0bc358 2

protocols/0bc358-2/0bc358-2.ot2.apiv2.py

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+from opentrons import protocol_api
+
+metadata = {
+    'apiLevel': '2.13',
+    'protocolName': '#2 Making Calibrator levels in 20 ml Scintillation vials',
+    'description': '''This protocol creates calibrators from Working Stocks by performing a dilutional series in methanol.''',
+    'author': 'Parrish Payne <[email protected]>'
+    }
+
+# Calibrator 10 (C10)=WS1 in A1
+# C9=2000ul from C10+2000ul MeOH, mix in A2
+# C8=2000ul from C9+2000ul MeOH, mix in A3
+# C7=2000ul from C8+3000ul MeOH, mix in A4 (email Aug 10)
+# C6=2000ul from C7+2000ul MeOH, mix in B1
+# C5=2000ul from C6+2000ul MeOH, mix in B2
+# C4=2000ul from C5+3000ul MeOH, mix in B3 (email Aug 10)
+# C3=2000ul from C4+2000ul MeOH, mix in C1
+# C2=2000ul from C3+2000ul MeOH, mix in C2
+# C0=2000ul pure MeOH in C3
+# pure MeOH used as source vial in C4
+# Repeat for WS2, WS3 and WS4
+
+
+def run(protocol: protocol_api.ProtocolContext):
+
+    tips = [protocol.load_labware('opentrons_96_filtertiprack_1000ul', 1)]
+    scint_vial = protocol.load_labware('chemglass_11x20mL', 2)
+
+    p1000 = protocol.load_instrument(
+        'p1000_single_gen2', 'right', tip_racks=tips)
+
+    def slow_withdraw(pip, well, z=0, delay_seconds=0):
+        pip.default_speed /= 10
+        if delay_seconds > 0:
+            protocol.delay(seconds=delay_seconds)
+        pip.move_to(well.top(z))
+        pip.default_speed *= 10
+
+    def transfer(pip, vol, source, destination):
+        pip.aspirate(vol, source)
+        slow_withdraw(pip, source)
+        pip.dispense(vol, destination)
+        slow_withdraw(pip, destination)
+
+    meoh = scint_vial.wells_by_name()['C4']
+    dilution_sources = [well for row in scint_vial.rows() for well in row][:8]
+    dilution_destinations = [well for row in scint_vial.rows() for well in row][1:9]
+    meoh_destinations = [well for row in scint_vial.rows() for well in row][1:10]
+    vols_meoh = [2000, 2000, 3000, 2000, 2000, 3000, 2000, 2000, 2000]
+
+    # pre-addition of meoh
+    p1000.pick_up_tip()
+    for d in meoh_destinations:
+        p1000.transfer(vols_meoh, meoh, d, new_tip='never', air_gap=20)
+    p1000.drop_tip()
+
+    dil_transfer_vol = 2000
+    for s, d in zip(dilution_sources, dilution_destinations):
+        p1000.pick_up_tip()
+        p1000.transfer(dil_transfer_vol, s, d.top(-5), new_tip='never', air_gap=20)
+        p1000.mix(5, 500, d.bottom(5))
+        p1000.drop_tip()

