Updated metadata.

Author: daemontus

models/[id-001]__[var-302]__[in-19]__[SIGNALING-IN-MACROPHAGE-ACTIVATION]/metadata.json

@@ -1 +1,17 @@
-{"id": 1, "name": "SIGNALING-IN-MACROPHAGE-ACTIVATION", "url-publication": "https://doi.org/10.1186/1752-0509-2-36", "url-model": "https://research.cellcollective.org/?dashboard=true#module/1582:1/signaling-in-macrophage-activation/1", "keywords": ["cell-collective", "curated", "repaired", "grn-principles"], "variables": 302, "inputs": 19, "regulations": 533}
+{
+    "id": 1,
+    "name": "SIGNALING-IN-MACROPHAGE-ACTIVATION",
+    "url-publication": "https://doi.org/10.1186/1752-0509-2-36",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/1582:1/signaling-in-macrophage-activation/1",
+    "keywords": [
+        "cell-collective",
+        "curated",
+        "repaired",
+        "grn-principles"
+    ],
+    "variables": 302,
+    "inputs": 19,
+    "regulations": 533,
+    "notes": "### Modifications\n\nThe following changes have been made to make sure the regulatory graph is consistent with the network's update functions:\n\n - Regulation `IRF3_IRF7nucleus (S_289) -> IFNB1gene (S_185)` marked as non-essential.\n - Regulation `RELAp65_NFBK1p50nucleus (S_200) -> IFNB1gene (S_185)` marked as non-essential.\n - Regulation `ATF2 (S_170) -> IFNB1gene (S_185)` marked as non-essential.\n - Regulation `CBP (S_161) -> IFNB1gene (S_185)` marked as non-essential.",
+    "bib": "@article{bbm-001,\n  title={A logic-based diagram of signalling pathways central to macrophage activation},\n  author={Raza, Sobia and Robertson, Kevin A and Lacaze, Paul A and Page, David and Enright, Anton J and Ghazal, Peter and Freeman, Tom C},\n  journal={BMC systems biology},\n  volume={2},\n  number={1},\n  pages={1--15},\n  year={2008},\n  publisher={Springer}\n}"
+}

models/[id-002]__[var-130]__[in-9]__[SIGNAL-TRANSDUCTION-IN-FIBROBLASTS]/metadata.json

