From 04e4391cfd6fc337f7183ee72275a6d59735417c Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 16:33:06 +0530 Subject: [PATCH 1/8] revert --- Schema_V2 | 1 + 1 file changed, 1 insertion(+) create mode 160000 Schema_V2 diff --git a/Schema_V2 b/Schema_V2 new file mode 160000 index 0000000..23ee042 --- /dev/null +++ b/Schema_V2 @@ -0,0 +1 @@ +Subproject commit 23ee042b89ddd69c1f86ff4c37931dee6120a04c From 24fd39daf648bc8305d3b63ec2d2675065a2ced9 Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 17:18:11 +0530 Subject: [PATCH 2/8] delete Schema_V2 folder --- Schema_V2 | 1 - 1 file changed, 1 deletion(-) delete mode 160000 Schema_V2 diff --git a/Schema_V2 b/Schema_V2 deleted file mode 160000 index 23ee042..0000000 --- a/Schema_V2 +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 23ee042b89ddd69c1f86ff4c37931dee6120a04c From 694d38493c90f159f4f6cfb8f29632f5db22dea7 Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 17:40:40 +0530 Subject: [PATCH 3/8] Added Schema v2 version along with changes made to fidnsim,simWrapMoose and simWrapHillTau --- FindSim-Schema.json | 582 +++++++++++++--------- __pycache__/simError.cpython-38.pyc | Bin 0 -> 1179 bytes __pycache__/simWrap.cpython-38.pyc | Bin 0 -> 6409 bytes __pycache__/simWrapHillTau.cpython-38.pyc | Bin 0 -> 17304 bytes __pycache__/simWrapMoose.cpython-38.pyc | Bin 0 -> 22707 bytes findSim.py | 81 +-- simWrapHillTau.py | 4 +- simWrapMoose.py | 4 +- 8 files changed, 394 insertions(+), 277 deletions(-) create mode 100644 __pycache__/simError.cpython-38.pyc create mode 100644 __pycache__/simWrap.cpython-38.pyc create mode 100644 __pycache__/simWrapHillTau.cpython-38.pyc create mode 100644 __pycache__/simWrapMoose.cpython-38.pyc diff --git a/FindSim-Schema.json b/FindSim-Schema.json index cca5dc6..9454af8 100644 --- a/FindSim-Schema.json +++ b/FindSim-Schema.json @@ -1,247 +1,347 @@ { - "title" : "FindSim schema", - "description" : "This is a schema for descriptors of experiments used by the FindSim package.", - "type": "object", - "properties": { - "FileType": {"type": "string"}, - "Version": {"type": "string"}, - "Metadata": { - "type": "object", - "properties": { - "transcriber": {"type": "string"}, - "organization": {"type": "string"}, - "email": {"type": "string"}, - "source": { - "type": "object", - "properties": { - "sourceType": { - "type": "string", - "enum": ["paper", "inhouse", "database", "simulation", "other"] - }, - "PMID": {"type": "number"}, - "doi": {"type": "string"}, - "authors": {"type": "string"}, - "journal": {"type": "string"}, - "journalDetail": {"type": "string"}, - "year": {"type": "number"}, - "figure": {"type": "string"}, - "table": {"type": "string"} - }, - "anyOf": [ - {"required": ["sourceType", "PMID", "year"]}, - {"required": ["sourceType", "doi", "year"]} - ], - "additionalProperties": false - }, - "notes": { "type": "string" }, - "testModel": { "type": "string", - "description": "This is a reference model against which the findSim expt file should work, typically provided along with it." }, - "testMap": { "type": "string", - "description": "Map file to go along with expt file and reference model" - } - }, - "required": ["transcriber", "organization", "source"], - "additionalProperties": false - }, + "$schema": "http://json-schema.org/draft-07/schema#", + "title" : "FindSim schema", + "description" : "This is a schema for descriptors of experiments used by the FindSim package.", + "definitions": { + "entityDefinition": { "type": "object", + "properties": { + "name": { "type": "string" }, + "alias": { "type": "string" }, + "identifier-type": { "enum": ["UnitProt", "ChEMBL"] }, + "identifier": { "type": "string" }, + "notes": { "type": "string" } + }, + "required": ["name"], + "additionalProperties": false, + "dependencies": { + "identifier-type": ["identifier"] + } + } + }, + "type": "object", + "properties": { + "FileType": {"type": "string"}, + "Version": {"type": "string"}, + "Metadata": { + "type": "object", + "properties": { + "transcriber": {"type": "string"}, + "organization": {"type": "string"}, + "email": {"type": "string"}, + "source": { + "type": "object", + "properties": { + "sourceType": { + "type": "string", + "enum": ["paper", "inhouse", "database", "simulation", "personal_communication","other"], + "description": "If the source type, 1. \"paper\", specify PMID and/or Doi.\\n 2.\"database/inhouse\" a URL must be specified.\\n 3.\"personal_communication\" authors infomation should be specified and optional field like affiliation,basedon, year can be provided" + }, + "PMID": {"type": "number"}, + "doi": {"type": "string" }, + "url": {"type": "string"}, + "descriptor":{"type":"string"}, + "authors": {"type": "string"}, + "affiliation":{"type":"string"}, + "journal": {"type": "string"}, + "journalDetail": {"type": "string"}, + "year": {"type": "number"}, + "figure": {"type": "string"}, + "table": {"type": "string"} + }, + "oneOf": [ + { "properties": { + "sourceType": { "enum": ["database","inhouse"] }, + "url": { "type": "string" } + }, + "required": ["url"] + }, + {"properties": { + "sourceType": { "const": "paper" }, + "PMID": { "type": "number" }, + "doi": { "type": "string" } + }, + "anyOf": [ + { "required": ["PMID"] }, + { "required": ["doi"] } + ] + }, + {"properties": { + "sourceType": {"const": "simulation"}, + "descriptor": {"type": "string"}, + "authors": {"type": "string"} + }, + "required": ["authors"] + }, + {"properties": { + "sourceType": {"const": "personal_communication"}, + "authors": {"type": "string"}, + "affiliation": {"type": "string"}, + "basedon": {"type": "string"}, + "year": {"type": "number"} + }, + "required": ["authors","year"] + }, + {"properties": { + "sourceType": {"const": "other"}, + "doi": { "type": "string" }, + "year": {"type": "number"} + }, + "required": ["doi","year"] + } + ], + "additionalProperties": false + }, + "notes": { "type": "string" }, + "testModel": { "type": "string", + "description": "This is a reference model against which the findSim expt file should work, typically provided along with it." }, + "testMap": { "type": "string", + "description": "Map file to go along with expt file and reference model" + } + }, + "required": ["transcriber", "organization", "source"], + "additionalProperties": false + }, - "Experiment": { - "type": "object", - "properties": { - "design": { "type": "string", - "enum": ["TimeSeries", "DoseResponse", "BarChart", "DirectParameter" ] - }, - "species": { "type": "string" }, - "cellType": { "type": "string" }, - "samplePrep": { "type": "string" }, - "sampleType": { "type": "string" }, - "temperature": { "type": "number" }, - "notes": { "type": "string" } - }, - "required": ["design"], - "additionalProperties": false - }, + "Experiment": { + "type": "object", + "properties": { + "design": { "type": "string", + "enum": ["TimeSeries", "DoseResponse", "BarChart", "DirectParameter" ] + }, + "species": { "type": "string" }, + "cellType": { "type": "string" }, + "samplePrep": { "type": "string" }, + "sampleType": { "type": "string" }, + "temperature": { "type": "number" }, + "notes": { "type": "string" } + }, + "required": ["design"], + "additionalProperties": false + }, - "Stimuli":{ "type": "array", - "items": { - "type": "object", - "properties": { - "timeUnits": {"type": "string", - "enum": ["s", "sec", "min", "hr", "day", "ms", "msec", "us", "usec"] - }, - "quantityUnits": {"type": "string", - "enum": ["nM", "uM", "mM", "M", "#", "uV", "mV", "V", "pA", "nA", "uA", "Hz", "ratio"], - "description": "Hz is used for synaptic input at a given freq. Ratio comes up for neuromodulation of synaptic weight and channels" - }, - "entity": {"type": "string" }, - "label": { - "type": "string", - "description" : "label is used only by BarCharts. It uniquely identifies stimulus blocks. By default the BarChart uses the _entity_ name, but in case there are multiple stimuli involving the same entity the _label_ lets one give each a unique identifier." - }, - "field": {"type": "string", - "enum": ["conc", "inject", "Vm", "Vclamp", "rate", "weight","EPSP_peak","synInput"], - "description": "rate and weight are used for synaptic input" - }, - "isBuffered": {"type": "number" }, - "data": {"type": "array", - "items": { "type": "array", - "items": {"type": "number" }, - "minItems": 2, "maxItems": 2 - } - }, - "value": {"type": "number"} - }, - "required": ["quantityUnits", "entity", "field"], - "additionalProperties": false - } - }, + "Stimuli":{ "type": "array", + "items": { + "type": "object", + "properties": { + "timeUnits": {"type": "string", + "enum": ["s", "sec", "min", "hr", "day", "ms", "msec", "us", "usec"] + }, + "quantityUnits": {"type": "string", + "enum": ["nM", "uM", "mM", "M", "#", "uV", "mV", "V", "pA", "nA", "uA", "Hz", "ratio"], + "description": "Hz is used for synaptic input at a given freq. Ratio comes up for neuromodulation of synaptic weight and channels" + }, + "entity": {"$ref": "#/definitions/entityDefinition" }, + "label": { + "type": "string", + "description" : "label is used only by BarCharts. It uniquely identifies stimulus blocks. By default the BarChart uses the _entity_ name, but in case there are multiple stimuli involving the same entity the _label_ lets one give each a unique identifier." + }, + "field": {"type": "string", + "enum": ["conc", "inject", "Vm", "Vclamp", "rate", "weight","EPSP_peak","synInput"], + "description": "rate and weight are used for synaptic input" + }, + "isBuffered": {"type": "number" }, + "data": {"type": "array", + "items": { "type": "array", + "items": {"type": "number" }, + "minItems": 2, "maxItems": 2 + } + }, + "value": {"type": "number"} + }, + "required": ["quantityUnits", "entity", "field"], + "additionalProperties": false + } + }, - "Readouts":{ - "type": "object", - "properties": { - "timeUnits": {"type": "string", - "enum": ["s", "sec", "min", "hr", "day", "ms", "msec", "us", "usec"] - }, - "quantityUnits": {"type": "string", - "enum": ["nM", "uM", "mM", "M", "#", "uV", "mV", "V", "pA", "nA", "uA", "ratio"] - }, - "entities": {"type": "array", - "items": {"type": "string"} - }, - "field": {"type": "string" }, - "window": {"type": "object", - "properties": { - "startt": {"type": "number"}, - "endt": {"type": "number"}, - "dt": {"type": "number"}, - "operation": {"type": "string", - "enum": ["min", "max", "mean", "sdev", "oscPk", "oscVal"] - } - }, - "required": ["startt", "endt", "dt", "operation"], - "additionalProperties": false - }, - "settleTime": {"type": "number", - "minimum": 0.0, - "maximum": 5000 - }, - "normalization": {"type": "object", - "properties": { - "sampling": {"type": "string", - "enum": ["none", "start", "end", "min", "max", "each", "presetTime", "dose"] - }, - "time": {"type": "number"}, - "dose": {"type": "number"}, - "entities": {"type": "array", - "items": {"type": "string"}, - "minitems":1, - "description": "If the entities here are different from the primary readout entities, it is a ratio calculation. If they are the same, it is a normalization." - } - }, - "required": ["sampling", "entities"], - "additionalProperties": false - }, - "display": {"type": "object", - "properties": { - "useXlog": {"type": "boolean"}, - "useYlog": {"type": "boolean"}, - "plotDt": {"type": "number", "minimum": 1e-6} - }, - "additionalProperties": false - }, - "epsp": {"type": "object", - "description": "Params to define field recordings", - "properties": { - "epspFreq": {"type": "number", "minumum": 0}, - "epspWindow": {"type": "number", - "minimum": 1e-6, - "description": "Time window to search for peak." - }, - "electrodePosition": {"type": "array", - "items": {"type": "number" }, - "minItems": 2, "maxItems": 3, - "description": "position of recording electrode" - }, - "epspDepthIntegMin": {"type": "number" }, - "epspDepthIntegMax": {"type": "number" } - }, - "additionalProperties": false - }, - "data": {"type": "array", - "items": { "type": "array", - "items": {"type": "number" }, - "minItems": 2, "maxItems": 3 - } - }, - "bardata": {"type": "array", - "items": { "type": "object", - "properties": { - "stimulus": {"type": "array", - "items": {"type": "string"} - }, - "value": {"type": "number" }, - "stderr": {"type": "number" } - }, - "required": ["stimulus", "value", "stderr"] - }, - "minItems": 1 - }, - "paramdata": {"type": "array", - "items": { "type": "object", - "properties": { - "entity": {"type": "string"}, - "field": {"type": "string"}, - "units": {"type": "string", - "enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA"] - }, - "value": {"type": "number" }, - "stderr": {"type": "number" } - }, - "required": ["entity", "field", "units", "value"], - "additionalProperties": false - }, - "minItems": 1 - } - }, - "oneOf": [ - { "required": ["timeUnits", "quantityUnits", "entities", "field", "data"]}, - { "required": ["timeUnits", "quantityUnits", "entities", "field", "bardata"]}, - { "required": ["paramdata"]} - ], - "additionalProperties": false - }, + "Readouts":{ + "type": "object", + "properties": { + "timeUnits": {"type": "string", + "enum": ["s", "sec", "min", "hr", "day", "ms", "msec", "us", "usec"] + }, + "quantityUnits": {"type": "string", + "enum": ["nM", "uM", "mM", "M", "#", "uV", "mV", "V", "pA", "nA", "uA", "ratio"] + }, + "entity": {"$ref": "#/definitions/entityDefinition"}, + "field": {"type": "string" }, + "window": {"type": "object", + "properties": { + "startt": {"type": "number"}, + "endt": {"type": "number"}, + "dt": {"type": "number"}, + "operation": {"type": "string", + "enum": ["min", "max", "mean", "sdev", "oscPk", "oscVal"] + } + }, + "required": ["startt", "endt", "dt", "operation"], + "additionalProperties": false + }, + "settleTime": {"type": "number", + "minimum": 0.0, + "maximum": 5000 + }, + "normalization": {"type": "object", + "properties": { + "sampling": {"type": "string", + "enum": ["start", "end", "min", "max", "each", "presetTime", "dose"] + }, + "sampTime": {"type": "number"}, + "dose": {"type": "number"}, + "entity": { "$ref": "#/definitions/entityDefinition", + "minItems":1, + "description": "If the entities here are different from the primary readout entities, it is a ratio calculation. If they are the same, it is a normalization." + } + }, + "required": ["sampling"], + "additionalProperties": false, + "if":{ + "properties": { "sampling": { "const": "presetTime" } } + }, + "then": { + "required": ["sampling", "sampTime"] + + }, + "else": { + "if": { + "properties": { "sampling": { "const": "dose" } } + }, + "then": { + "required": ["sampling", "dose"], + "not":{"required":["sampTime"]} + }, + "else": { + "required": ["sampling"], + "allOf": [ + { "not": {"required": ["sampTime"] } }, + { "not": {"required": ["dose"] } } + ] + } + } + }, + "display": {"type": "object", + "properties": { + "useXlog": {"type": "boolean"}, + "useYlog": {"type": "boolean"}, + "plotDt": {"type": "number", "minimum": 1e-6} + }, + "additionalProperties": false + }, + "epsp": {"type": "object", + "description": "Params to define field recordings", + "properties": { + "epspFreq": {"type": "number", "minumum": 0}, + "epspWindow": {"type": "number", + "minimum": 1e-6, + "description": "Time window to search for peak." + }, + "electrodePosition": {"type": "array", + "items": {"type": "number" }, + "minItems": 2, "maxItems": 3, + "description": "position of recording electrode" + }, + "epspDepthIntegMin": {"type": "number" }, + "epspDepthIntegMax": {"type": "number" } + }, + "additionalProperties": false + }, + "data": {"type": "array", + "items": { "type": "array", + "items": {"type": "number" }, + "minItems": 2, "maxItems": 3 + } + }, + "bardata": {"type": "array", + "items": { "type": "object", + "properties": { + "stimulus": {"type": "array", + "items": {"type": "string"} + }, + "value": {"type": "number" }, + "stderr": {"type": "number" } + }, + "required": ["stimulus", "value", "stderr"] + }, + "minItems": 1 + }, + "paramdata": {"type": "array", + "items": { "type": "object", + "properties": { + "entity": {"$ref": "#/definitions/entityDefinition"}, + "field": {"type": "string"}, + "units": {"type": "string", + "enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA"] + }, + "value": {"type": "number" }, + "stderr": {"type": "number" } + }, + "required": ["entity", "field", "units", "value"], + "additionalProperties": false + }, + "minItems": 1 + } + }, + "oneOf": [ + { "required": ["timeUnits", "quantityUnits", "field", "data"]}, + { "required": ["timeUnits", "quantityUnits", "field", "bardata"]}, + { "required": ["paramdata"]} + ], + "additionalProperties": false + }, + + "Modifications":{ + "type": "object", + "properties": { + "subset": {"type": "array", + "items": {"$ref": "#/definitions/entityDefinition"} + }, + "itemsToDelete": {"type": "array", + "items": {"$ref": "#/definitions/entityDefinition"} + }, + "parameterChange": {"type": "array", + "items": {"type": "object", + "properties": { + "entity": {"$ref": "#/definitions/entityDefinition" }, + "field": {"type": "string" }, + "value": {"type": "number" }, + "units": {"type": "string", + "enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA", "none"] + } + }, + "required": [ "field", "value", "units"] + } + }, + "notes": {"type": "string" } + }, + "anyOf": [ + { "required": ["subset"] }, + { "required": ["itemsToDelete"] }, + { "required": ["parameterChange"] } + ], + "additionalProperties": false + } + }, + "required": ["Metadata", "Experiment", "Readouts"], + "additionalProperties": false, + "if": { + "required": [ "Experiment" ], + "properties": { + "Experiment": { + "required": ["design"], + "properties": + {"design": { "type": "string", "enum": ["DoseResponse", "BarChart"] } + } + } + } + }, + "then": { + "properties": { + "Readouts": { "required": [ "settleTime" ] } + } + }, + "else": { + "properties": { + "Readouts": { "not": { "required": [ "settleTime"] } } + } + } - "Modifications":{ - "type": "object", - "properties": { - "subset": {"type": "array", - "items": {"type": "string"} - }, - "itemsToDelete": {"type": "array", - "items": {"type": "string"} - }, - "parameterChange": {"type": "array", - "items": {"type": "object", - "properties": { - "enitity": {"type": "string" }, - "field": {"type": "string" }, - "value": {"type": "number" }, - "units": {"type": "string", - "enum": ["nM", "uM", "mM", "M", "#", "s", "sec", "1/s", "1/sec", "uV", "mV", "V", "pA", "nA", "uA", "none"] - } - }, - "required": ["entity", "field", "value", "units"] - } - }, - "notes": {"type": "string" } - }, - "anyOf": [ - { "required": ["subset"] }, - { "required": ["itemsToDelete"] }, - { "required": ["parameterChange"] } - ], - "additionalProperties": false - } - }, - "required": ["Metadata", "Experiment", "Readouts"], - "additionalProperties": false } diff --git a/__pycache__/simError.cpython-38.pyc b/__pycache__/simError.cpython-38.pyc new file mode 100644 index 0000000000000000000000000000000000000000..2599603aa8d5b9dbf0da06d71e554c5dc5686663 GIT binary patch literal 1179 zcmb_bL2uJA6n4^f>mnuwCk`B*Kxm}e($ZbfG@-GQO&r!9!Z`F|xv|%JBu=o?!BB78 zpV_bBo+}6b11J1a6*6&TpY*Kv{GQ+YY<)i4-1LaW!Ow^1-&=(Iz@Uz%4GyiDCwAdv zOil=QxO+pmE1c`b*yW9g_)SJ#LcGrZ!-EbS%S7x$4MwJ+)|n3SE6l$WCe|`9WTy5p zemgH_nXa8U%cbH%LlnT#j3o)fs&F@DGO1Nfs??#1CnnIs1X9_udqCIoy7$n=w(vR~ z_%M?Oa-B^zO95S`3&_r4`*bvl!tEU>W&-O@g)wX@)f7gP3lSGE(o(2GaEN3&PZ+)y zgz8f2OrQDdvXJFt>lYV)ae1Q|P4pYBqf;|6c=<_#G)dCTf^ zt!&#@s5BJgsTI&i8(1^=5f;vZP^T^;Wgq+9npDd+rBca)(&yN|n(KUfv?3C$vaw^+E1-XeQ9%~u!nt-LqH!Oo zXp!rRitlLrpB10wvS!0_ol;Y1N?+JuHFm2uwn`5D77|n}6_l19rD?|J3HlEx{XA#M zGNadVz{cGvcz=zfG}3)$%^;7q({`(!q2E9fJd16+jqqzMs?S>GYGnVkDcc9j>2Drm JFT7`S>o+Hh{L}yd literal 0 HcmV?d00001 diff --git a/__pycache__/simWrap.cpython-38.pyc b/__pycache__/simWrap.cpython-38.pyc new file mode 100644 index 0000000000000000000000000000000000000000..e514d4a7787655fd0c646fdd214211671adeafb7 GIT binary patch literal 6409 zcmb_gTaVku73NKsmG&ZEVtZ{TX45o|ob|eObF1s5No;T9B3?VuCUKOeDwi|T(o2!d z4CO={EegaAP@rgw0tNcg2m8?