) - if X == 'A3': - p300.move_to(A3_p300_loc3) - if X == 'A5': - p300.move_to(A5_p300_loc3) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(PCRMixRep, PCRMixVol) - p300.move_to(sample_plate_mag[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - protocol.comment('--> Adding Barcodes') - BarcodeVol = 10 - BarcodeMixRep = 10 - BarcodeMixVol = 10 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - p20.pick_up_tip() - p20.aspirate(BarcodeVol, Barcodes1.bottom( - z=p20_offset_Temp), rate=0.25) - p20.dispense( - BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.mix(BarcodeMixRep, BarcodeMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - p20.pick_up_tip() - p20.aspirate(BarcodeVol, Barcodes2.bottom( - z=p20_offset_Temp), rate=0.25) - p20.dispense( - BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.mix(BarcodeMixRep, BarcodeMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - p20.pick_up_tip() - p20.aspirate(BarcodeVol, Barcodes3.bottom( - z=p20_offset_Temp), rate=0.25) - p20.dispense( - BarcodeVol, sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.mix(BarcodeMixRep, BarcodeMixVol) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if DRYRUN == 'NO': - protocol.pause("PLACE sample_plate on THERMO") - - if STEP_PCRDECK == 1: - ####################################################################### - protocol.pause('Seal, Run PCR (25min)') - - thermocycler.close_lid() - profile_PCR_1 = [ - {'temperature': 68, 'hold_time_minutes': 3}, - {'temperature': 98, 'hold_time_minutes': 3} - ] - thermocycler.execute_profile( - steps=profile_PCR_1, repetitions=1, block_max_volume=50) - profile_PCR_2 = [ - {'temperature': 98, 'hold_time_seconds': 45}, - {'temperature': 62, 'hold_time_seconds': 30}, - {'temperature': 68, 'hold_time_minutes': 2} - ] - thermocycler.execute_profile( - steps=profile_PCR_2, repetitions=5, block_max_volume=50) - profile_PCR_3 = [ - {'temperature': 68, 'hold_time_minutes': 1} - ] - thermocycler.execute_profile( - steps=profile_PCR_3, repetitions=1, block_max_volume=50) - thermocycler.set_block_temperature(4) - ####################################################################### - thermocycler.open_lid() - protocol.pause("Remove Seal") - else: - protocol.pause('Seal, Run PCR (60min)') - - Liquid_trash = reservoir['A11'] - - if STEP_POSTPCR == 1: - protocol.pause("PLACE sample_plate on MAGNET") - protocol.comment('==============================================') - protocol.comment('--> CLEANUP') - protocol.comment('==============================================') - - if DRYRUN == 'NO': - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - protocol.comment('--> Transferring Supernatant') - TransferSup = 45 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A1' - Y = 'A7' - p300.pick_up_tip() - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag + 1), rate=0.5) - protocol.delay(seconds=0.1) - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag), rate=0.5) - p300.dispense( - TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag)) - protocol.delay(seconds=0.1) - p300.blow_out(sample_plate_mag[Y].top(z=-2)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A3' - Y = 'A9' - p300.pick_up_tip() - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag + 1), rate=0.5) - protocol.delay(seconds=0.1) - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag), rate=0.5) - p300.dispense( - TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag)) - protocol.delay(seconds=0.1) - p300.blow_out(sample_plate_mag[Y].top(z=-2)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A5' - Y = 'A11' - p300.pick_up_tip() - p300.aspirate( - TransferSup / 2, sample_plate_mag[X]. - bottom(z=p300_offset_Mag + 1), rate=0.5) - protocol.delay(seconds=0.1) - p300.aspirate( - TransferSup / 2, sample_plate_mag[X].bottom(z=p300_offset_Mag), - rate=0.5) - p300.dispense( - TransferSup + 5, sample_plate_mag[Y].bottom(z=p300_offset_Mag)) - protocol.delay(seconds=0.1) - p300.blow_out(sample_plate_mag[Y].top(z=-2)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - protocol.comment('--> ADDING AMPure (0.8x)') - AMPureVol = 40 - AMPureMixRep = 50 - AMPureMixVol = 80 