@@ -1 +1,16 @@
-{"id": 2, "name": "SIGNAL-TRANSDUCTION-IN-FIBROBLASTS", "url-publication": "https://doi.org/10.1073/pnas.0705088105", "url-model": "https://research.cellcollective.org/?dashboard=true#module/1557:1/signal-transduction-in-fibroblasts/1", "keywords": ["cell-collective", "curated", "repaired"], "variables": 130, "inputs": 9, "regulations": 557}
+{
+    "id": 2,
+    "name": "SIGNAL-TRANSDUCTION-IN-FIBROBLASTS",
+    "url-publication": "https://doi.org/10.1073/pnas.0705088105",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/1557:1/signal-transduction-in-fibroblasts/1",
+    "keywords": [
+        "cell-collective",
+        "curated",
+        "repaired"
+    ],
+    "variables": 130,
+    "inputs": 9,
+    "regulations": 557,
+    "notes": "### Modifications\n\nThe following changes have been made to make sure the regulatory graph is consistent with the network's update functions:\n\n - Regulation `PIP3_345 (S_91) -> RalGDS (S_5)` sign changed to `unknown`.\n - Regulation `PDK1 (S_28) -> RalGDS (S_5)` sign changed to `unknown`.\n - Regulation `PKA (S_80) -> MLCP (S_18)` sign changed to `unknown`.\n - Regulation `SAPK (S_26) -> SAPK (S_26)` sign changed to `unknown`.\n - Regulation `Crk (S_15) -> WASP (S_38)` marked as non-essential.\n - Regulation `Cas (S_48) -> Cas (S_48)` sign changed to `unknown`.\n - Regulation `PTEN (S_55) -> PTEN (S_55)` sign changed to `unknown`.\n - Regulation `Src (S_103) -> Cdc42 (S_57)` sign changed to `unknown`.\n - Regulation `Src (S_103) -> Csk (S_66)` sign changed to `unknown` and marked as non-essential.\n - Regulation `Fak (S_128) -> Csk (S_66)` sign changed to `unknown` and marked as non-essential.\n - Regulation `PKC (S_67) -> PKC (S_67)` sign changed to `unknown`.\n - Regulation `DAG (S_70) -> DAG (S_70)` sign changed to `unknown`.\n - Regulation `PKA (S_80) -> PKA (S_80)` sign changed to `unknown`.\n - Regulation `PIP3_345 (S_91) -> PIP3_345 (S_91)` sign changed to `unknown`.\n - Regulation `Src (S_103) -> Src (S_103)` sign changed to `unknown`.\n - Regulation `PP2A (S_130) -> IP3R1 (S_104)` sign changed to `unknown`.\n - Regulation `EGF (S_68) -> PTP1b (S_111)` sign changed to `unknown`.\n - Regulation `Mek (S_123) -> Mek (S_123)` sign changed to `unknown`.\n - Regulation `PAK (S_137) -> Mek (S_123)` marked as non-essential.\n - Regulation `Fak (S_128) -> Fak (S_128)` sign changed to `unknown`.\n",
+    "bib": "@article{bbm-002,\n  title={Emergent decision-making in biological signal transduction networks},\n  author={Helikar, Tom{\\'a}{\\v{s}} and Konvalina, John and Heidel, Jack and Rogers, Jim A},\n  journal={Proceedings of the National Academy of Sciences},\n  volume={105},\n  number={6},\n  pages={1913--1918},\n  year={2008},\n  publisher={National Acad Sciences}\n}"
+}

models/[id-003]__[var-19]__[in-1]__[MAMMALIAN-CELL-CYCLE]/metadata.json

@@ -1 +1,17 @@
-{"id": 3, "name": "MAMMALIAN-CELL-CYCLE", "url-publication": "https://doi.org/10.1186/1752-0509-3-1", "url-model": "https://research.cellcollective.org/?dashboard=true#module/1607:1/mammalian-cell-cycle/1", "keywords": ["cell-collective", "grn-principles", "curated", "repaired"], "variables": 19, "inputs": 1, "regulations": 51}
+{
+    "id": 3,
+    "name": "MAMMALIAN-CELL-CYCLE",
+    "url-publication": "https://doi.org/10.1186/1752-0509-3-1",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/1607:1/mammalian-cell-cycle/1",
+    "keywords": [
+        "cell-collective",
+        "grn-principles",
+        "curated",
+        "repaired"
+    ],
+    "variables": 19,
+    "inputs": 1,
+    "regulations": 51,
+    "notes": "### Modifications\n\nThe following changes have been made to make sure the regulatory graph is consistent with the network's update functions:\n\n - Regulation `CDK2 (S_2) -> pRB (S_18)` marked as non-essential.",
+    "bib": "@article{bbm-003,\n  title={Modeling {ERBB} receptor-regulated {G1/S} transition to find novel targets for de novo trastuzumab resistance},\n  author={Sahin, {\\\"O}zg{\\\"u}r and Fr{\\\"o}hlich, Holger and L{\\\"o}bke, Christian and Korf, Ulrike and Burmester, Sara and Majety, Meher and Mattern, Jens and Schupp, Ingo and Chaouiya, Claudine and Thieffry, Denis and others},\n  journal={BMC systems biology},\n  volume={3},\n  number={1},\n  pages={1--20},\n  year={2009},\n  publisher={BioMed Central}\n}"
+}