|TA+W2kL^R?w?5~o-x-P&rQODeQxZHgrF>;+w~nO?QSS+a1VSZM$HRiF1n7((}u1Wu$I@SKHeC_ zTcIcjc`rgE7j|paesjz5eTTTNob5ZFU*OtQO|J*;rd$@3QoY?Ylud5m3TKVs*> zvCMwVUci^*>_zqx$`kBm_6o|A>?iQ6SCa~`Altj}ul%x5o5OP*kGu;q0tn06Nb69| zP&M77cY~RrfCdzf4O(K>$k;B6t+)(cYgxOav(mPO_e%Eu$Ai0OT)j6pGVkm7qxOOJ zqV|sVu67eHkN3Ljd0x>4MHiVyL9m`Qyj~Cre$A883wqZ#ZzW|3XAa`8prpEzO5cgd z!5^0JE)0<7l2G+B>PfvHGVZ?}hTDTEsfa-kdwrf%{m@~mwiG$S>A&H^r{xAUndm;T z!ieZC8G;gTyBu!by5>afit6twOG=R+#y%{@=v0+!U-(0e4c2!WR;<Er>>6TtLYI*}V)h*r7t9XpBcMfGJ7XEa}sj`bQ1_7&p z{2?j;g1`d^yT-^6heycY1d@2F2PckArr)!u^^X1pvI_t*)^|>grChMP$cLQS1tzlyJtpx5+yHOeyR z&SEyglxff4$WzqdeuYY`ji5NwF@ZHm`SH7P1k>HNDOO{hnfHurcr@6IH_Qc8saX=drZIuKf{$ zaK-L=+-EDcV*hx>?uGFM`}F6#r-9lcIug{Icm^aX2`A|BWU-@ouLo)G8GdCI`ZCeI zSpetLACxZg9rRRyv4OBVtnVDoU@Wpufl28n54o4{f=~lgfaSSeb7bBFg!lDd8oSnR zX=K2ID6lAukYaz2L*A3r!1SFX)0k%VdbBX{GI~+snyI*C!HaocZiJUPe24ED zGNuH4zDhjZf&!E1pR_-Y^mNi`4L0T8;H*paS;_YHlU-(1i14=ru-Do zw*gPk>@X{G-rb_~k!Ar&632d;$9|DvO&kY{tCT{8E~@VdjDoLPX&x`j(7(+^GB=R? zeJs2C5mqf;aFrI@w;g|0t@`G`^I1#%a~l#et#aorw0|26ve2}R7|&%T89Omg>X8Ew-bw+P&KAicf+=lj5$^~cXG6~u$2801jJ_(k!@@x< zXAx-hoo)VZ+IWMOe!nRwkcZDK)6_DXa3DNX_|U}MLjd)#+vu9e^X7UFpK$%>XKDqd z6nLPg>2n5)xvuB?N{cV>Lk7cvEDrM4$3ejOWZ!)0!9`o}j4ulUbC*L{X6<`MJZ*g) zQ-iTCXqAy7O#A0qtQRrWTp9?0g+8sxe_Ifln|hjM<1qrSU3b`RCvdr1_m^2nfMPor zws;)-dq6la<_5^L9ma0?cLlwcGwkBA-Nu@h~M;z9&6Ol_{KN`e1)Q~aad)QIA z$VL*t*YpGgi%}1YCk76({y^Gp*x&R5>^aC08}7JUHf@UR zD8#uz{$nGqbZo?zk5BOKp0CZx_|gF@ zv}sJ^EWB!yy3;+Lo9fAy$~HL28ecF^Ogjc!`4bK2)2$HaSqfj6cq<(E%-#eDgMJ^N z5mu?hbZ`?>UJYy+_JJ>s!_W)2x18JDc2bFsZ}*wg}zi4!VZs40g`HlS~8#YN4}JB0o>K<9By-bTUE1`)m53j)eaMf>Y+K8R5~3Nx}A<_prfP| zV6!w7Pg1?!=|qmZ?eqwfs>F;!XWZ)eBWbLqXY;H1XHsZCO_S=y6xi1eftCi27WGI?1vu*=Jf3C6bbC=_K z?%nR}-aE6Dc$!NMQYefxapeR^n<6ldZjeH0;-pAFjTTJ}!%foyMT5dE21Wl!Tn9o^ zqXmNgkp^vlzvrFZ+uft=0PP;;otgK2-tXu8dFNi6nJMS+`_F$eyMF2`x!fP~W&G#h zk+T00_Bq$E(pq1)!+3Rl5Uz1D%gFLnD-PmzH%JNK zVG0+t?rA(1@yxZ@ao<~7e0*bfjg5@|@_2a$S2T|u335#fsAOYf?e}v)pS*H#cT_>S zxEEAWdAPe~OMyleRmHofW>gLLlA2X@+{@~an!~-K4y$?GtLlh4iu;T@rWSCospIMd z?z8F+brScwx>KFP{gAq-?pCMYx0-Y69(6Br4y*gr{kYGo2h@YOA5jhU5bj6SPpLDw zA5#yjMcfzE^XgIc3Di8U9#fx0&I$Fn`V{VWs3+8uxSv#?R-eKBPW6IXQlACnDfOcI zoO%jRcd4hUdjqSW1bhxZS2dLBLe`TdW?-M(BGS5{Znt_I!K>yJGWO%s$RZ+aY8 zR6~-p<}8?B+ez)O-or@d3_=V{_WX`bqhH+ zu#zf&9BZ|i-*mQIeJw61Cw7^4ldLWuJrfsiSg{AV0`joVgfz9z<|gt>%0)}k-dQls zmFyWc%3DRfhkHeTjrr)K$Pus?j>2O9W%GU7|b zC!0ZDRkqv@Ed7#wBOA4E_XU%gx zdv;K(q-HRi!sa22s3uQyXLBD|;n^gwX3?LmzbgG5&iZo`j3K&_^>;1nuRiK;*rF>f zqSeIRoWl%@Xm4)I#u&esIElMDk9=N74g+HKsJs;w`VPMX$io8pzY}NIi;wLsp!7Jd z6Sr9ZPZJL{PDsk!<4I8+M!layy?NBL^$F?W1Z$vd9%UiQj!4-PQg#Q*?m*cQlwCsE zQ7OA5WhYT~5@knG_5{j~Nm(dmccSc0lpRCa36w2J*;l3P6v|GaY{6hfIUk$UKquGJ2dU=_x2G9rs+y?wDZYH zDqNZ#S{S$E>(aCIvK98;2|wZ(GNyvT9G|N5-Yy2y>AmAW`k|dVYrSwS^_ad0CbM&L z3i!29n)JIp2)xvNUiSw52m%Hx(hi~zi>dvEb7?+q4N?cmW2twg1wPXbgVfn*wZqi; z0=QD@oI|>E=f||IgVq`vFI>Vs(mn>S?`CqE$vsT&WpW>r`;j#6O7oo{)Z`?o3lZLJ z#hNTBt?aLClomu};?~mLD6O4~qCiu2ij+(X>z!UJPQA^j7oKmg#c4&@=S#ib)}Wud z5!8z?PK%iLi{W}N&2I#;zJq-fs1dxYPx3jxq5G-BPE(JwAgD|rEm3Sd*9+FyQ+w-b zYKQ%_*pAjZJq+TmzKYwmPxsPa!YTNOD%ys#$ehp0!||upGMvF7DWK_8fAmxN24zmy0LIuG%N9Qxoqe z@aCetYL{&%lLS@Clhhu2Mr(xKxpP`VOpI(oPEgQ{rXLhFz*n^ zpbcD8s2y}n<$e#?tAM^Oto5j@( zjor1Yt#Bhqi@htGqNL>Ukh&X&uh>eZc@0XN!s3c)Nv3`iql^}j=1GDE)ct%H)vc%F41}C#1#6CHMvH%Kl~N(Fv7j}@se1?J?!c=V%8qC6<`x&zJ4r$ ztcPy$SmHqH+r$eSI12rOP?@aPZvd(Qs5g?rZJ>ymkkHx#lnW?G%1Nkg;M+>>LuXk( zfU)RPNK)s*b{Kt_Pu**+&LD_nGxduoX%uB6^s5B@B0=qqjnvjUwWBDtgJ5c5^%ns1 z>$sw$NXQe)xUhJmbk5qj`?d==zW)=nOPzJJeqY5)0^JNVt0op!M(7x88A6k?v$e#k z>L&n|2hFDpF;wLQ-@)R!?B{W_9{ zYgUNryMBYoPcvyU`57it=vSkOD5CF`b)i_KS;dMnEqg!tPqO(Eeq=5L#EfPwKJ$avs+7QRNB$P ziD3(XtnRn*fwf)T{)@x|6D=+a+e=HLGPS}u5-QQJVO@o2VEPQMM4*iqm_yE|FEDu? z3B);hR$9Dj{03R!+EpfS`DOuEDh z#b7&JhHB7s@ql{z%k0lygJz5jT+R;Qipl-pk5DugqxT0y1jFHih^&`#RNu@9rAh(S9B2x$(Dv0iI$kDY+&Ju z4YE4(PI3Ft*t>)GXU)EHA6LZe;!Z7~wW;mV`-o?X^CJoyXy#G8fRTPjtOWr?? z_X3!CL00GS?bE`_xoSli8B`WdC!k6&sp5u1L1Bc&_UY}p7zzv26u?sTP)-!bg&SaC z!0tkZ-Nm(Dw+kV<^JURrm;Bel)|F1+$31ai`P2ga-nt)AGpGFadsjALwuo)8=$~&Z z|9WrW8>#2F#qx-+24dW3xDUb@?R0{t#ee~W6k1uu%niYe6a@V+^5B}FlB#82MA(pv zHk}P1w21c0*ZaWln6LSRNUqlb{oim!WVAV;ZC%jT$ngar@6O4o?V3P~iLGK2qpkY; zV4owOg01UZLTnu*30Y|jKg=eUSmZdoGL$3q)a*L30|p1*%&sd>MM>dX00TM;T`#vu z=2pU1mXk7AZ5jEecPmLHu_14M7J6YZsR*lF2a6g#Z!afBK+c017NA+?_DV_h7B(5$ z8um3T0po^5haj`jCOu*X z&AnwoJmKVqKZv?>4>ngHXF_h?n9&dNnYfuc#CXwq3^yOCwT7>|gFgMEI$(tjCPcc_ zZT0&>s2cNvz|HC^)ZL&%W)H2CnA|K=SOl?XzJ(2T(kvT>32KVu`9cUqI*6LH1~d+g zau7A^qYQ8&f~QtnFSGNJs?oH2y|e&w)7LfSif(gQRELeMz{Bg13NrC2HKbx%7cKaI zp;km)CRZhcD~mXQSb#AGcbw?H)P<_fs-o-IPdp^i)?&xi?9AM3;Xlc#yq zKA=&*3P1TC%F8JKo+`zlmYdeG926;mLrZy87D~DoUdBrH zG#mjq5GWG%Lt;FQt|Cw3D9Y?5gjWn>Wk1!V3dkPrs9!%b%6}pBv?a*GMmQ$^YgkznoCQoG59KtAZKqJleF%C9wVC=l!_zB7+hyi++SpUqX`R zv3`(iqE4Mf1_ew%hJ=CBPt#qO76b=VyW7>DBY?fRF=el&mQJl{+di$1FU9A{SgEAt zDs@qb;rO#*EEtJkQ}cphk=^T%BJ;?p=OJ72ln;(;>|447Z+Agr+%dTmi{rgdu<9ZP zF;duW-~~*V7H(!==pCqGux^zd=Os9lznOc&|$v)B;RwAo_rN zX8a74@!S*R(<)<6<{;S}`+$&~ZsS1Mk}_JXnk#sKsw@gI)G(^X_8!g-Knx)G2Igk- zuJRB@C{dP#q6pyt0(M~ZEFfqPVs&GO0uyQ>);5E8vY<+FIjxLE;f;s$b4&g!y1mg3 zTb+zSflV1^aOL_iATP|w=pAI5YlBXU?)zvlbxoXp=bwzv&Ki(>AGYaoxjv=H}H>pEhov0i70 zJu^g8I3h;}3ZP5Mae=9Q)aTK_-{#iM;Q>B1_`b|pEO@3l1Eqzg z4`9l86VnAo0rn0G3(O+46{D<5mwQ-FY?ufohF#;Cy_s7%_uH{o=|>> z>Wgx=9Q|imPjjk}cz1}Q6~jnS?oIozFYH$0`OPC}VJ@lgc)>5^t=yM#pUQnPcPaNq zF092zRcY^-v4;^7%{jTv1=Dv@UdTNO%XxJ{=(fCkd8e>Qxw~`nOD!Ez5;3GED!hd3 zC>fW0L)acxGPU0Mh%^9SgUd(`Eb51|5Whji$ZzSumo^uD+Obp7wZ`$Z5)X9v%KG|+ zPOz5Ry(o4149a^^zXNX){6}xIqY45{Dr?#x*;kldM6 z<9Z)PqF@lb-0BNfA;!i)e;JBP6ueBs#e}`8Cdgy7n{g8fnhHX2TppN9gKl3!X2#F& zadd*(RimUA)~QOQWg(*L7je);|18H_V#SN5Of)9*?9p35W|hJ_+6h)M?I4UmpQ*ha zrB$>Nbg~^u?fB8uTA!kmbcQ34S@0~+Zg$f*~T=5F(d8} zigU;W5!kX8T#F3EAc?KwhGVwcHK(7_(jW?6U+c8GeMCRo z;fo>c<%8auv?3#1krPw@b2J%lkA1*S90Q$LevTehC+$QXadZ@eLrW2!uXcB85wrfy zK>vdMvoRQm(-9r%+kj0(bjZlz=zewT;{c&|I*{AUa}9TqaFV zvr&CYX*C>lUq&GRRh&19V91kg!S!L3TE^VT)-PTrs5I1W}J;aD|(Mf>kAW#{irU%1#4{IW5nRkHD zrdyfNjYwi6{=i6344srqy$Q+2*aWm8aRZ94_h`m5uz+xQ+v+2LA}QO=#;4(i%1> z588SnhVKUo6gFIZLdZ>c<_pvZIy(cy11c^Y_-vB7oPB`PQ#7y4c&uavTmqa2>5&?7y0^C? zO(J3#>wmyjzR6^2Z4PC1fm@k<^Z=KKB*^GAm8ZIOw0JQ5WyZ2!ZDQ-Vx}&9{QU*?h zGZ4Z8tv#D&fhgs9lb=}Gg5-(yW_ul(wAo`<G4eTks2_WhxNYv2wc+3al5;>WZqR_|9q$r%#h%mEJUx;g}PVC|rm@L&e~HDHA}gerL^1*3#Y0#Cs9Ce;v>Z)WAP z>QG~{a#(yW4qp|A79WnY&Z7q1?Z2G$LMQt#OWO#`VQ0Xmlfr5#{8PZ;;0&DGI)kJu z{o4YGqr2Q!X`LZDh*Dwfw(`*O572_UT4B0bJw z$i;(!RI5_}*^g z$Ubi|>gR~8j31X+Yph(J!H`3l9JqdxiO=NIOg_Wp#|}>a8-Qd!J}v4gJ+hiQg)p#Y z9_{OMe4XUW`kx{1B1w>fhMd^5tMH*N;JyF@mPa#;N3{k+)`Jeq)DS5Nb?U;gOlUvT zN9>3DIl=Qd_Yu`TYK^ECp)OFZjl*jDRQuRLTIE>{K$4cfJO=ruKu%CCA;W(RSRC7u zAe3pBhuCfiv@6u-fcnhA%6;l1T_YH_S(3h7y!|HL%JPP=F{szstjHVb^!M>rl{Zr6 z_whC(Z=g%iu(Mf{H_~Jdbn9%+;vj!fRpIj*r=+5q8P5?)s!wrnIWEwsE$H z!b8mvF1t@je|d!0f5;{eVEw@+r?LLfPr!P??h)$$B}mU;cjn62$8HLo+u?NT4aazm zh)og_#1^Rn*xN9*`0-1E^HoF{x#LD7Uh&vU**!~={$NfTuS;^uKEF0bFrV8wZA$_xWGESld_ zfGxvy3A>?q%SL~rcd}{-eQ%j34EX!KgK9qJ_R5t_an9Xd&0j#hoeR@!aID&c;CV~_ ziuss;F*yG!zVY!tksa~D7YRK4OWOg*@s%;+eKZQ5F52ircot10ts}D6)4|JaMC&Br zzV8t<>gvB|wG1T~Z89M!uN|$xM~6cT|CV`^ye_Sb4fR)u8pbj=$J5HN&}lsEM=)?8 zZQ64))_|tcw#Ka={$}w|#wBR*O>i{ChvcXZwm}YsXQBQZ4Atwe$)T7xaQwyNsYHad zi6;1DN4$Gg)WKmHgyG9cWj-fHTuHdyX;Xqvwf0K{7Jl(j4$gGZC`9y$AIH&a9ey99 znUOyGAKT{)B2w%V#|n7AWv`33{A0%gJ%^+G31cCYng4K1MX^+7pv69eV-Ho#A71)w zzP0_if?My;*5nUoDsMQVa~j8z;BtbwE9Np%tl%vimVn~#j!H`KeLz1NmTcqTZQ`zz zAS$ij%4663?Drhp5CcZcqZnSC>#O2v^Wn`wt_kyuPOZ@aIOq%zhwpW-AV35^n*@DE zZ4rRlF=OSAJ$&A$uYw2PMgZ*dK|&dmdi1@Hgi*84b{alnE}ehz8OL*I59xB)-pXJ zG`P{}UBL~*LEs&h^Jx7!>h}K82&~lR02|kW>*OlF)+M95K0HA%#FzbU!OYAyaC`M2 z@Z07<0;_R4jQ>OfvCQBPIfGr;;;0lR`S5Uu#&#R63_r`|p22x+=4@(c1|l&pMy6zt zT>J=5m{AKOq(cAvm@B@Dk0Ca|?76i(j{$5NVGYJGhA)>8I@F;-(jl%4M~FikJSW2L zhDC^yuJN45{)&#ZWyHqFe7JZSmiqU=cJ;qR(!f`Me5R<<$Cw;tZc+bhK8rJo8n6CW zOc)r~6eRlJA;}I=GnQ%yH?0nbNc2r9TV#HkXSnnwB>V;h-%a)Ted~yhjWzr(VV)Kk z7{aO3Ll`-AdmXql4jiSf8*U@6`W3Vj{ap$t9IF%s*!6i)aCO1^o5QV!ij-l3-R zD=4bzJR-+GdcfxF6V}OtE{N$~COjz+SNoA0u9+BJI6(T+_Yz51T^8GCGbRlBe#+CHw*@4A2-W6udHOGx!9gg8gV`G?(uTOz4 zH*6DOYuJ}BHmr+$rOwf~hhJJV&WSIr%d0#XIzU`=HLb3$ZVy@=QzG9$>t_M4SD1W( z$(u|9CR79EpsCh;8Zb$ie1*w*Ccnny>r8%w$!{|GZ6^Pa$v@So&9bq0lpP$4PJ%a>hX4$*o-Q&%8v)*a1F5dE9-E;AtFV}Fdc#nGbl;_Gzc+N{}jU#DsbyfA&%v!Avz=yC_8ruNB zln(S?!-M`Cd@CT>)4y)Q2zloI5_2o7tNqs6R%?SR>_rgPJlJJE=`7-v|Gq#zf7fpl zynYd}df@xw5Hg(|%OP-6zTn`8sP4*(&#zp*B;&l@a-`l_v$s#tJr?;$oU(~B(*&;; QJQ&-eydw6Dd>pg+zW|O}tpET3 literal 0 HcmV?d00001 diff --git a/__pycache__/simWrapMoose.cpython-38.pyc b/__pycache__/simWrapMoose.cpython-38.pyc new file mode 100644 index 0000000000000000000000000000000000000000..1e24616d9f2c5bcc49fa28f78609c90d153c8a2b GIT binary patch literal 22707 zcmb_^3v681ncmzxuRC{!!x2SM)Wi1GBetl>q@y@?%yn$pdc=w)T5HOWOe{0QIhWLs z^WwRemNg!3TFc$KMY3^&wA})Wlu8$Aou)~#-R*9R6b<@Fv%xmqEP_RFfwtQQNNN;K zlOot|-5}}r{pZebW+XdBw&dSp%JMzqxb9koeZX;jLTM0k6 zR#55ng#NhXj+Munrkq=LRi<3*lq7w;Jg&0k;&X}S;Z(vet-JbjR-(MiN_0}sB|eZ) z$?~p`?Rq}((L~dJKH*QO>bFN zHaRL^-lq!X{c5ayKo!de)p+?1RZ_cNOO)?a6KXe}cd1FW2TxB;sl9j}QqyW5o`=Y%y<&!g&2br+uRQJy-4=iMJpsKe^WYYBD4pSqDO-=mJI_aOb4x?A0Y=Zre0 zX7D_&l8cF%qp?Kkp6v1+~U=y3)SbY6bpm`#Q^<@q?Z!%EUacAWdZkkJy_J^sR%%VPSZlESW1HdCmL6#JnKm+g?JdrFk6*3S>lKzd zdvBvss}Gb~maJ3F>T)ov{b07%M6v%5e{-()76Et0ii&NGQ7^4*HmjV?0+LdjVXZ!6 zzm-IZw^9hsU5;4P!DP;A-O`9>5$B@(;HPi?_>V3wUwU-)mB}xE_&;@Cdvx{Q(+B_S ze}2I2MfN|s%C7!!qWV}ByVU<<+{W)Te!(PyZek6GWZiC0AcljpFM+L1E=1V{e>2pT zdO3Ics^2)>YP7={JIYn-l^|HCH2f%83m$vZijsc4@n%Agqp7!#&V`M({LU>dEml#l z^6bgEk&TSrCQ`-b!^-YbippJd^tpdlN{1ek&cO zyXhO&R;HU#DInep8~1PA-_2m@v-*BO4$=j37)!5Z8JE`6XdOAydTA@$O(H*Q@;5qY z<6svsw?a6}EOd^(a^Ke6ks}{FzxddP&Ne%bR|5aaiGj4I{Yv#plngePqhwnv+1}2= zK!HoGR{fS*@7U5{)8}GLa%ILr2Ywi(8$_H@;aaV(suiuyVQZoc5M-kgM!BY6TfMs6 z(t)gal&mNvTR7v$enn{@$Mel7Tdy_O0bx;A=~kN&o2R4M6p)MTm6efAjq(J63#L{T z+Z7PP5;z~35p+;~kcS2m-u=4NAYb2$J(3H>0-NK^XD|14hKefedf)A2%sl^oav8_S+p%XV!p@fwzU61e7o(58XKerRVE zMnDlWd{OUrfia zbZIW!bV@U42yT-|=r3FoFYmr^J-F@KVFn!ZNkSkX(hjqe3A~>(u`R%8ii>A=tpkaN zKqvvXOvw$T80byL(ECul=K!mL1ts|Yq6K{yV3p}c`HSZl&R=}y;?m{Eo{4r1yevKa z*yZz24M3_P!m_00OslRin31K8+?