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p300.pick_up_tip() - p300.mix(10, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res)) - p300.aspirate(AMPureVol, AMPure.bottom( - z=p300_offset_Res), rate=0.25) - p300.dispense(AMPureVol, sample_plate_mag[X].bottom( - z=p300_offset_Mag), rate=0.25) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(AMPureMixRep, AMPureMixVol) - p300.blow_out(sample_plate_mag[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p300.pick_up_tip() - p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res)) - p300.aspirate(AMPureVol, AMPure.bottom( - z=p300_offset_Res), rate=0.25) - p300.dispense(AMPureVol, sample_plate_mag[X].bottom( - z=p300_offset_Mag), rate=0.25) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(AMPureMixRep, AMPureMixVol) - p300.blow_out(sample_plate_mag[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p300.pick_up_tip() - p300.mix(3, AMPureVol + 10, AMPure.bottom(z=p300_offset_Res)) - p300.aspirate(AMPureVol, AMPure.bottom( - z=p300_offset_Res), rate=0.25) - p300.dispense(AMPureVol, sample_plate_mag[X].bottom( - z=p300_offset_Mag), rate=0.25) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.mix(AMPureMixRep, AMPureMixVol) - p300.blow_out(sample_plate_mag[X].top(z=-5)) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - if DRYRUN == 'NO': - protocol.delay(minutes=5) - - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=8.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7.5) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=7) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=6) - protocol.delay(minutes=1) - mag_block.engage(height_from_base=5) - protocol.delay(minutes=1) - - if TIPREUSE == 'NO': - if all(STEPS) is True: - protocol.pause('RESET TIPS') - p300.reset_tipracks() - p20.reset_tipracks() - - protocol.comment('--> Removing Supernatant') - RemoveSup = 100 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.1) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.1) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p300.pick_up_tip() - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(RemoveSup - 30, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(20, rate=0.2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - protocol.delay(minutes=0.1) - p300.aspirate(10, rate=0.1) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(bypass) - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - - protocol.comment('--> Repeating 2 washes') - washreps = 2 - for wash in range(washreps): - protocol.comment('--> ETOH Wash #' + str(wash + 1)) - ETOHMaxVol = 150 - WASHNUM = 1 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_washtip_1) - elif WASHNUM == 2: - pass # # FIXME: W2_ETOH_washtip_1 is never defined - # p300.pick_up_tip(W2_ETOH_washtip_1) - p300.aspirate(ETOHMaxVol, EtOH_1.bottom(z=p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - p300.dispense(ETOHMaxVol - 50, rate=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.dispense(50, rate=0.5) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 5 - p300.move_to(sample_plate_mag[X].top(z=-2)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_washtip_2) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_washtip_2 is never defined - # p300.pick_up_tip(W2_ETOH_washtip_2) - p300.aspirate(ETOHMaxVol, EtOH_2.bottom(z=p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - p300.dispense(ETOHMaxVol - 50, rate=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.dispense(50, rate=0.5) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 5 - p300.move_to(sample_plate_mag[X].top(z=-2)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_washtip_3) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_washtip_3 is undefined - # p300.pick_up_tip(W2_ETOH_washtip_3) - p300.aspirate(ETOHMaxVol, EtOH_3.bottom(z=p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - p300.dispense(ETOHMaxVol - 50, rate=0.5) - p300.move_to(sample_plate_mag[X].center()) - p300.dispense(50, rate=0.5) - p300.move_to(sample_plate_mag[X].top(z=2)) - p300.default_speed = 5 - p300.move_to(sample_plate_mag[X].top(z=-2)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.default_speed = 400 - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - protocol.delay(minutes=0.5) - - protocol.comment('--> Remove ETOH Wash #' + str(wash + 1)) - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_removetip_1) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_removetip_1 is never defined - # p300.pick_up_tip(W2_ETOH_removetip_1) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(ETOHMaxVol, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(200 - ETOHMaxVol, rate=0.25) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(Liquid_trash.top(z=5)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_removetip_2) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_removetip_2 