protocols/0bc358-2/README.md

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+# Protocol Title (#2 Making Calibrator levels in 20 ml Scintillation vials)
+
+### Author
+[Opentrons](https://opentrons.com/)
+
+## Categories
+* Sample Prep
+	* Standard Curve
+
+## Description
+This section of the README (especially the first paragraph) should grip a prospective user with the overarching purpose/flow of the protocol, but should not include fine details of the protocol steps themselves.
+
+### Labware
+* [OT-2 Filter Tips, 1000µL (999-00082)](https://shop.opentrons.com/opentrons-1000ul-filter-tips-1000-racks/)
+* [Chemglass 11-Position Block for 28 mm 20mL Scintillation Flat Bottom Vials](https://chemglass.com/blocks-for-centrifugal-vacuum-evaporators-optichem?sku=OP-6600-11)
+
+### Pipettes
+* [P1000 GEN2 Single Channel Pipette](https://shop.opentrons.com/single-channel-electronic-pipette-p20/)
+
+### Reagents
+* [Methanol](link to product not available)
+
+---
+
+### Deck Setup
+* If the deck layout of a particular protocol is more or less static, it is often helpful to attach a preview of the deck layout, most descriptively generated with Labware Creator. Example:
+![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/bc-rnadvance-viral/Screen+Shot+2021-02-23+at+2.47.23+PM.png)
+
+### Reagent Setup
+* This section can contain finer detail and images describing reagent volumes and positioning in their respective labware. Examples:
+* Reservoir 1: slot 5
+![reservoir 1](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/1ccd23/res1_v2.png)
+
+
+---
+
+### Protocol Steps
+1. Transfer diluent volume of MeOH into empty scintillation vials in A2 - C3.
+2. Perform dilutional series starting with Working Stock in A1 through C2 creating specified calibrator levels.
+
+
+### 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
+0bc358-2

protocols/0bc358-2/labware/Chemglass 11x20mL Vial.json

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+{
+  "wells": {
+    "A1": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 17.6,
+      "y": 70.9,
+      "z": 4.2
+    },
+    "C1": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 17.6,
+      "y": 15.4,
+      "z": 4.2
+    },
+    "A2": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 48.1,
+      "y": 70.9,
+      "z": 4.2
+    },
+    "C2": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 48.1,
+      "y": 15.4,
+      "z": 4.2
+    },
+    "A3": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 78.6,
+      "y": 70.9,
+      "z": 4.2
+    },
+    "C3": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 78.6,
+      "y": 15.4,
+      "z": 4.2
+    },
+    "A4": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 109.1,
+      "y": 70.9,
+      "z": 4.2
+    },
+    "C4": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 109.1,
+      "y": 15.4,
+      "z": 4.2
+    },
+    "B1": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 33.3,
+      "y": 43,
+      "z": 4.2
+    },
+    "B2": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 63.8,
+      "y": 43,
+      "z": 4.2
+    },
+    "B3": {
+      "totalLiquidVolume": 20000,
+      "diameter": 26,
+      "shape": "circular",
+      "depth": 56.2,
+      "x": 94.3,
+      "y": 43,
+      "z": 4.2
+    }
+  },
+  "groups": [
+    {
+      "metadata": {
+        "displayName": "20 mL Scintillation Vial",
+        "displayCategory": "tubeRack",
+        "wellBottomShape": "flat"
+      },
+      "brand": {
+        "brand": " ",
+        "brandId": [
+          ""
+        ],
+        "links": [
+          ""
+        ]
+      },
+      "wells": [
+        "A1",
+        "C1",
+        "A2",
+        "C2",
+        "A3",
+        "C3",
+        "A4",
+        "C4"
+      ]
+    },
+    {
+      "metadata": {
+        "displayName": "20 mL Scintillation Vial",
+        "displayCategory": "tubeRack",
+        "wellBottomShape": "flat"
+      },
+      "brand": {
+        "brand": "",
+        "brandId": [
+          ""
+        ],
+        "links": [
+          ""
+        ]
+      },
+      "wells": [
+        "B1",
+        "B2",
+        "B3"
+      ]
+    }
+  ],
+  "brand": {
+    "brand": "chemglass",
+    "brandId": [],
+    "links": [
+      "https://chemglass.com/blocks-for-centrifugal-vacuum-evaporators-optichem?sku=OP-6600-11"
+    ]
+  },
+  "metadata": {
+    "displayName": "Chemglass 11x20mL Vial",
+    "displayCategory": "tubeRack",
+    "displayVolumeUnits": "mL",
+    "tags": []
+  },
+  "dimensions": {
+    "xDimension": 127.05,
+    "yDimension": 85.86,
+    "zDimension": 60.4
+  },
+  "parameters": {
+    "format": "irregular",
+    "isTiprack": false,
+    "isMagneticModuleCompatible": false,
+    "loadName": "chemglass_11x20ml"
+  },
+  "ordering": [
+    [
+      "A1",
+      "B1",
+      "C1"
+    ],
+    [
+      "A2",
+      "B2",
+      "C2"
+    ],
+    [
+      "A3",
+      "B3",
+      "C3"
+    ],
+    [
+      "A4",
+      "C4"
+    ]
+  ],
+  "namespace": "custom",
+  "version": 1,
+  "schemaVersion": 2,
+  "cornerOffsetFromSlot": {
+    "x": 0,
+    "y": 0,
+    "z": 0
+  }
+}