{cLjw?)3o&edMOc@+l04AKU^utIco*eq)TA#u% z_zwvDMA=e_G6pW2USQ5{eR@f=ros5|j2sk@Yi=Pq?f9maD)9Z^T| z+^yzCBCyJnu|%*({gQgGI)S#Q)V*pJW%jB$bswJ7>S6UhbrL!I)ce)_NZGGGpdP^U zfO-%I+W@?4gA3CgD2mYSoS{P;oY+qsptl#IrL;V_vbdC7UCUofoCgDA6pjn9#7(~qF`SJ)j9MFKn2*)ur2*=Xw&@#g_8x^YbE3J+-{%)mv5KZm+ex<^yeeo6XwBrVp|j zwEb#rrRFPd`MOu}fa7b;)mg9K(B-RsTuDgrvL834yh`X*n%6z$x5KLt;=B+g8|>C2 z6FxiCLQR2pXE!?T!3(dqYoHGpLABKkY5~U7T9G!I5KkB<;g`{#=r^^z8G5zQYgDd# z7)a9x4;@tWbuVmrsuoll%eB=_Op|3Wn_9D4-&B|m-UH9b5B;X3mrCGW^Xv7Uv7Unj z>c3oRwCnx}uO{QsXfD9Yth8El%N31bVd`F|rTBJ&BW|J*4~$xUXVtD&Uh+ArHpDIO za9sE>Q$`jZWA88U&M*vXnF2F9H*}&Xi4d|E@e|f;73b&5#1=42*IG+}83rHm*C2ra zAgs>BoNUL(?z=L_QxqWbrX}3an|5T+-WOT5k@FL|57)63Rfvm^{7d#h-aZ4o?j}0N zh7J<>M8MVT!vw5)@CYKkibC`{cf=*;J+m#X&A{WD8;(tr59yrfmsx1_fNZ6;i3N@s zI;jCBkj&izSmUfr=)7TewTCwJAp}vf?l*V1z9{S0{RRLI{NO2Or#IPilx?=2uGGL) zr}$cSbgLCoYAi!)y#783PmV4~HXh<{qaDFvi998*3H%qqsqhDR%r1c;cI?jN?bc|B z4imj`QBSkIOIQU6Xg~=f0`HGGWFP?Hjlr-$5CXr9eSM>w*v8&61t^FTDA*bxgO4LW z6TA^-RT{jtsbQ%MN&#&^4+XJ$%~>TcnKZc%vqe)Qd%GIwC)ewTy-`?~p1w>h9lG0j zA~6xv97+GW;SJa)P-6jgoqYxkj&;*v@rE7zu$$fZ#`E zmxfwA=Do5t`^uI#<273$umix>K>qzftonM_S~wR<0qX)KG%9WHEgtQdF~{H!ippr- zTOjjp(h#<-Y(9c18k`~34 zk%%&NQ_5qhkFZpFrQU*g>DGc;GYF}ofG`^BD5Lx;5WBGB!tz88_~LV1z{mlkBr(XI zr`QM;HI+sXIkF_c5m6TFO%fg@5kV(XFD;81C10x4N6%bwc%i?IRs%9x3AK#d*4IUzwO$qui3MC=|ZFX0@? zhQ<>m6EIk_bI<8Yley;AlsFG8u07&d?!7r%o%?=q|02-$kJL;dN|PsP>tDuJM5Wql zv!(ruwE!TxilOSKk*rA%jlll|V-)y>Iz$=&WwI8!$`rDBGZ_P=V>Qn9a_fvt0Oe$^ zQKov8C#;+Yq;l97P+L>WH43Bofi?RxmNPrp;5UENmA}m@qVp9OW3A}Zthd^+k zfg$)Sp&e3*B!0oKgF@7xFoWt;7}8ZTq!v_YX$dpfeZbgOR^A}Q0`4Zaa$Sc?HPDOP zO~5GNW>#{xkrStGxm_1!Ke?4h3u)c#=BY&1&5d%H+0J(Jfb2rIux3l@Ye;pv1*j3f z32d7S-EN_qy#eT@suuL1AnLY4H{W$`*f<|!TSZ{}WOqzTWDqOLD9X3gPH&H~7n8g3 z1nHkjf{{*=k-lO5mBe3$v;cW2`I^Hs1?C#FS7|9D??@T%j$#@p@u9(M?Y$s7yr7`?qo^KhCuR?dc$1VjQ$*3Tv|qbn3+r z)*et9r1HF?r5ELF<&1{+77mR&Cmb4uM&Zz0NXp>P3}z2__u-T2@5Wh&S7>$4bdWUbw9jUONEqyt|2V^=ySpR4F55X-#5 zWMmdptJMIR20j28o~LA?T9BiNpai#o1Pji&i_0UL#>{40K?u>8nc_3>7?8q>vYkjN zgjQdS4SElgsYcaD860A;!l24v7`x4s4DvEWo*Fqn1gg@t)di!VgUDagz}|gJM^K&s zqduB8-fT7dMHbOU#>`SrvCsD~IESE|_KEw+PB(}QMZc%-X7)Xj4KASv9qUXbh(!4T z0L^oaIdK|U$TvfgY&+=;ViUFlLQOnr3&ymQj#aYUWDy#`0{H1t3OsglBI{U(lO^O8 zK>S&21d9%IHiSiq>k0WhW`RZ^81U)~Nm6fM5pcoVpw>Lmg5wTvq90|H7T8w?}dSv(@Ejr3E9jUcs^A#Cuzq1i8Q!U%JbnhnEO|6ie9u8I(W zgNO(bm^4H{CBWW6lw0cy>H;7bAUSozyVUywlwItj-c^p0OJHPj0WT=V(!$IbI3k+_ zRs1PD%H!a1V1e%sJW8(n*C7MoEC>1plrW2MoiRDPrO~M>cIYBMfx}6Ww_tVdc-O_L za(KNzHrhXh(-3h&oI3K&dLp!yD7L`eWWwYc`C+63XtG;Q*AYJX3`)bq2l}7BnS243 zqowRtuK7B0GdOoIA{QKw$z@)%i5#lZ{vgb4y9#+X?JXDaeAmT^MYvV~zX9F`d`o`2 z2#K^H;{ja{z9uo0)4zq-xI&C=Zu|k>N(v>U2bLf2y#ZhB0*5dm?ZK3=mf9La{%)1u zo+R%hM#sCiis7DaacxQ!C>6)?F~(K#Hz50Vivaf@sd4ZziS50y0UR39^(45FdFau> zvrrONC5&L&%n&&tX0R{jyf`NG#t{yV31iuRGXX>B9ywyW)>EkWeW)@gj5NblM9LRX z?f~Y2@f+;bJQdg2Ej7N28k2DiNH3`IUDP-@RHKO9+=E%Cj9h~HP=Kl_)VH-0-Vv8g za~|QHH#nw&G0RckyYP0#sH-|hAcUIZW}Hd{fIWzbennk3L^tT9W?yd9X(a`4>tg`3 zjy=2DNy5_vN+RQC(ixkp*OoQ(gLCv{7<`4!Z^+t9E7Xvww`a7~cc5ua-X7i)R-j+z zD7!sxt;alwvoP!Smz4+yY0`d|naCN{Sxf?pBO2pm;yVkm($AlVxfA4?Rm zfQ(b2sMIzd;hV~YSu!?YfgpHpI|_Axw!s7~K}mrSs=V#IARB9&Dv7bRq7lEKpv$7w z{{p0LQ3(jQxs3iIS^{wlOQ==oIw+f?s0Nhbf)DtH$&JhBQU3cVw@b15^;Svk=_V(kY!$IkZG2Xc+0??hw`1k|9P|s-xvN2|{*vFh{DeIFxU7l; z9{Ot5yHxk#Y~pEOj*<6He*&PeG{7wm>X;`M+30MiWbmfxDQGn+Z;7R!Is}*iVtO-U^lq#aqNtZ;>rt#Sedf^61Py{V7C7F=<+qq@tKS4V<_Rc?)}R z26|0CFToOW1`>~1y~tK!lnG%2Hg<@CNObHA<7r(3@*ol{XFe>WEN7mSXOuB3 zRnC~j5mZ{v(|A(RA?**aQkoh?Y;<+;dH{Zmg49f2_%mo_xq~{&Z3h0caLsG9qkN;* zJWq#6>P63S1j%p}!!-~D{S-achjWmG)LgAe<>|#>b!J>7y2ug5 zV$BZ(O3RsNPjj0Mmrqt*fF?@uWE+13JFG=^sLJ-~MwD8Gmt~ZNs0dT1fzOz=2OSG* zjdD)FKxFgZV`IO=Ktu)!gr_%fV8H7?5)QjyED`tW4Q?@K8B)|0`vOgnKJxO9kTkD$FYG>E1>wvroag$@9=8WYGh`o~}0%A*~Q zyC}RpMhL=mH*4XSWB-&B!VKSfDL4<~Yy-7QJGBD+?xoO+i!uHTW6X5jfib!pKkJgm z|2+005548*!-Cp{li(P=WjBqyuf};_Mczag^P@(yOCtJ*VNvZyX-Ga~6@-vYE_8}L z3SfBTw@bbE9*cZV_~9K!SxCg?$a3GdJpC65kYt)WyL$Edu8w6#R2Dcl9eeI&2(isJ zqGvs~uY@}%wqUrwuELRVRlNR4VCK;E^#%;|a1aN%1N9L<0;5m|HHEpX^VfG;xqKD& zdm>;VPBidK^?L&EX;9w_m1}S$@Kr!d9GnWOEu7{msImv=0QwD3!z7MxG-tGp+Zzo2 za0`e#^sZe6ODN_1kOoH3bKP16gKC@taD0)v>BFg_^WR)C?A=mj9u{vnJ%ISax&b2# zRze2U^DsAVj&RNO8piZ7>z!Zm`niJ>=#9#FCcwx@oh9Z*KZ9#6y&hck;cW#w&PB>j z;Pv5Dzv|ul2#UcX5;74ACNIDuV6A7pvvuK2kb~aE$HR;OLj^en#}JIn7iv-3imuJN zK!SZrYN+%f!UKf~qvI6WLVPr~}xKu#VLwX9-cJLn>Q2eJrS*H%T@45Lf-u>3$hGH1d$AAdWXXEZ=-#^jer#M z^Pk<{cwFB^3}!bE53}okm$ARc;7tZ!L;!!sQ+UwUhkc9k?Fv{T!!64;jIMJLif5C( z$O?BswPgH9KXn+URB{!r50G2nv#uaN z!H*qkD=4SnEr#-tu%J=_^VrW%H4n2cSP}SXt$}TkC%n+*>994BElOSUAUC$krW0`Z zNUvocghCaL8n(*BDcOFC6{k2RWupld5!Km1+LMV7%H;&~2_v0xE9^pAp(*Vq95k^* z?tI6n-=c%k1T`9bZF>;vw0v@xRXk z*7eBhfM43sA$|87u?1NFwq#x?r#M|hsK{@Rj1zkEfq~3$z{VxMfYZs-ODX;^P9>#y zp4d^%`9SRQg{x@Z!dqF4XkYt*>PZi3jPZYok9$Txc>XO@%28 z8emeu>cA&@t$-h7YyEkYDt2+7V#^U%BBn#8*56=l1;?GW5?CWC1M{ejQZC+hnHpWF zBiAO-?ry@ev^j~oKT_E(xB1;T#YpI6;9O|Q?IlX!Q(Jjui*j}^m91N2nCUcCs$d59 zb)mu)8N3c<@%UB={q66T!0eBMbs_VA0LsZ?cYN&*^l&Fkz2j?lA?8W!5Mqa?6F7PH z)~@gf-i~&6-LNJ09>!o6oQ$hfY3Lv-_ zA!txC4)i}kl5R1$%wUBj;1I;jr*I9!$SawqIL<}RGSn8-$eC$~Axfld@d$#LdbzR; zEnj}cZwGCYRvt%p1A`6987Xv9Kg#|@=yrFCN6BjtcatwcX(znHA8|a%4#@F8WASgw zt7?T>&bsZttp6>OZ2!9cmWgyCSGuQEy$Y`+wtcbkaxYeEiU~F@B>q-V6tshCZwl~% zsrxg#4Sf=oER-*SF_4aftyFkDYYe1;Zg5Z=42lTK;=L^T#T2)^oQvmA^EL>@>( z`@9C}3xqwZckgf863gIyu^BaXBLqG>2%KdBpQXV|P#m!(4(x){b97^Z7Y~3*vMac@ zYTU#f0hTBu0z{1Q|2=v$TbTj0fLqmnpDEu#&~y4pa}xrSPFx>lnLyZ*eH-EButW8_ zEbb?`xFu9DW^9VhWW!2!XKILM^(zcvdMe_$E`sTQhzMOlcu`QEHkBc~@g|u4TXeU? zT1s7#T*T;!jT{QRx?8~X+C z#p)J85pO>ZJz@V|uy~%;paENiG6No(#@}q%0qlea<4twF=N=4SNimm38KacYzl#N> zilotiV|J9HSzQNAvzk#Fsx+7vicuO(>+51DHwaEtFVtTcuQ87?qB=ouTI}u>zCMQ_ zvSQUs?BHl`_@J!{A5w>)~>jtK{r@e~c&blc5nea%i;p8nSARwJpOE zAwY*cksx1DFVPj1eZ%3f#S?Di`|1nOxox>ydFa^S3%F(j%{&X^5D~6;x5a?My!hD~f!# zmjho!n9bzkalY~oa4=ji{v&I&$(uSb7Qo)UBmyzrzmY07&;^x4W+>2}^#{j~Izah$)q_)9#cQ|l;e>wwmr(D}`Pe6E`4;k$)T}4EB*<*RI*3hKFz6uDzB{QRVG?z?_7KcQ2reJ9Kr`i1oTQkDZ zWI!~Gzv)L&ILZO&jF8iFz;Jp15EXh$!($UUJur}Kv7ox7#rj8V1i}ffWYPr{U)>1H zE?YP&n`3ySO%Chh3^o{uRKzQ{I02)iyJRq)DD)Q5Oz;&_%a5R1VuC&v_=ok9I#b9t zV3Cadir%C29G$SC^Rstyrl5^+!CcX*$+9JTzjbg_mKp8w76t&A*$~_lh>$Rd^V%e0 z;MZp&6I=4;}&cz`zNdg9?c@*%atGd|i=pQa-L>!?J{XXy#Uy#N-1Sf#+%eB;N5t&i7O=Po{W>B-)6slC)jymRs$JB4UjZ`^L+12^f$4f0&TG8kpn zj&w+g&OkLa&Ia8Qv?Ckx2l119CPY3$pb6-)xAuT@HW4Ungdm#qx-I8pnNgshC~*`O z<_8u&1soL2q7XDY(AW_B0n0H49S-A@)_!?HXcW5G*akY|t>IsPw0B(!=7~_;!i%jNp{a!rOg|asRVAo%_zvOd9h# zFz0|2d7u=yAvr&La%GErOdK;@WnlFBoFG2GmE;$rc10=H(0L*kmjOQY7H{eyl#A@( z+K$zds?WzaSIAT;{lAf|r&xNCvBNB#46fs21VKne9PdwV23LD78g_^q*4Kng-qwbd zYlFzj9FB5}jah-4N9o^OmY^AsWX4?1`~WvpP#cE_t(x)1pETb1UHRq` z(ZEvD_}CjkHl;f#Z6I3!`lop93E=z`1{V5E4K66Ju$a*F5hcMmF1q7x-lg7@-p?s< zJaioI92`8Fvm-_E^|W&{_Br#J6#KHo3s_|)ALOSXs3gUwAl#+ca~1Kz($dCerEYTM zs}JU~>oUi;#y~T8i2?mu_2(G;V+Q}6!M|qk4F*&w>mM`tQwB+HZ<>L?hCs<4zRJFn z`sjlU?qM*)U}qsDM!KXwgy75g1t$?;OVjQh&OOd<=OfOzlXWh*$DBRRdmYy)Ip>_b zbI?h;N&HSDFYkKJxYQroSr_f}g@1)^Y4KCm4LF&6dI5Gw671O72FLLPwTNqQxq$;z z5+0QY@%0GWCvA{=IMb*U2oIcz+rC-OTZFyP= zeiZSS6Hh1pjwnI~S~exWBt7t37rh>ykL!M2aMF0I1`We&5-(`gCEx*&c^j6q;-}uws+@6=Y@hbV<+~PYJkj3c~ zL6|%Ux#lX53!6>sUkP1&^-9N)>?c>;UTnD^Q*I|Gx%keFtG~v^;?fPb<4VptKGEUM zz&Kv^?InqWd^!jpxPsFdo59C&KEc$_Ai#IN z+6DnpPAT&?Hk;V_9*%}}3tuT>umj8j$8Vs*Lp;g%BVz6f(F1{$hL^AD8AvNA`7iu% zYpa(|ODJs)nk@`LGFehWv*4%_`c%MCfKE6En($@{@GK5iV5O3PFWS}Z^;9q$rsc~i zd?#CWigox|B3zlKqhLzf0gELq$@69g%oy9Eu6wYp&PZFI#Yw>lVBNj6^07^}n!$Bz zj*eeqG3~~&n>ZWNGHs)SEq`aE& zntNsI1R}3&87cEVtXgNXm($N={sgo34`dDIBHnrb5cJHG7vgtJ@PI4uz2=)FCp>5> zj2klX>MTB4MH*tbA&;>`49EjT#m53j+Eh1*Ka=@Npm0oNmhdS6fj-_tE6a7G_m%By zEArJj^M10Ng@aU6wJYZR{iBe_Zqsjt*bLz?yh~ID7i!B(PrzJ-FIg>>v+zf& z1Id`LnlogfL>Jz2GZm6bIn zCW@SgVH}6E*&_t?po}2p@><2te<2I$*mmG7#fywaB|wlVCh4Lf>I1UL87JvDPR_|V U`|ukBK`xa(k?8%G9M75hKeO$(djJ3c literal 0 HcmV?d00001 diff --git a/findSim.py b/findSim.py index 3bf40d1..06b6223 100644 --- a/findSim.py +++ b/findSim.py @@ -166,7 +166,7 @@ def __init__( self, s ): if "label" in s: self.label = s["label"] else: - self.label = self.entities[0] + self.label = self.entities[0]['name'] if not self.data: if "value" in s: @@ -221,7 +221,7 @@ def configure( self, modelLookup ): """Sanity check on all fields. First, check that all the entities named in experiment have counterparts in the model definition""" #self.minInterval() - for i in self.entities: + for i in [self.entities[0]['name']]: #if not i.encode( 'ascii' ) in modelLookup: if not i in modelLookup: raise SimError( "Stim::configure: Error: object {} not defined in model lookup.".format( i ) ) @@ -254,7 +254,7 @@ def __init__( self, findsim, isPlotOnly = False ): self.timeScale = convertTimeUnits[self.timeUnits] self.quantityUnits = ro["quantityUnits"] self.quantityScale = convertQuantityUnits[self.quantityUnits] - self.entities = ro["entities"] + self.entities = ro["entity"] self.field = ro["field"] self.settleTime = ro.get("settleTime") if not self.settleTime: @@ -283,7 +283,7 @@ def __init__( self, findsim, isPlotOnly = False ): self.ratioReferenceValue = 1.0 if norm: self.useNormalization = True - self.ratioReferenceEntities = norm["entities"] + self.ratioReferenceEntities = norm["entity"] #if len( self.ratioReferenceEntities ) > 0 and not self.entities[0] in self.ratioReferenceEntities: self.normMode = norm["sampling"] if self.normMode == "none": @@ -291,7 +291,7 @@ def __init__( self, findsim, isPlotOnly = False ): elif self.normMode == "start": self.ratioReferenceTime = 0 elif self.normMode == "presetTime": - self.ratioReferenceTime = norm["time"] + self.ratioReferenceTime = norm["sampTime"] elif self.normMode == "each": self.ratioReferenceTime = -1 elif self.normMode == "dose": @@ -361,14 +361,15 @@ def plotCopy( self, entity, field): def configure( self, modelLookup ): """Sanity check on all fields. First, check that all the entities named in experiment have counterparts in the model definition""" - for i in self.entities: + for i in [self.entities['name']]: #if not i.encode("ascii") in modelLookup: if not i in modelLookup: raise SimError( "Readout::configure: Error: object {} not defined in model lookup.".format( i ) ) - for i in self.ratioReferenceEntities: - #if not i.encode("ascii") in modelLookup: - if not i in modelLookup: - raise SimError( "Readout::configure: Error: ratioReferenceEntity '{}' not defined in model lookup.".format( i ) ) + if