is never defined - # p300.pick_up_tip(W2_ETOH_removetip_2) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(ETOHMaxVol, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(200 - ETOHMaxVol, rate=0.25) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(Liquid_trash.top(z=5)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - if TIPREUSE == 'NO': - p300.pick_up_tip() - elif WASHNUM == 1: - p300.pick_up_tip(W1_ETOH_removetip_3) - elif WASHNUM == 2: - pass - # FIXME: W2_ETOH_removetip_3 is never defined - # p300.pick_up_tip(W2_ETOH_removetip_3) - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag + 4)) - p300.aspirate(ETOHMaxVol, rate=0.25) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_bead_side) - if X == 'A9': - p300.move_to(A9_p300_bead_side) - if X == 'A11': - p300.move_to(A11_p300_bead_side) - protocol.delay(minutes=0.1) - p300.aspirate(200 - ETOHMaxVol, rate=0.25) - p300.default_speed = 400 - p300.dispense(200, Liquid_trash) - p300.move_to(Liquid_trash.top(z=5)) - protocol.delay(minutes=0.1) - p300.blow_out() - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - wash += 1 - - if DRYRUN == 'NO': - protocol.delay(minutes=2) - - protocol.comment('--> Removing Residual ETOH') - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate( - 10, rate=0.25) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate( - 10, rate=0.25) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(20, rate=0.25)if NOMODULES == 'NO' else p20.aspirate( - 10, rate=0.25) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if DRYRUN == 'NO': - mag_block.engage(height_from_base=6) - protocol.comment('AIR DRY') - protocol.delay(minutes=0.5) - - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() - - protocol.comment('--> Adding RSB') - RSBVol = 32 - RSBMixRep = 5 - RSBMixVol = 25 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - p300.pick_up_tip() - p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(RSBVol, rate=0.5) - if X == 'A7': - p300.move_to(A7_p300_bead_top) - if X == 'A9': - p300.move_to(A9_p300_bead_top) - if X == 'A11': - p300.move_to(A11_p300_bead_top) - p300.dispense(RSBVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name() - [X].bottom(z=p300_offset_Mag)) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name()[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag.wells_by_name()[X].center()) - p300.default_speed = 400 - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - p300.pick_up_tip() - p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(RSBVol, rate=0.5) - if X == 'A7': - p300.move_to(A7_p300_bead_top) - if X == 'A9': - p300.move_to(A9_p300_bead_top) - if X == 'A11': - p300.move_to(A11_p300_bead_top) - p300.dispense(RSBVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name() - [X].bottom(z=p300_offset_Mag)) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name()[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag.wells_by_name()[X].center()) - p300.default_speed = 400 - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - p300.pick_up_tip() - p300.aspirate(RSBVol, RSB.bottom(p300_offset_Res)) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - p300.default_speed = 5 - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.dispense(RSBVol / 5, rate=0.75) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.dispense(RSBVol / 5, rate=0.75) - reps = 5 - for x in range(reps): - p300.move_to(sample_plate_mag[X].bottom(z=p300_offset_Mag)) - p300.aspirate(RSBVol, rate=0.5) - if X == 'A7': - p300.move_to(A7_p300_bead_top) - if X == 'A9': - p300.move_to(A9_p300_bead_top) - if X == 'A11': - p300.move_to(A11_p300_bead_top) - p300.dispense(RSBVol, rate=1) - reps = 3 - for x in range(reps): - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc1) - if X == 'A9': - p300.move_to(A9_p300_loc1) - if X == 'A11': - p300.move_to(A11_p300_loc1) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc2) - if X == 'A9': - p300.move_to(A9_p300_loc2) - if X == 'A11': - p300.move_to(A11_p300_loc2) - p300.mix(RSBMixRep, RSBMixVol) - if X == 'A7': - p300.move_to(A7_p300_loc3) - if X == 'A9': - p300.move_to(A9_p300_loc3) - if X == 'A11': - p300.move_to(A11_p300_loc3) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name() - [X].bottom(z=p300_offset_Mag)) - p300.mix(RSBMixRep, RSBMixVol) - p300.move_to(sample_plate_mag.wells_by_name()[X].top()) - protocol.delay(seconds=0.5) - p300.move_to(sample_plate_mag.wells_by_name()[X].center()) - p300.default_speed = 400 - if TIPREUSE == 