protocols/0bc358-3/#3 Quality Control Levels.py

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+from opentrons import protocol_api
+
+metadata = {
+    'apiLevel': '2.13',
+    'protocolName': '#3 Making Quality Control Levels in 20 ml Scintillation Vials',
+    'description': '''This protocol creates quality controls from Working Stocks by performing a dilutional series in methanol.''',
+    'author': '[email protected]'
+    }
+
+# WS1 in A1
+# Quality control 8 (QC8)= 3000ul WS1 + 1000 MeOH ul MeOH in A2
+# QC7=1500 ul QC8 + 1500 MeOH in A3
+# QC6=1200 ul QC8 + 3300 MeOH in A4
+# QC5=1500 ul QC6 + 2500 MeOH in B1
+# QC4=2000 ul QC5 + 2000 MeOH in B2
+# QC3=2000 ul QC4 + 3000 MeOH in B3
+# QC2=2000 ul QC3 + 3000 MeOH in C1
+# QC1=2000 ul QC2 + 2000 MeOH in C2
+# # pure MeOH in C4 used as source vial
+# Repeat for WS2, WS3 and WS4
+
+
+def run(protocol: protocol_api.ProtocolContext):
+
+    tips = [protocol.load_labware('opentrons_96_filtertiprack_1000ul', 1)]
+    scint_vial = protocol.load_labware('chemglass_11x20mL', 2)
+
+    p1000 = protocol.load_instrument(
+        'p1000_single_gen2', 'right', tip_racks=tips)
+
+    def slow_withdraw(pip, well, z=0, delay_seconds=2.0):
+        pip.default_speed /= 10
+        if delay_seconds > 0:
+            protocol.delay(seconds=delay_seconds)
+        pip.move_to(well.top(z))
+        pip.default_speed *= 10
+
+    def transfer(pip, vol, source, destination):
+        pip.aspirate(vol, source)
+        slow_withdraw(pip, source)
+        pip.dispense(vol, destination)
+        slow_withdraw(pip, destination)
+
+    meoh = scint_vial.wells_by_name()['C4']
+    dilution_sources = [
+        [well for row in scint_vial.rows() for well in row][0]] + [
+            [well for row in scint_vial.rows() for well in row][1]]*2 + [well for row in scint_vial.rows() for well in row][3:8]
+    dilution_destinations = [well for row in scint_vial.rows() for well in row][1:9]
+    meoh_destinations = [well for row in scint_vial.rows() for well in row][1:9]
+    vols_meoh = [1000, 1500, 3300, 2500, 2000, 3000, 3000, 2000]
+    vols_dilution = [3000, 1500, 1200, 1500, 2000, 2000, 2000, 2000]
+
+# pre-addition of meoh
+    p1000.pick_up_tip()
+    for vol, d in zip(vols_meoh, meoh_destinations):
+        p1000.transfer(vol, meoh, d, new_tip='never', air_gap=20)
+    p1000.drop_tip()
+
+    for vol, s, d in zip(
+            vols_dilution, dilution_sources, dilution_destinations):
+        p1000.pick_up_tip()
+        p1000.transfer(vol, s, d.top(-5), new_tip='never', air_gap=20)
+        p1000.mix(5, 500, d.bottom(5))
+        p1000.drop_tip()