len(self.ratioReferenceEntities) > 0: + for i in [self.ratioReferenceEntities['name']]: + #if not i.encode("ascii") in modelLookup: + if not i in modelLookup: + raise SimError( "Readout::configure: Error: ratioReferenceEntity '{}' not defined in model lookup.".format( i ) ) def digestSteadyStateRun( self, ref, ret ): if self.useNormalization: @@ -416,9 +417,9 @@ def displayPlots( self, fname, modelLookup, stims, hideSubplots, exptType, bigFo else: separator = "." if not deferPlot: - plt.figure( self.entities[0] + "." + self.field ) + plt.figure( self.entities['name'] + "." + self.field ) if "doseresponse" in exptType: - for i in stims[0].entities: + for i in [stims[0].entities[0]['name']]: #elms = modelLookup[i.encode("ascii")] #elms = modelLookup.get( i.encode("ascii") ) elms = modelLookup.get( i ) @@ -429,7 +430,7 @@ def displayPlots( self, fname, modelLookup, stims, hideSubplots, exptType, bigFo pp.plotme( fname, pp.ylabel, joinSimPoints = True, labelPos = labelPos ) elif "barchart" in exptType: - for i in self.entities: + for i in [self.entities['name']]: #elms = modelLookup[i.encode("ascii")] #elms = modelLookup.get( i.encode("ascii") ) elms = modelLookup.get( i ) @@ -615,7 +616,7 @@ def directParamScore( readouts, scoringFormula ): score = 0.0 numScore = 0.0 for d in readouts.directParamData: - entity = d["entity"] + entity = d['entity']["name"] qs = convertQuantityUnits[ d["units"] ] expt = d["value"] * qs sem = d["stderr"] * qs @@ -856,9 +857,13 @@ def __init__( self, findsim, mapFile ): mod = findsim.get( "Modifications" ) if mod: if "subset" in mod: - self.modelSubset = mod[ "subset" ] + #self.modelSubset = mod[ "subset" ] + for modelss in mod['subset']: + self.modelSubset.append(modelss["name"]) if "itemsToDelete" in mod: - self.itemsToDelete = mod[ "itemsToDelete" ] + #self.itemsToDelete = mod[ "itemsToDelete" ] + for modeli2D in mod['itemsToDelete']: + self.itemsToDelete.append(modeli2D["name"]) if "parameterChange" in mod: self.parameterChange = mod[ "parameterChange" ] @@ -916,7 +921,7 @@ def modify( self, erSPlist, modelWarning): #Function call for checking dangling Reaction/Enzyme/Function's sw.pruneDanglingObj( erSPlist) #print( "{}".format( self.parameterChange ) ) - sw.changeParams( [ [i["entity"], i["field"], i["value"] * convertQuantityUnits[ i["units"] ] ] for i in self.parameterChange] ) + sw.changeParams( [ [i["name"], i["field"], i["value"] * convertQuantityUnits[ i["units"] ] ] for i in self.parameterChange] ) ########################################################################## @@ -1017,7 +1022,7 @@ def doReadout( qe, model ): readout.plots, readout.plotDt, readout.numMainPlots = sw.fillPlots() doFepspReadout( readout ) elif val == -1: # This is a special event to get RatioReferenceValue - readout.ratioReferenceValue = sw.sumFields( readout.ratioReferenceEntities, readout.field ) + readout.ratioReferenceValue = sw.sumFields( [readout.ratioReferenceEntities['name']], readout.field ) else: doEntityAndRatioReadout(readout, readout.field) @@ -1062,12 +1067,12 @@ def doEpspReadout( readout ): readout.ratioData.append( v ) def doEntityAndRatioReadout( readout, field ): - sim = sw.sumFields( readout.entities, field ) + sim = sw.sumFields( [readout.entities['name']], field ) # print( "Appending simData: ", len( readout.simData ), len( readout.ratioData ) ) readout.simData.append( sim/readout.quantityScale ) ratioReference = 1.0 if readout.useNormalization: - ratioReference = sw.sumFields( readout.ratioReferenceEntities, field ) + ratioReference = sw.sumFields( [readout.ratioReferenceEntities['name']], field ) readout.ratioData.append( ratioReference ) def processReadouts( readouts, scoringFormula ): @@ -1179,12 +1184,18 @@ def runDoser( model, stim, readout ): responseList = [] EPS = 1e-9 for dose, response, sem in readout.data: - stimList.append( [ (stim.entities[0], stim.field, dose, stim.quantityScale), ] ) + stimList.append( [ (stim.entities[0]['name'], stim.field, dose, stim.quantityScale), ] ) if len( readout.ratioReferenceEntities ) > 0 and readout.ratioReferenceTime > EPS: # Add another entry for the global reference readout. - stimList.append( [ (stim.entities[0], stim.field, readout.ratioReferenceDose, stim.quantityScale), ] ) + stimList.append( [ (stim.entities[0]['name'], stim.field, readout.ratioReferenceDose, stim.quantityScale), ] ) #print( ">>>>>>>>> {} {} {} {}".format( stim.entities[0], stim.field, readout.ratioReferenceDose, stim.quantityScale ) ) - responseList = [ readout.entities, readout.field, readout.ratioReferenceEntities, readout.field ] + + if 'name' in readout.ratioReferenceEntities: + readout_ratioReferenceEntities = [readout.ratioReferenceEntities['name']] + else: + readout_ratioReferenceEntities = [] + responseList = [ [readout.entities['name']], readout.field, readout_ratioReferenceEntities, readout.field ] + #responseList = [ readout.entities, readout.field, readout.ratioReferenceEntities, readout.field ] ret, ref = sw.steadyStateStims( stimList, responseList, isSeries = True, settleTime = readout.settleTime ) if len( readout.ratioReferenceEntities ) > 0 and readout.ratioReferenceTime < EPS: # Special case where the extra entry is the value at reset time. @@ -1211,13 +1222,17 @@ def runBarChart( model, stims, readout ): stimSource = {} for s in stims: #print ("SSSSSSSSSSSSS= {}".format( s.data ) ) - stimEntry = ( s.entities[0], s.field, s.data[0][1], s.quantityScale ) + stimEntry = ( s.entities[0]['name'], s.field, s.data[0][1], s.quantityScale ) stimSource[ s.label ] = stimEntry for i in readout.bardata: stimLine = [ stimSource[ j ] for j in i["stimulus"] ] stimList.append( stimLine ) - - responseList = [ readout.entities, readout.field, readout.ratioReferenceEntities, readout.field ] + if 'name' in readout.ratioReferenceEntities: + readout_ratioReferenceEntities = [readout.ratioReferenceEntities['name']] + else: + readout_ratioReferenceEntities = "" + responseList = [ [readout.entities['name']], readout.field, readout_ratioReferenceEntities, readout.field ] + #responseList = [ readout.entities, readout.field, readout.ratioReferenceEntities, readout.field ] #print( responseList ) # Some fuzzy normalization stuff if readout.useNormalization and readout.normMode == "presetTime": @@ -1251,7 +1266,7 @@ def parseAndRunBarChart( model, stims, readouts ): class PlotPanel: def __init__( self, readout, exptType, xlabel = '', useBigFont=False ): self.name=[] - for i in readout.entities: + for i in [readout.entities['name']]: self.name.append( i ) self.exptType = exptType self.useXlog = readout.useXlog @@ -1311,6 +1326,7 @@ def plotbar( self, readout, stims, scriptName, labelPos = None ): simBar = plt.bar(barpos + width/2, self.sim, width, color='IndianRed', label='Sim') plt.xlabel( "Stimulus combinations", fontsize=self.labelFontSize) plt.ylabel( self.ylabel, fontsize = self.labelFontSize ) + scriptName = "FindSim comparison for: "+os.path.basename(scriptName) plt.title( scriptName, fontsize = self.labelFontSize ) plt.legend( loc=labelPos, fontsize = self.tickFontSize, frameon=False ) #ticklabels = [ i["stimulus"] for i in readout.bardata ] @@ -1383,7 +1399,7 @@ def saveTweakedModel( origFname, dumpFname, mapFile, scaleParam ): for i in scaleParam: sp.extend( i ) localSW.deleteSimulation() - localSW.loadModelFile( origFname, None, sp, dumpFname, "") + localSW.loadModelFile( origFname, silentDummyModify, sp, dumpFname, "") localSW.deleteSimulation() def dummyModify( erSPlist, modelWarning ): @@ -1541,7 +1557,7 @@ def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile = elapsedTime = time.time() - t0 if not hidePlot: - print( "Score = {:.3f} for\t{}\tElapsed Time = {:.1f} s".format( score, os.path.basename(exptFile), elapsedTime ) ) + print( "Score = {:.3f} for {} Elapsed Time = {:.1f} s".format( score, os.path.basename(exptFile), elapsedTime ) ) #plt.figure(1) #readouts.displayPlots( exptFile, model._tempModelLookup, stims, hideSubplots, expt.exptType, bigFont = bigFont ) #plt.show() @@ -1561,10 +1577,10 @@ def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile = model._tempModelLookup['vclamp'] = [vpath,] elif i.field.lower() == 'inject': readoutStim = i - if len(i.entities) > 0 and i.entities[0].lower() == 'syninput': + if len(i.entities) > 0 and i.entities[0]['name'].lower() == 'syninput': readoutStim = i if expt.exptType in ['barchart', 'doseresponse'] and i.isBuffered: - sw.changeParams( [( i.entities[0], "isBuffered", 1 ),] ) + sw.changeParams( [( i.entities[0]['name'], "isBuffered", 1 ),] ) if readouts.field in Readout.postSynFields: readouts.stim = readoutStim readoutVec = [readouts] @@ -1622,7 +1638,8 @@ def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile = deferPlot = deferPlot ) print( "Score= {:.4f} for {:34s} UserT= {:.1f}s, evalT= {:.3f}s".format( score, os.path.basename(exptFile), elapsedTime, sw.runtime ) ) if not deferPlot: - plt.show() + pass + #plt.show() ''' plt.figure( "Main FindSim Plots" ) diff --git a/simWrapHillTau.py b/simWrapHillTau.py index 37fef31..eb93e77 100644 --- a/simWrapHillTau.py +++ b/simWrapHillTau.py @@ -515,7 +515,7 @@ def makeReadoutPlots( self, readouts ): numPlots = 0 self.numMainPlots = 0 for i in readouts: - for j in i.entities: + for j in [i.entities['name']]: if not j in self.modelLookup: continue objList = self.modelLookup[ j ] @@ -535,7 +535,7 @@ def fillPlots( self ): # takes plots from sim and puts the numpy arrays of the p def deliverStim( self, qe ): field = qe.entry.field - for name in qe.entry.entities: + for name in [qe.entry.entities[0]['name']]: #print( "in deliver stim setting {} to {}".format( name, field, qe.val ) ) if not name in self.modelLookup: raise SimError( "SimWrapHillTau::deliverStim: Entity {} not found".format( name ) ) diff --git a/simWrapMoose.py b/simWrapMoose.py index 0078be0..88f3e94 100644 --- a/simWrapMoose.py +++ b/simWrapMoose.py @@ -571,7 +571,7 @@ def makeReadoutPlots( self, readouts ): self.numMainPlots = 0 for i in readouts: readoutElmPaths = [] - for j in i.entities: + for j in [i.entities['name']]: readoutElmPaths.extend( self.lookup(j) ) for elmPath in readoutElmPaths: ######Creating tables for plotting for full run ############# @@ -650,7 +650,7 @@ def fillPlots( self ): def deliverStim( self, qe ): field = qe.entry.field #field = model.fieldLookup[s.field] - for name in qe.entry.entities: + for name in [qe.entry.entities[0]['name']]: if not name in self.modelLookup: raise SimError( "simWrapMoose::deliverStim: entity '{}' not found, check object map".format( name ) ) elmPaths = self.modelLookup[name] From 00ab4ff5bb425c01cc2c9ccc9dc46cd54fac5ac6 Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 17:54:53 +0530 Subject: [PATCH 4/8] plot.show() is enabled --- findSim.