'NO': - p300.drop_tip() if DRYRUN == 'NO' else p300.return_tip() - else: - p300.return_tip() - - if DRYRUN == 'NO': - protocol.delay(minutes=2) - - protocol.comment('MAGNET ENGAGE') - mag_block.engage(height_from_base=5) - - protocol.delay(minutes=4) - - protocol.comment('--> Transferring Supernatant') - - if NOMODULES == 'NO': - TransferSup = 30 - else: - TransferSup = 20 - if samplecolumns >= 1: # ---------------------------------------- - X = 'A7' - Y = 'A8' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 2: # ---------------------------------------- - X = 'A9' - Y = 'A10' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - if samplecolumns >= 3: # ---------------------------------------- - X = 'A11' - Y = 'A12' - p20.pick_up_tip() - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(sample_plate_mag[X].bottom(z=p20_offset_Mag)) - p20.aspirate(TransferSup / 2, rate=0.25) - p20.dispense( - TransferSup / 2, sample_plate_mag[Y].bottom(z=p20_offset_Mag)) - p20.move_to(bypass) - p20.drop_tip() if DRYRUN == 'NO' else p20.return_tip() - - if DRYRUN == 'NO': - protocol.comment('MAGNET DISENGAGE') - mag_block.disengage() diff --git a/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py b/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py index 57eb9e518a..7f5228cfa7 100644 --- a/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py +++ b/protocols/zymo-ribofree-cleanup/cleanup.ot2.apiv2.py @@ -8,7 +8,7 @@ MagBead Clean-up (robot 2)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py b/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py index 66db610837..f3d496ba68 100644 --- a/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py +++ b/protocols/zymo-ribofree-first-strand-cdna-synth-universal-depletion/1_first_strand_synth_uni_depletion.ot2.apiv2.py @@ -6,7 +6,7 @@ cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py b/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py index a2aeff63d1..693d013170 100644 --- a/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py +++ b/protocols/zymo-ribofree-library-index-pcr/4_library_index_pcr.ot2.apiv2.py @@ -7,7 +7,7 @@ PCR (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py b/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py index 227c59a304..d2f286d3d9 100644 --- a/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py +++ b/protocols/zymo-ribofree-p5-adapter-ligation/3_p5_adapter_ligation.ot2.apiv2.py @@ -7,7 +7,7 @@ Ligation (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py b/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py index bc7e8c565d..1caf96e0c0 100644 --- a/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py +++ b/protocols/zymo-ribofree-p7-adapter-ligation/2_p7_adapter_ligation.ot2.apiv2.py @@ -6,7 +6,7 @@ Ligation (robot 1)', 'author': 'Nick ', 'source': 'Custom Protocol Request', - 'apiLevel': '2.0' + 'apiLevel': '2.3' } diff --git a/protolib/parse/parseOT2v2.py b/protolib/parse/parseOT2v2.py index aa01e0d5b0..6ee662b420 100644 --- a/protolib/parse/parseOT2v2.py +++ b/protolib/parse/parseOT2v2.py @@ -2,6 +2,10 @@ import sys from pathlib import Path import opentrons +from opentrons.hardware_control import ( + API as HardwareAPI, + ThreadManager, + ) from opentrons.protocols.execution.execute import run_protocol from opentrons.protocols.parse import parse as parse_protocol from opentrons.protocols.context.simulator.protocol_context \ @@ -106,10 +110,14 @@ def parse(protocol_path): assert protocol.api_level >= (2, 0) # Use a simulating protocol context - context_impl = ProtocolContextSimulation() + sh_arg = ThreadManager(HardwareAPI.build_hardware_simulator).sync + + context_impl = ProtocolContextSimulation( + sync_hardware=sh_arg, api_version=protocol.api_level) context = opentrons.protocol_api.contexts.ProtocolContext( implementation=context_impl) + # NOTE:(IL, 2020-05-13)L there’s no deck calibration, and the # identity deck calibration is about 25 mm too high (as of v1.17.1). # Because of this, tall labware can cross the threshold and cause a diff --git a/protolib/parse/readme_map.json b/protolib/parse/readme_map.json index 956dafea57..281282cc16 100644 --- a/protolib/parse/readme_map.json +++ b/protolib/parse/readme_map.json @@ -61,6 +61,10 @@ "thermocycler": { "displayText": "Opentrons Thermocycler Module", "link": "https://shop.opentrons.com/thermocycler-module-1/" + }, + "heatershaker": { + "displayText": "Opentrons Heater-Shaker Module", + "link": "https://shop.opentrons.com/heater-shaker-module/" } } }