models/[id-004]__[var-225]__[in-22]__[ERBB-RECEPTOR-SIGNALING]/metadata.json

@@ -1 +1,17 @@
-{"id": 4, "name": "ERBB-RECEPTOR-SIGNALING", "url-publication": "https://doi.org/10.1371/journal.pone.0061757", "url-model": "https://research.cellcollective.org/?dashboard=true#module/1776:1/erbb-14-receptor-signaling/1", "keywords": ["cell-collective", "grn-principles", "curated", "repaired"], "variables": 225, "inputs": 22, "regulations": 1100}
+{
+    "id": 4,
+    "name": "ERBB-RECEPTOR-SIGNALING",
+    "url-publication": "https://doi.org/10.1371/journal.pone.0061757",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/1776:1/erbb-14-receptor-signaling/1",
+    "keywords": [
+        "cell-collective",
+        "grn-principles",
+        "curated",
+        "repaired"
+    ],
+    "variables": 225,
+    "inputs": 22,
+    "regulations": 1100,
+    "notes": "### Modifications\n\nThe following changes have been made to make sure the regulatory graph is consistent with the network's update functions:\n\n - Regulation `Mek (S_27) -> Mek (S_27)` sign set to `unknown`.\n - Regulation `PAK (S_205) -> Mek (S_27)` set as non-essential.\n - Regulation `Cas (S_29) -> Cas (S_29)` sign set to `unknown`.\n - Regulation `Rab5 (S_33) -> Rab5 (S_33)` sign set to `unknown`.\n - Regulation `ErbB2_ErbB3 (S_40) -> ErbB2_ErbB3 (S_40)` sign set to `unknown`.\n - Regulation `DAG (S_49) -> DAG (S_49)` sign set to `unknown`.\n - Regulation `Crk (S_165) -> WASP (S_56)` set as non-essential.\n - Regulation `PKA (S_62) -> PKA (S_62)` sign set to `unknown`.\n - Regulation `Src (S_190) -> Cdc42 (S_71)` sign set to `unknown`.\n - Regulation `PIP3_345 (S_79) -> PIP3_345 (S_79)` sign set to `unknown`.\n - Regulation `Hsp90 (S_88) -> Hsp90 (S_88)` sign set to `unknown`.\n - Regulation `Rac (S_194) -> E_cadherin (S_120)` sign set to `unknown`.\n - Regulation `Cdc42 (S_71) -> E_cadherin (S_120)` sign set to `unknown`.\n - Regulation `p120_catenin (S_192) -> E_cadherin (S_120)` sign set to `unknown`.\n - Regulation `Fak (S_121) -> Fak (S_121)` sign set to `unknown`.\n - Regulation `PKA (S_62) -> MLCP (S_142)` sign set to `unknown`.\n - Regulation `Ca (S_81) -> IQGAP1 (S_145)` sign set to `unknown`.\n - Regulation `PP2A (S_162) -> IP3R1 (S_148)` sign set to `unknown`.\n - Regulation `PIP3_345 (S_79) -> RalGDS (S_159)` sign set to `unknown`.\n - Regulation `PDK1 (S_220) -> RalGDS (S_159)` sign set to `unknown`.\n - Regulation `EGFR_EGFR (S_106) -> EGFR_Free (S_163)` sign set to `unknown`.\n - Regulation `EGFR_EGFR_EGF_PM (S_153) -> EGFR_Free (S_163)` sign set to `unknown`.\n - Regulation `EGFR_ErbB2 (S_168) -> EGFR_Free (S_163)` sign set to `unknown`.\n - Regulation `EGFR_EGFR_TGFa_PM (S_107) -> EGFR_Free (S_163)` sign set to `unknown`.\n - Regulation `EGFR_ErbB3 (S_86) -> EGFR_Free (S_163)` sign set to `unknown`.\n - Regulation `SAPK (S_167) -> SAPK (S_167)` sign set to `unknown`.\n - Regulation `PKC (S_195) -> PKC (S_195)` sign set to `unknown`.\n - Regulation `EGFR_Y992 (S_211) -> EGFR_Y992 (S_211)` sign set to `unknown`.\n - Regulation `Fak (S_121) -> Csk (S_243)` set as non-essential.\n - Regulation `Src (S_190) -> Csk (S_243)` set as non-essential.\n - Regulation `Spry2 (S_78) -> Cbl_RTK (S_245)` sign set to `unknown`.\n",
+    "bib": "@article{bbm-004,\n  title={A comprehensive, multi-scale dynamical model of {ErbB} receptor signal transduction in human mammary epithelial cells},\n  author={Helikar, Tom{\\'a}{\\v{s}} and Kochi, Naomi and Kowal, Bryan and Dimri, Manjari and Naramura, Mayumi and Raja, Srikumar M and Band, Vimla and Band, Hamid and Rogers, Jim A},\n  journal={PloS one},\n  volume={8},\n  number={4},\n  pages={e61757},\n  year={2013},\n  publisher={Public Library of Science}\n}"
+}