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/findSim.py b/findSim.py index 06b6223..a571280 100644 --- a/findSim.py +++ b/findSim.py @@ -1638,8 +1638,7 @@ def innerMain( exptFile, scoreFunc = defaultScoreFunc, modelFile = "", mapFile = deferPlot = deferPlot ) print( "Score= {:.4f} for {:34s} UserT= {:.1f}s, evalT= {:.3f}s".format( score, os.path.basename(exptFile), elapsedTime, sw.runtime ) ) if not deferPlot: - pass - #plt.show() + plt.show() ''' plt.figure( "Main FindSim Plots" ) From 906c9e8a18b0eed2148ef7214ac426079cca9154 Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 21:23:36 +0530 Subject: [PATCH 5/8] converted all curated and Non-curated json files to new format and editing map file for supporting new format --- Non-Curated/Bhalla1999_Fig2C.json | 86 ++++++++---------------- Non-Curated/HH_Fig13.json | 64 ++++++------------ Non-Curated/HH_vclamp4.json | 106 ++++++++---------------------- Non-Curated/Jain2009_Fig2C.json | 50 +++++--------- Non-Curated/Jain2009_Fig2D_n.json | 70 ++++++++++++++++++++ Non-Curated/Jain2009_Fig3B.json | 62 +++++------------ Non-Curated/Jain2009_Fig4B.json | 102 +++++++--------------------- Non-Curated/Jain2009_Fig4F.json | 52 +++++---------- Non-Curated/PKC_SB_Fig7.json | 82 +++++++++++------------ Non-Curated/PKC_SB_Fig8.json | 93 ++++++++++++-------------- Non-Curated/directParamsDemo.json | 22 +++++-- models/synSynth7_map.json | 39 ++++++++++- 12 files changed, 355 insertions(+), 473 deletions(-) create mode 100644 Non-Curated/Jain2009_Fig2D_n.json diff --git a/Non-Curated/Bhalla1999_Fig2C.json b/Non-Curated/Bhalla1999_Fig2C.json index 0d0489c..983524f 100644 --- a/Non-Curated/Bhalla1999_Fig2C.json +++ b/Non-Curated/Bhalla1999_Fig2C.json @@ -25,7 +25,10 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Ca", + "entity" : { + "name": "Ca", + "alias": "Ca" + }, "field": "conc" } ], @@ -33,15 +36,16 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "ratio", - "entities": [ - "CaPLCgp" - ], + "entity" : { + "name": "aPLCg", + "alias": "CaPLCgp" + }, "field": "conc", "normalization": { - "time": 300, - "entities": [ - "CaPLCgp" - ], + "entity" : { + "name": "aPLCg", + "alias": "CaPLCgp" + }, "dose": 100, "sampling": "dose" }, @@ -50,75 +54,41 @@ "useYlog": false }, "data": [ - [ - 0, - 0, - 0 - ], - [ - 0.032, - 0.15, - 0 - ], - [ - 0.065, - 0.2, - 0 - ], - [ - 0.1, - 0.25, - 0 - ], - [ - 0.21, - 0.35, - 0 - ], - [ - 0.43, - 0.6, - 0 - ], - [ - 1, - 0.9, - 0 - ], - [ - 100, - 1, - 0 - ] + [0, 0, 0], + [0.032, 0.15, 0], + [0.065, 0.2, 0], + [0.1, 0.25, 0], + [0.21, 0.35, 0], + [0.43, 0.6, 0], + [1, 0.9, 0], + [100, 1, 0] ] }, "Modifications": { "subset": [ - "Ca_g", - "PLCg_g", - "EGFR_g" + {"name":"Ca_g","alias":"Ca_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"EGFR_g","alias":"EGFR_g"} ], "itemsToDelete": [ - "PLCgp_deph", - "EGFR_act_SHC", - "CaPLCg_PIP2hydr", - "CaPLCgp_PIP2hydr" + {"name":"PLCgp_deph","alias":"PLCgp_deph"},{"name":"eEGFR+SHC","alias":"EGFR_act_SHC"},{"name":"eCaPLCg+PIP2","alias":"CaPLCg_PIP2hydr"},{"name":"eCaPLCgp+PIP2","alias":"CaPLCgp_PIP2hydr"} ], "parameterChange": [ { - "entity": "EGF", + "name": "EGF", + "alias": "EGF", "field": "concInit", "value": 0.0001, "units": "mM" }, { - "entity": "PLCg", + "name": "PLCg", + "alias": "PLCg", "field": "concInit", "value": 0.00082, "units": "mM" }, { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "isBuffered", "value": 1, "units": "none" diff --git a/Non-Curated/HH_Fig13.json b/Non-Curated/HH_Fig13.json index 98fd944..841dafe 100644 --- a/Non-Curated/HH_Fig13.json +++ b/Non-Curated/HH_Fig13.json @@ -24,65 +24,39 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity": "soma", + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "inject", "data": [ - [ - 0, - 2000 - ], - [ - 0.1, - 0 - ] + [0,2000], + [0.1,0] ] } ], "Readouts": { "timeUnits": "msec", "quantityUnits": "mV", - "entities": [ - "soma" - ], + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "Vm", "data": [ - [ - 0, - -45.0 - ], - [ - 1, - 25 - ], - [ - 2, - -20.0 - ], - [ - 3, - -75.0 - ], - [ - 4, - -74.0 - ], - [ - 5, - -73.0 - ], - [ - 10, - -66.0 - ], - [ - 15, - -65.0 - ] + [0, -45.0], + [1, 25], + [2, -20.0], + [3, -75.0], + [4, -74.0], + [5, -73.0], + [10, -66.0], + [15, -65.0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/Non-Curated/HH_vclamp4.json b/Non-Curated/HH_vclamp4.json index 1dd8138..017d2b5 100644 --- a/Non-Curated/HH_vclamp4.json +++ b/Non-Curated/HH_vclamp4.json @@ -11,7 +11,7 @@ "year": 117, "figure": "Figure 13" }, - "testModel": "models/loadhh.py", + "testModel": "models/loadhh.py", "testMap": "models/loadhh.json" }, "Experiment": { @@ -24,97 +24,47 @@ { "timeUnits": "msec", "quantityUnits": "mV", - "entity": "soma", + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "Vclamp", "data": [ - [ - 0, - -65.0 - ], - [ - 10, - -25.0 - ], - [ - 60, - -65.0 - ], - [ - 100, - -65.0 - ] + [0,-65.0], + [10,-25.0], + [60,-65.0], + [100,-65.0] ] } ], "Readouts": { "timeUnits": "msec", "quantityUnits": "uA", - "entities": [ - "soma" - ], + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "current", "data": [ - [ - 0, - 0 - ], - [ - 10, - 0 - ], - [ - 11, - -7.0 - ], - [ - 12, - -2.0 - ], - [ - 13, - 1.5 - ], - [ - 14, - 3.2 - ], - [ - 16, - 6 - ], - [ - 20, - 6.9 - ], - [ - 60, - 6.9 - ], - [ - 61, - 1.2 - ], - [ - 62, - 0.8 - ], - [ - 63, - 0.6 - ], - [ - 64, - 0.4 - ], - [ - 100, - 0 - ] + [0, 0], + [10, 0], + [11, -7.0], + [12, -2.0], + [13, 1.5], + [14, 3.2], + [16, 6], + [20, 6.9], + [60, 6.9], + [61, 1.2], + [62, 0.8], + [63, 0.6], + [64, 0.4], + [100, 0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/Non-Curated/Jain2009_Fig2C.json b/Non-Curated/Jain2009_Fig2C.json index 4ad750b..b808ffd 100644 --- a/Non-Curated/Jain2009_Fig2C.json +++ b/Non-Curated/Jain2009_Fig2C.json @@ -25,7 +25,10 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "BDNF", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, "field": "conc" } ], @@ -33,48 +36,25 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "nM", - "entities": [ - "SHCp" - ], + "entity" : { + "name": "aSHC", + "alias": "SHCp" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 1, - 6.5, - 0 - ], - [ - 2, - 12.5, - 0 - ], - [ - 3.8, - 14, - 0 - ], - [ - 7.5, - 18, - 0 - ] + [0, 0, 0], + [1, 6.5, 0], + [2, 12.5, 0], + [3.8, 14, 0], + [7.5, 18, 0] ] }, "Modifications": { "subset": [ - "BDNF_g", - "TrKB_g", - "SHC", - "SHCp", - "SHCp_deph" + {"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"SHC","alias":"SHC"},{"name":"aSHC","alias":"SHCp"},{"name":"SHCp_deph","alias":"SHCp_deph"} ], "itemsToDelete": [ - "TrKB_act_PLCg" + {"name":"eTrKB+PLCg","alias":"TrKB_act_PLCg"} ], "notes": "Jain2009_Fig2C" } diff --git a/Non-Curated/Jain2009_Fig2D_n.json b/Non-Curated/Jain2009_Fig2D_n.json new file mode 100644 index 0000000..538dc25 --- /dev/null +++ b/Non-Curated/Jain2009_Fig2D_n.json @@ -0,0 +1,70 @@ +{ + "Metadata": { + "transcriber": "Nisha Ann Viswan", + "organization": "NCBS", + "email": "nishaav@ncbs.res.in", + "source": { + "sourceType": "paper", + "PMID": 10486198, + "authors": "Yuen and Mobley", + "journal": "Exp Neurol ", + "year": 1999, + "figure": "Fig3" + }, + "testModel": "models/synSynth7.g", + "testMap": "models/synSynth7_map.json" + }, + "Experiment": { + "design": "DoseResponse", + "species": "cell-line", + "cellType": "NIH 3T3 cells (murine fibroblasts)", + "temperature": 37, + "notes": "Deleting the rest of the model for convenience" + }, + "Stimuli": [ + { + "timeUnits": "sec", + "quantityUnits": "nM", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, + "field": "conc" + } + ], + "Readouts": { + "timeUnits": "sec", + "settleTime": 300, + "quantityUnits": "nM", + "entity" : { + "name": "PLCgp", + "alias": "PLCgp" + }, + "field": "conc", + "data": [ + [0, 3, 0], + [1, 15, 0], + [2, 24, 0], + [3.8, 34, 0], + [7.5, 41, 0] + ] + }, + "Modifications": { + "subset": [ + {"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"PLCg_g","alias":"PLCg_g"} + ], + "itemsToDelete": [ + {"name":"eTrKB+SHC","alias":"TrKB_act_SHC"},{"name":"Ca_PLCg","alias":"CaPLCg"},{"name":"aPLCg","alias":"CaPLCgp"},{"name":"Ca+PLCg","alias":"Ca_act_PLCg"},{"name":"Ca+PLCgp","alias":"Ca_act_PLCgp"},{"name":"dephosph_PLC_g","alias":"dephosph_PLC_g"} + ], + "parameterChange": [ + { + "name": "PLCg", + "alias": "PLCg", + "field": "concInit", + "value": 0.0001, + "units": "mM" + } + ], + "notes": "Jain2009_Fig2D" + } +} diff --git a/Non-Curated/Jain2009_Fig3B.json b/Non-Curated/Jain2009_Fig3B.json index 70409e5..8edc8d6 100644 --- a/Non-Curated/Jain2009_Fig3B.json +++ b/Non-Curated/Jain2009_Fig3B.json @@ -25,7 +25,10 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "mTOR", + "entity" : { + "name": "mTOR", + "alias": "mTOR" + }, "field": "conc" } ], @@ -33,60 +36,31 @@ "timeUnits": "sec", "settleTime": 3600, "quantityUnits": "uM", - "entities": [ - "S6KpT412" - ], + "entity" : { + "name": "S6Kpqr", + "alias": "S6KpT412" + }, "field": "conc", "data": [ - [ - 0.45, - 0.01, - 0 - ], - [ - 0.66935, - 0.05, - 0 - ], - [ - 0.8925, - 0.08, - 0 - ], - [ - 1.785, - 0.15, - 0 - ], - [ - 3.57, - 0.21, - 0 - ], - [ - 7.14, - 0.53, - 0 - ] + [0.45, 0.01, 0], + [0.66935, 0.05, 0], + [0.8925, 0.08, 0], + [1.785, 0.15, 0], + [3.57, 0.21, 0], + [7.14, 0.53, 0] ] }, "Modifications": { "subset": [ - "S6K_g", - "mTORC1_g" + {"name":"S6K_g","alias":"S6K_g"},{"name":"mTORC1_g","alias":"mTORC1_g"} ], "itemsToDelete": [ - "S6_phos", - "S6_phospho", - "S6Kp_act_CaMKIII", - "bS6K", - "TOR_4EBPp", - "TOR_4EBP_phospho", - "S6_dephosph" + {"name":"eS6Kpqr+40S","alias":"S6_phos"},{"name":"eS6Kpqrs+40S","alias":"S6_phospho"},{"name":"eS6Kpqrs+CaMKIII","alias":"S6Kp_act_CaMKIII"},{"name":"bS6K","alias":"bS6K"},{"name":"emTORC1+4EBP","alias":"TOR_4EBPp"},{"name":"emTORC1+4EBPhospho","alias":"TOR_4EBP_phospho"},{"name":"S6_dephosph","alias":"S6_dephosph"} ], "parameterChange": [ { - "entity": "S6K", + "name": "S6K", + "alias": "S6K", "field": "concInit", "value": 0.0009, "units": "mM" diff --git a/Non-Curated/Jain2009_Fig4B.json b/Non-Curated/Jain2009_Fig4B.json index 92aacd3..75979d2 100644 --- a/Non-Curated/Jain2009_Fig4B.json +++ b/Non-Curated/Jain2009_Fig4B.json @@ -25,7 +25,10 @@ { "timeUnits": "sec", "quantityUnits": "M", - "entity": "CaMCa4", + "entity" : { + "name": "CaMCa4", + "alias": "CaMCa4" + }, "field": "conc" } ], @@ -33,103 +36,46 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "uM", - "entities": [ - "eEF2p" - ], + "entity" : { + "name": "eEF2p", + "alias": "eEF2p" + }, "field": "conc", "display": { "useXlog": true, "useYlog": false }, "data": [ - [ - 5e-12, - 0, - 0 - ], - [ - 3e-11, - 0.01, - 0 - ], - [ - 3.2e-10, - 0.12, - 0 - ], - [ - 5e-10, - 0.22, - 0 - ], - [ - 1.75e-09, - 0.35, - 0 - ], - [ - 3.16e-09, - 0.44, - 0 - ], - [ - 8e-09, - 0.5, - 0 - ], - [ - 1e-08, - 0.5, - 0 - ], - [ - 3.1e-08, - 0.51, - 0 - ], - [ - 6.2e-08, - 0.51, - 0 - ] + [5e-12, 0, 0], + [3e-11, 0.01, 0], + [3.2e-10, 0.12, 0], + [5e-10, 0.22, 0], + [1.75e-09, 0.35, 0], + [3.16e-09, 0.44, 0], + [8e-09, 0.5, 0], + [1e-08, 0.5, 0], + [3.1e-08, 0.51, 0], + [6.2e-08, 0.51, 0] ] }, "Modifications": { "subset": [ - "CaMCa4", - "CaMKIII_bind_CaMCa4", - "CaMKIII", - "aCaMKIII", - "eEF2", - "eEF2p", - "PP2A" + {"name":"CaMCa4","alias":"CaMCa4"},{"name":"CaMCa4+CaMKIII","alias":"CaMKIII_bind_CaMCa4"},{"name":"CaMKIII","alias":"CaMKIII"},{"name":"aCaMKIII","alias":"aCaMKIII"},{"name":"eEF2","alias":"eEF2"},{"name":"eEF2p","alias":"eEF2p"},{"name":"PP2A","alias":"PP2A"} ], "itemsToDelete": [ - "CaMCa3_bind_Ca", - "elongation", - "PP2A_dephos_I1", - "PP2A_dephos_PP1_Ip", - "clus_S6K_deph", - "S6K_deph", - "S6K_dephospp", - "AKTpS473_deph", - "AKTpT308_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "mGluR_deph", - "dephos_FMRP" + {"name":"CaMCa3+Ca","alias":"CaMCa3_bind_Ca"},{"name":"elongation","alias":"elongation"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"S6K_dephospp","alias":"S6K_dephospp"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"mGluR_deph","alias":"mGluR_deph"},{"name":"dephos_FMRP","alias":"dephos_FMRP"} ], "parameterChange": [ { - "entity": "eEF2", + "name": "eEF2", + "alias": "eEF2", "field": "concInit", "value": 0.00054555, "units": "mM" }, { - "entity": "CaMKIII", + "name": "CaMKIII", + "alias": "CaMKIII", "field": "concInit", "value": 3.65e-05, "units": "mM" diff --git a/Non-Curated/Jain2009_Fig4F.json b/Non-Curated/Jain2009_Fig4F.json index 14bd754..18e27d0 100644 --- a/Non-Curated/Jain2009_Fig4F.json +++ b/Non-Curated/Jain2009_Fig4F.json @@ -24,7 +24,10 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "S6p", + "entity" : { + "name": "aS6", + "alias": "S6p" + }, "field": "conc" } ], @@ -32,53 +35,34 @@ "timeUnits": "sec", "settleTime": 2400, "quantityUnits": "nM", - "entities": [ - "43S" - ], + "entity" : { + "name": "43S", + "alias": "43S" + }, "field": "conc", "data": [ - [ - 6.8, - 3.61, - 0 - ], - [ - 20.4, - 15.3, - 0 - ], - [ - 68, - 30.7, - 0 - ], - [ - 204, - 42.4, - 0 - ], - [ - 612, - 45.3, - 0 - ] + [6.8, 3.61, 0], + [20.4, 15.3, 0], + [68, 30.7, 0], + [204, 42.4, 0], + [612, 45.3, 0] ] }, "Modifications": { "subset": [ - "Transl_init_g", - "40S_g", - "43S_g" + {"name":"Transl_init_g","alias":"Transl_init_g"},{"name":"_40S_g","alias":"40S_g"},{"name":"_43S_g","alias":"43S_g"} ], "parameterChange": [ { - "entity": "M_clx", + "name": "M_clx", + "alias": "M_clx", "field": "concInit", "value": 0.0015, "units": "mM" }, { - "entity": "Q_clx", + "name": "Q_clx", + "alias": "Q_clx", "field": "concInit", "value": 4.97e-05, "units": "mM" diff --git a/Non-Curated/PKC_SB_Fig7.json b/Non-Curated/PKC_SB_Fig7.json index fd25318..219d98d 100644 --- a/Non-Curated/PKC_SB_Fig7.json +++ b/Non-Curated/PKC_SB_Fig7.json @@ -25,21 +25,30 @@ "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "Ca", + "entity" : { + "name": "Ca", + "alias": "Ca" + }, "value": 1.0 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "DAG", + "entity" : { + "name": "DAG", + "alias": "DAG" + }, "value": 50 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "AA", + "entity" : { + "name": "AA", + "alias": "AA" + }, "value": 50 } ], @@ -47,15 +56,16 @@ "timeUnits": "sec", "settleTime": 15, "quantityUnits": "ratio", - "entities": [ - "aPKC" - ], + "entity" : { + "name": "aPKC", + "alias": "aPKC" + }, "field": "conc", "normalization": { - "time": 15, - "entities": [ - "aPKC" - ], + "entity" : { + "name": "aPKC", + "alias": "aPKC" + }, "sampling": "start" }, "bardata": [ @@ -65,39 +75,27 @@ "stderr": 0 }, { - "stimulus": [ - "AA" - ], + "stimulus": ["AA"], "value": 2.5, "stderr": 0 }, { - "stimulus": [ - "DAG" - ], + "stimulus": ["DAG"], "value": 3.0, "stderr": 0 }, { - "stimulus": [ - "Ca" - ], + "stimulus": ["Ca"], "value": 5.5, "stderr": 0 }, { - "stimulus": [ - "Ca", - "AA" - ], + "stimulus": ["Ca","AA"], "value": 12.1, "stderr": 0 }, { - "stimulus": [ - "Ca", - "DAG" - ], + "stimulus": ["Ca","DAG"], "value": 12.0, "stderr": 0 } @@ -105,52 +103,50 @@ }, "Modifications": { "subset": [ - "Ca", - "AA", - "PKC_g", - "DAG" + {"name":"Ca","alias":"Ca"},{"name":"AA","alias":"AA"},{"name":"PKC_g","alias":"PKC_g"},{"name":"DAG","alias":"DAG"} ], "itemsToDelete": [ - "PKC_act_raf", - "PKC_inact_GAP", - "PKC_act_GEF", - "PKC_phosph_neurogranin", - "PKC_phosph_ng_CaM", - "phosph_AC2" + {"name":"ePKC+craf","alias":"PKC_act_raf"},{"name":"PKC_inact_GAP","alias":"PKC_inact_GAP"},{"name":"PKC_act_GEF","alias":"PKC_act_GEF"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"phosph_AC2","alias":"phosph_AC2"} ], "parameterChange": [ { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "concInit", "value": 0.0001, "units": "mM" }, { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "isBuffered", "value": 1, "units": "none" diff --git a/Non-Curated/PKC_SB_Fig8.json b/Non-Curated/PKC_SB_Fig8.json index 1e300fc..b00f3b3 100644 --- a/Non-Curated/PKC_SB_Fig8.json +++ b/Non-Curated/PKC_SB_Fig8.json @@ -25,21 +25,30 @@ "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "Ca", + "entity" : { + "name": "Ca", + "alias": "Ca" + }, "value": 1.0 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "DAG", + "entity" : { + "name": "DAG", + "alias": "DAG" + }, "value": 100 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "AA", + "entity" : { + "name": "AA", + "alias": "AA" + }, "value": 50 } ], @@ -47,15 +56,16 @@ "timeUnits": "sec", "settleTime": 150, "quantityUnits": "ratio", - "entities": [ - "aPKC" - ], + "entity" : { + "name": "aPKC", + "alias": "aPKC" + }, "field": "conc", "normalization": { - "time": 150, - "entities": [ - "aPKC" - ], + "entity" : { + "name": "aPKC", + "alias": "aPKC" + }, "sampling": "start" }, "bardata": [ @@ -65,56 +75,37 @@ "stderr": 0 }, { - "stimulus": [ - "AA" - ], + "stimulus": ["AA"], "value": 2.5, "stderr": 0 }, { - "stimulus": [ - "DAG" - ], + "stimulus": ["DAG"], "value": 12.0, "stderr": 0 }, { - "stimulus": [ - "DAG", - "AA" - ], + "stimulus": ["DAG","AA"], "value": 19.5, "stderr": 0 }, { - "stimulus": [ - "Ca" - ], + "stimulus": ["Ca"], "value": 9.0, "stderr": 0 }, { - "stimulus": [ - "Ca", - "AA" - ], + "stimulus": ["Ca","AA"], "value": 18.0, "stderr": 0 }, { - "stimulus": [ - "Ca", - "DAG" - ], + "stimulus": ["Ca","DAG"], "value": 17.0, "stderr": 0 }, { - "stimulus": [ - "Ca", - "DAG", - "AA" - ], + "stimulus": ["Ca","DAG","AA"], "value": 19.5, "stderr": 0 } @@ -122,52 +113,50 @@ }, "Modifications": { "subset": [ - "Ca", - "AA", - "PKC_g", - "DAG" + {"name":"Ca","alias":"Ca"},{"name":"AA","alias":"AA"},{"name":"PKC_g","alias":"PKC_g"},{"name":"DAG","alias":"DAG"} ], "itemsToDelete": [ - "PKC_act_raf", - "PKC_inact_GAP", - "PKC_act_GEF", - "PKC_phosph_neurogranin", - "PKC_phosph_ng_CaM", - "phosph_AC2" + {"name":"ePKC+craf","alias":"PKC_act_raf"},{"name":"PKC_inact_GAP","alias":"PKC_inact_GAP"},{"name":"PKC_act_GEF","alias":"PKC_act_GEF"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"phosph_AC2","alias":"phosph_AC2"} ], "parameterChange": [ { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "concInit", "value": 0.0001, "units": "mM" }, { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "isBuffered", "value": 1, "units": "none" diff --git a/Non-Curated/directParamsDemo.json b/Non-Curated/directParamsDemo.json index 8a84bad..c451cb4 100644 --- a/Non-Curated/directParamsDemo.json +++ b/Non-Curated/directParamsDemo.json @@ -23,28 +23,40 @@ "Readouts": { "paramdata": [ { - "entity": "MAPK_phosph_PLA2", + "entity" : { + "name": "MAPK_phosph_PLA2", + "alias": "MAPK_phosph_PLA2" + }, "field": "kcat", "units": "1/sec", "value": 20, "stderr": 0 }, { - "entity": "MAPK_phosph_4EBP", + "entity" : { + "name": "MAPK_phosph_4EBP", + "alias": "MAPK_phosph_4EBP" + }, "field": "kcat", "units": "1/sec", "value": 0.1, "stderr": 0 }, { - "entity": "MAPK_phosph_PLA2", + "entity" : { + "name": "MAPK_phosph_PLA2", + "alias": "MAPK_phosph_PLA2" + }, "field": "Km", "units": "uM", "value": 27, "stderr": 0 }, { - "entity": "MAPK_phosph_4EBP", + "entity" : { + "name": "MAPK_phosph_4EBP", + "alias": "MAPK_phosph_4EBP" + }, "field": "Km", "units": "uM", "value": 20, @@ -54,7 +66,7 @@ }, "Modifications": { "subset": [ - "all" + {"name":"all"} ], "notes": "Test for direct