models/[id-005]__[var-28]__[in-0]__[FA-BRCA-PATHWAY]/metadata.json

@@ -1 +1,17 @@
-{"id": 5, "name": "FA-BRCA-PATHWAY", "url-publication": "https://doi.org/10.1093/bioinformatics/bts036", "url-model": "https://research.cellcollective.org/?dashboard=true#module/1778:1/fa-brca-pathway/1", "keywords": ["cell-collective", "grn-principles", "curated", "repaired"], "variables": 28, "inputs": 0, "regulations": 123}
+{
+    "id": 5,
+    "name": "FA-BRCA-PATHWAY",
+    "url-publication": "https://doi.org/10.1093/bioinformatics/bts036",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/1778:1/fa-brca-pathway/1",
+    "keywords": [
+        "cell-collective",
+        "grn-principles",
+        "curated",
+        "repaired"
+    ],
+    "variables": 28,
+    "inputs": 0,
+    "regulations": 123,
+    "notes": "### Modifications\n\nThe following changes have been made to make sure the regulatory graph is consistent with the network's update functions:\n\n - Regulation `FAcore (S_17) -> PCNATLS (S_5)` set as non-essential.\n - Regulation `FANCD2I (S_4) -> MRN (S_8)` sign set to `unknown`.\n - Regulation `ATR (S_27) -> NHEJ (S_9)` sign set to `unknown`.\n - Regulation `ssDNARPA (S_16) -> NHEJ (S_9)` sign set to `unknown`.\n - Regulation `FAN1 (S_28) -> XPF (S_20)` sign set to `unknown`.\n - Regulation `FANCD2I (S_4) -> XPF (S_20)` sign set to `unknown`.\n",
+    "bib": "@article{bbm-005,\n  title={A Boolean network model of the {FA/BRCA} pathway},\n  author={Rodriguez, Alfredo and Sosa, David and Torres, Leda and Molina, Bertha and Frias, Sara and Mendoza, Luis},\n  journal={Bioinformatics},\n  volume={28},\n  number={6},\n  pages={858--866},\n  year={2012},\n  publisher={Oxford University Press}\n}"
+}

models/[id-006]__[var-62]__[in-6]__[HGF-SIGNALING-IN-KERATINOCYTES]/metadata.json

@@ -1 +1,16 @@
-{"id": 6, "name": "HGF-SIGNALING-IN-KERATINOCYTES", "url-publication": "https://doi.org/10.1093/bioinformatics/bts410", "url-model": "https://research.cellcollective.org/?dashboard=true#module/1969:1/hgf-signaling-in-keratinocytes/1", "keywords": ["cell-collective", "grn-principles", "curated"], "variables": 62, "inputs": 6, "regulations": 103}
+{
+    "id": 6,
+    "name": "HGF-SIGNALING-IN-KERATINOCYTES",
+    "url-publication": "https://doi.org/10.1093/bioinformatics/bts410",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/1969:1/hgf-signaling-in-keratinocytes/1",
+    "keywords": [
+        "cell-collective",
+        "grn-principles",
+        "curated"
+    ],
+    "variables": 62,
+    "inputs": 6,
+    "regulations": 103,
+    "notes": "### Modifications\n\nThe model is given without modifications.",
+    "bib": "@article{bbm-006,\n  title={Boolean approach to signalling pathway modelling in {HGF}-induced keratinocyte migration},\n  author={Singh, Amit and Nascimento, Juliana M and Kowar, Silke and Busch, Hauke and Boerries, Melanie},\n  journal={Bioinformatics},\n  volume={28},\n  number={18},\n  pages={i495--i501},\n  year={2012},\n  publisher={Oxford University Press}\n}"
+}

models/[id-007]__[var-5]__[in-0]__[CORTICAL-AREA-DEVELOPMENT]/metadata.json

@@ -1 +1,15 @@
-{"id": 7, "name": "CORTICAL-AREA-DEVELOPMENT", "url-publication": "https://doi.org/10.1371/journal.pcbi.1000936", "url-model": "https://research.cellcollective.org/?dashboard=true#module/2035:1/cortical-area-development/1", "keywords": ["cell-collective", "curated"], "variables": 5, "inputs": 0, "regulations": 14}
+{
+    "id": 7,
+    "name": "CORTICAL-AREA-DEVELOPMENT",
+    "url-publication": "https://doi.org/10.1371/journal.pcbi.1000936",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/2035:1/cortical-area-development/1",
+    "keywords": [
+        "cell-collective",
+        "curated"
+    ],
+    "variables": 5,
+    "inputs": 0,
+    "regulations": 14,
+    "notes": "### Modifications\n\nThe model is given without modifications.",
+    "bib": "@article{bbm-007,\n  title={A Boolean model of the gene regulatory network underlying Mammalian cortical area development},\n  author={Giacomantonio, Clare E and Goodhill, Geoffrey J},\n  journal={PLoS Comput Biol},\n  volume={6},\n  number={9},\n  pages={e1000936},\n  year={2010},\n  publisher={Public Library of Science}\n}"
+}

models/[id-008]__[var-25]__[in-3]__[DEATH-RECEPTOR-SIGNALING]/metadata.json

@@ -1 +1,19 @@
-{"id": 8, "name": "DEATH-RECEPTOR-SIGNALING", "url-publication": "https://doi.org/10.1371/journal.pcbi.1000702", "url-model": ["https://research.cellcollective.org/?dashboard=true#module/2084:1/death-receptor-signaling/1", "http://ginsim.org/node/227"], "keywords": ["cell-collective", "ginsim", "curated"], "variables": 25, "inputs": 3, "regulations": 45}
+{
+    "id": 8,
+    "name": "DEATH-RECEPTOR-SIGNALING",
+    "url-publication": "https://doi.org/10.1371/journal.pcbi.1000702",
+    "url-model": [
+        "https://research.cellcollective.org/?dashboard=true#module/2084:1/death-receptor-signaling/1",
+        "http://ginsim.org/node/227"
+    ],
+    "keywords": [
+        "cell-collective",
+        "ginsim",
+        "curated"
+    ],
+    "variables": 25,
+    "inputs": 3,
+    "regulations": 45,
+    "notes": "### Modifications\n\nThe model is given without modifications.",
+    "bib": "@article{bbm-008,\n  title={Mathematical modelling of cell-fate decision in response to death receptor engagement},\n  author={Calzone, Laurence and Tournier, Laurent and Fourquet, Simon and Thieffry, Denis and Zhivotovsky, Boris and Barillot, Emmanuel and Zinovyev, Andrei},\n  journal={PLoS Comput Biol},\n  volume={6},\n  number={3},\n  pages={e1000702},\n  year={2010},\n  publisher={Public Library of Science}\n}"
+}

models/[id-009]__[var-60]__[in-13]__[YEAST-APOPTOSIS]/metadata.json

@@ -1 +1,15 @@
-{"id": 9, "name": "YEAST-APOPTOSIS", "url-publication": "https://doi.org/10.3389/fphys.2012.00446", "url-model": "https://research.cellcollective.org/?dashboard=true#module/2135:1/yeast-apoptosis/1", "keywords": ["cell-collective", "curated"], "variables": 60, "inputs": 13, "regulations": 114}
+{
+    "id": 9,
+    "name": "YEAST-APOPTOSIS",
+    "url-publication": "https://doi.org/10.3389/fphys.2012.00446",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/2135:1/yeast-apoptosis/1",
+    "keywords": [
+        "cell-collective",
+        "curated"
+    ],
+    "variables": 60,
+    "inputs": 13,
+    "regulations": 114,
+    "notes": "### Modifications\n\nThe model is given without modifications.",
+    "bib": "@article{bbm-009,\n  title={Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations},\n  author={Kazemzadeh, Laleh and Cvijovic, Marija and Petranovic, Dina},\n  journal={Frontiers in physiology},\n  volume={3},\n  pages={446},\n  year={2012},\n  publisher={Frontiers}\n}"
+}

models/[id-010]__[var-13]__[in-2]__[CARDIAC-DEVELOPMENT]/metadata.json

@@ -1 +1,16 @@
-{"id": 10, "name": "CARDIAC-DEVELOPMENT", "url-publication": "https://doi.org/10.1371/journal.pone.0046798", "url-model": "https://research.cellcollective.org/?dashboard=true#module/2136:1/cardiac-development/1", "keywords": ["cell-collective", "curated", "repaired"], "variables": 13, "inputs": 2, "regulations": 37}
+{
+    "id": 10,
+    "name": "CARDIAC-DEVELOPMENT",
+    "url-publication": "https://doi.org/10.1371/journal.pone.0046798",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/2136:1/cardiac-development/1",
+    "keywords": [
+        "cell-collective",
+        "curated",
+        "repaired"
+    ],
+    "variables": 13,
+    "inputs": 2,
+    "regulations": 37,
+    "notes": "### Modifications\n\nTo ensure inputs are represented canonically in all models, identity regulation function was removed from the constant variable `exogen_CanWnt_I (S_13)`.",
+    "bib": "@article{bbm-010,\n  title={A boolean model of the cardiac gene regulatory network determining first and second heart field identity},\n  author={Herrmann, Franziska and Gro{\\ss}, Alexander and Zhou, Dao and Kestler, Hans A and K{\\\"u}hl, Michael},\n  journal={PloS one},\n  volume={7},\n  number={10},\n  pages={e46798},\n  year={2012},\n  publisher={Public Library of Science}\n}"
+}

models/[id-011]__[var-40]__[in-4]__[GUARD-CELL-ABSCISIC-ACID-SIGNALING]/metadata.json

@@ -1 +1,16 @@
-{"id": 11, "name": "GUARD-CELL-ABSCISIC-ACID-SIGNALING", "url-publication": "https://doi.org/10.1371/journal.pbio.0040312", "url-model": "https://research.cellcollective.org/?dashboard=true#module/2161:1/guard-cell-abscisic-acid-signaling/1", "keywords": ["cell-collective", "curated", "repaired"], "variables": 40, "inputs": 4, "regulations": 78}
+{
+    "id": 11,
+    "name": "GUARD-CELL-ABSCISIC-ACID-SIGNALING",
+    "url-publication": "https://doi.org/10.1371/journal.pbio.0040312",
+    "url-model": "https://research.cellcollective.org/?dashboard=true#module/2161:1/guard-cell-abscisic-acid-signaling/1",
+    "keywords": [
+        "cell-collective",
+        "curated",
+        "repaired"
+    ],
+    "variables": 40,
+    "inputs": 4,
+    "regulations": 78,
+    "notes": "### Modifications\n\nThe following changes have been made to make sure the regulatory graph is consistent with the network's update functions:\n\n - Regulation `NO (S_23) -> KOUT (S_11)` sign set to `unknown`.\n - Regulation `pH (S_31) -> KAP (S_35)` sign set to `unknown`.",
+    "bib": "@article{bbm-011,\n  title={Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling},\n  author={Li, Song and Assmann, Sarah M and Albert, R{\\'e}ka},\n  journal={PLoS Biol},\n  volume={4},\n  number={10},\n  pages={e312},\n  year={2006},\n  publisher={Public Library of Science}\n}"
+}