measure of parameters. Note that each Readouts entry can be used for a different parameter, but may apply to many objects." } diff --git a/models/synSynth7_map.json b/models/synSynth7_map.json index 511e29f..beb98cd 100644 --- a/models/synSynth7_map.json +++ b/models/synSynth7_map.json @@ -26,12 +26,14 @@ "S6K_g":["S6Kinase"], "4EBP_g":["kinetics/_4E_BP"], "43S_g":["_43S_complex"], + "_43S_g":["_43S_complex"], "protein_g":["kinetics/protein"], "BDNF_g":["kinetics/BDNF"], "CaMKIII_g":["kinetics/CaMKIII"], "Transl_init_g":["Translation_initiation"], "Transl_elong_g":["Translation_elongation"], "40S_g":["kinetics/_40S"], + "_40S_g":["kinetics/_40S"], "TSC1_TSC2_g":["kinetics/TSC1_TSC2"], "HomerPIKE_g":["HomerPIKE"], "barr2_g":["barr2_signaling"], @@ -44,15 +46,20 @@ "ERK":["MAPK/MAPK"], "pERK":["MAPK/MAPK_p_p","MAPK/MAPK_p"], "FMRP_synth":["FMRP_synth"], + "aSHC":["SHC_p"], "SHCp":["SHC_p"], "SHC":["SHC"], + "Gq_GDP":["G_GDP"], "G_GDP":["G_GDP"], "EGFR":["EGFR/EGFR"], "EGFRp":["L.EGFR"], "act_surface_EGFR":["L.EGFR"], + "eEGFR+SHC":["L.EGFR/SHC_phospho"], "EGFR_act_SHC":["L.EGFR/SHC_phospho"], "PLCg":["PLC_g/PLC_g"], + "Ca+PLCg":["Ca_act_PLC_g"], "Ca_act_PLCg":["Ca_act_PLC_g"], + "Ca+PLCgp":["Ca_act_PLC_g_p"], "Ca_act_PLCgp":["Ca_act_PLC_g_p"], "enolase":["GDP_Ras"], "enolase_p":["GTP_Ras"], @@ -77,7 +84,6 @@ "MAPKpp":["MAPK/MAPK_p_p"], "MAPKp":["MAPK/MAPK_p"], "EGF":["EGF"], - "DHPG":["Glutamate"], "Glutamate":["Glutamate"], "CaMKIII":["CaMKIII/CaMKIII"], "CaMKIII_deph":["CaMKIII_dephospho"], @@ -113,6 +119,7 @@ "Rheb_inact":["TSC2phospho"], "S6K":["S6K"], "S6KpT389":["S6K_thr_412"], + "S6Kpqr":["S6K_thr_412"], "S6KpT412":["S6K_thr_412"], "S6KpT229":["S6K_thr_252"], "S6KpT252":["S6K_thr_252"], @@ -137,6 +144,7 @@ "Act_PLC_Ca":["Act_PLC_Ca"], "PLC_Gq_bind_Ca":["PLC_Gq_bind_Ca"], "PLCb_Ca_Gq":["PLCb_Ca_Gq"], + "aPLCg":["Ca.PLC_g_p"], "CaPLCgp":["Ca.PLC_g_p"], "CaPLCg":["Ca.PLC_g"], "bPLCg":["PLCg_basal"], @@ -170,8 +178,11 @@ "eIF4E":["eIF4E"], "eIF4E_S209":["eIF4E"], "S6":["_40S_inact"], + "aS6":["_40S/_40S"], "S6p":["_40S/_40S"], + "eS6Kpqr+40S":["S6_phos"], "S6_phos":["S6_phos"], + "eS6Kpqrs+40S":["S6_phospho"], "S6_phospho":["S6_phospho"], "Glu_mGluR":["RecLigandBinding"], "Ligand_binding":["Ligand_binding"], @@ -188,6 +199,7 @@ "PDK1":["PDK1"], "APC":["APC"], "CaPLCgp_PIP2hydr":["Ca.PLC_g_p/PIP2_hydrolysis"], + "eCaPLCg+PIP2":["Ca.PLC_g/PIP2_hydrolysis"], "CaPLCg_PIP2hydr":["Ca.PLC_g/PIP2_hydrolysis"], "EGF_act_PLCg":["Ca.PLC_g_p/PIP2_hydrolysis"], "act_PLCg":["Ca.PLC_g/PIP2_hydrolysis"], @@ -222,9 +234,11 @@ "40SmRNA_bind_Q":["RM_binds_Q"], "QR":["Q.R"], "Rec_bind_Gq":["Rec_bind_Gq"], + "Glu_mGluR+Gq":["Rec_Glu_bind_Gq"], "Glu_mGluR_bind_Gq":["Rec_Glu_bind_Gq"], "Glu_bind_Rec_Gq":["Glu_bind_Rec_Gq"], "mGluR_Gq":["Rec_Gq"], + "amGluR":["Rec_Glu_Gq"], "Glu_mGluR_Gq":["Rec_Glu_Gq"], "eEF2":["eEF2"], "eEF2p":["eEFthr_56"], @@ -235,6 +249,7 @@ "CaMKIIT286_bind_CaM":["CaMKII_thr286_bind_CaM"], "CaMCaMKII_act_T286":["CaM_act_286"], "CaMCaMKII_act_T305":["CaM_act_305"], + "CaMCa4+CaMKIII":["CaMKIII_bind_CaM_Ca4"], "CaMKIII_bind_CaMCa4":["CaMKIII_bind_CaM_Ca4"], "aCaMKIII":["CaMKIII_CaM_Ca4"], "PP1_deph_T286":["Deph_thr286"], @@ -245,15 +260,19 @@ "Ca_bound":["CaM_Ca4","CaM_Ca3","CaM_Ca2","CaM_Ca"], "tot_Ca_on_CaM":["CaM_Ca4","CaM_Ca4","CaM_Ca4","CaM_Ca4","CaM_Ca3","CaM_Ca3","CaM_Ca3","CaM_Ca2","CaM_Ca2","CaM_Ca"], "eEF2_phospho":["CaMKIII_CaM_Ca4/phospho"], + "eS6Kpqrs+CaMKIII":["S6K_thr_252/CaMKIII_phospho"], "S6Kp_act_CaMKIII":["S6K_thr_252/CaMKIII_phospho"], "bS6K_act_CaMKIII":["S6K_basal/CaMKIII_basal"], "bS6K_act":["basal_S6K"], "bCaMKIII":["CaMKIII/CaMKIII_basal"], + "eMAPK+crafp":["MAPK_p_p_feedback"], "MAPKpp_feedback":["MAPK_p_p_feedback"], "MAPKKthr":["MAPKKthr"], "MAPKKtyr":["MAPKKtyr"], "MKP1":["MKP_1"], + "eMAPK+4EBPpq":["MAPK_4E_BP_p_p"], "MAPK_4EBPpp":["MAPK_4E_BP_p_p"], + "eMAPK+PLA2":["MAPK_p_p/MAPK_p_p"], "MAPKpp_act_PLA2":["MAPK_p_p/MAPK_p_p"], "TrKB_cycling":["LR_cycling"], "TrKB_Internalize":["LR_Internalize"], @@ -272,12 +291,17 @@ "MAPKKpp":["MAPKK_p_p"], "GEFp_actRas":["GEF_p_act_Ras"], "bGEF_act":["basal_GEF_activity"], + + "ePP2A+S6Kpq":["dephos_clus_S6K"], "clus_S6K_deph":["dephos_clus_S6K"], + "ePP2A+S6Kpqr":["dephos_S6K"], "S6K_deph":["dephos_S6K"], + "ePP2A+S6Kpqrs":["dephosp_S6K"], "S6K_dephosp":["dephosp_S6K"], "CaMCaN_deph_I1p":["dephosph_inhib1"], "CaN_deph_I1p":["dephosph_inhib1_noCaM"], "CaMCaN_deph_PP1_I1p":["dephosph_PP1_I_p"], + "ePP2A+I1p":["PP2A_dephospho_I1"], "PP2A_dephos_I1":["PP2A_dephospho_I1"], "PP2A_dephos_PP1_Ip":["PP2A_dephospho_PP1_I_p"], "Gab1":["Gab1"], @@ -306,15 +330,22 @@ "PIP2_Ca_PLA2_act":["PIP2_Ca_PLA2_act"], "CaM_bind_GEF":["CaM_bind_GEF"], "PIP2_phospho_RasGTP":["PIP2_phospho_Ras_GTP"], + "ePP2A+AKTpq":["Dephos_AKTser473"], "AKTpS473_deph":["Dephos_AKTser473"], + "ePP2A+AKTp":["Dephosph_AKTthr308"], "AKTpT308_deph":["Dephosph_AKTthr308"], + "ePP2A+eEF2p":["eEF2thr_56_dephospho"], "eEF2p_deph":["eEF2thr_56_dephospho"], "beEF2p":["eEF2thr56_basal"], "GST_PKBalpha":["AKT"], "pGST_PKBalpha":["PIP3_AKT_thr308"], + "ePP2A+4EBPpqr":["PP2A_4E_BP_p_p"], "PP2A_4EBPpp":["PP2A_4E_BP_p_p"], + "ePP2A+4EBPpq":["PP2A_4E_BP_p"], "PP2A_4EBPp":["PP2A_4E_BP_p"], + "ePP2A+eIF4EBPpqr":["PP2A_4E_BP"], "PP2A_eIF4EBPpp":["PP2A_4E_BP"], + "ePP2A+eIF4EBPpq":["PP2A_4EBP"], "PP2A_eIF4EBPp":["PP2A_4EBP"], "PLCgp_deph":["PLC_g_p_dephospho"], "Grb2_bind_SHC":["Grb2_bind_SHC"], @@ -323,7 +354,9 @@ "mTOR_act_S6K":["TOR_Rheb_GTP_clx/S6K_phospho"], "phospho_AKTpT308":["phospho_thr308"], "phospho_AKTpS473":["phosp_AKTser473"], + "eMAPK+S6K":["cluster_phospho_S6K"], "clus_S6K_phospho":["cluster_phospho_S6K"], + "eMAPK+eIF4EBPpq" :["MAPK_4E_BP_phospho"], "MAPK_4EBP_phospho":["MAPK_4E_BP_phospho"], "MEK_phospho":["MEK_phospho"], "MEKp_phospho":["MEKp_phospho"], @@ -358,7 +391,9 @@ "PKC_DAG_AA":["PKC_n_DAG_AA"], "mGluR_barr2Raf":["mGluR_barr2_Raf"], "PKC_act_DAG_AA":["PKC_act_by_DAG_AA"], + "eTrKB+PLCg":["BDNF_TrKB2_p_clx/PLC_g_phospho"], "TrKB_act_PLCg":["BDNF_TrKB2_p_clx/PLC_g_phospho"], + "eTrKB+SHC":["BDNF_TrKB2_p_clx/SHC_phospho"], "TrKB_act_SHC":["BDNF_TrKB2_p_clx/SHC_phospho"], "Act_Gq":["Activate_Gq"], "Sos_phospho":["phosph_Sos"], @@ -367,6 +402,8 @@ "MAPKKp_deph":["MAPKK_dephospho_ser"], "crafpp_deph":["craf_p_p_dephospho"], "S6_deph":["S6_dephosph"], + "emTORC1+4EBPhospho":["TOR_4E_BP_phospho"], "TOR_4EBP_phospho":["TOR_4E_BP_phospho"], + "emTORC1+4EBP":["TOR_4E_BP_p"], "TOR_4EBPp":["TOR_4E_BP_p"] } From 5d935b88d0f16d16539bb51958aa495eb6959d8a Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 21:29:19 +0530 Subject: [PATCH 6/8] converted all TestJson json files to new format --- TestJson/Non-Curated/dr_j2c.json | 53 +++++--------- TestJson/bc_ratio_sb8.json | 93 +++++++++++------------- TestJson/dp.json | 22 ++++-- TestJson/dp_Kd_tau.json | 25 +++++-- TestJson/dr_ratio_b2c.json | 86 ++++++++-------------- TestJson/epsc.json | 84 ++++++++-------------- TestJson/epsc_ratio.json | 120 ++++++++++++++++--------------- TestJson/fepsp.json | 93 +++++++----------------- TestJson/iclamp_hh13.json | 64 +++++------------ TestJson/ts_j4d.json | 80 ++++++--------------- TestJson/ts_norm_m3b.json | 79 ++++++-------------- TestJson/ts_ratio_t2a.json | 108 +++++++--------------------- TestJson/vclamp_hh.json | 118 +++++++----------------------- 13 files changed, 356 insertions(+), 669 deletions(-) diff --git a/TestJson/Non-Curated/dr_j2c.json b/TestJson/Non-Curated/dr_j2c.json index 6939803..82c583a 100644 --- a/TestJson/Non-Curated/dr_j2c.json +++ b/TestJson/Non-Curated/dr_j2c.json @@ -24,7 +24,10 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "BDNF", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, "field": "conc" } ], @@ -32,52 +35,30 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "nM", - "entities": [ - "SHCp" - ], + "entity" : { + "name": "aSHC", + "alias": "SHCp" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 1, - 6.5, - 0 - ], - [ - 2, - 12.5, - 0 - ], - [ - 3.8, - 14, - 0 - ], - [ - 7.5, - 18, - 0 - ] + [0, 0, 0], + [1, 6.5, 0], + [2, 12.5, 0], + [3.8, 14, 0], + [7.5, 18, 0] ] }, "Modifications": { "subset": [ - "BDNF_g", - "TrKB_g", - "SHC", - "SHCp", - "SHCp_deph" + {"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"SHC","alias":"SHC"},{"name":"aSHC","alias":"SHCp"},{"name":"SHCp_deph","alias":"SHCp_deph"} ], "itemsToDelete": [ - "TrKB_act_PLCg" + {"name":"eTrKB+PLCg","alias":"TrKB_act_PLCg"} ], "parameterChange": [ { - "entity": "SHCp_deph", + "name": "SHCp_deph", + "alias": "SHCp_deph", "field": "Kf", "value": 0.2, "units": "none" diff --git a/TestJson/bc_ratio_sb8.json b/TestJson/bc_ratio_sb8.json index 1e300fc..b00f3b3 100644 --- a/TestJson/bc_ratio_sb8.json +++ b/TestJson/bc_ratio_sb8.json @@ -25,21 +25,30 @@ "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "Ca", + "entity" : { + "name": "Ca", + "alias": "Ca" + }, "value": 1.0 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "DAG", + "entity" : { + "name": "DAG", + "alias": "DAG" + }, "value": 100 }, { "timeUnits": "sec", "quantityUnits": "uM", "field": "conc", - "entity": "AA", + "entity" : { + "name": "AA", + "alias": "AA" + }, "value": 50 } ], @@ -47,15 +56,16 @@ "timeUnits": "sec", "settleTime": 150, "quantityUnits": "ratio", - "entities": [ - "aPKC" - ], + "entity" : { + "name": "aPKC", + "alias": "aPKC" + }, "field": "conc", "normalization": { - "time": 150, - "entities": [ - "aPKC" - ], + "entity" : { + "name": "aPKC", + "alias": "aPKC" + }, "sampling": "start" }, "bardata": [ @@ -65,56 +75,37 @@ "stderr": 0 }, { - "stimulus": [ - "AA" - ], + "stimulus": ["AA"], "value": 2.5, "stderr": 0 }, { - "stimulus": [ - "DAG" - ], + "stimulus": ["DAG"], "value": 12.0, "stderr": 0 }, { - "stimulus": [ - "DAG", - "AA" - ], + "stimulus": ["DAG","AA"], "value": 19.5, "stderr": 0 }, { - "stimulus": [ - "Ca" - ], + "stimulus": ["Ca"], "value": 9.0, "stderr": 0 }, { - "stimulus": [ - "Ca", - "AA" - ], + "stimulus": ["Ca","AA"], "value": 18.0, "stderr": 0 }, { - "stimulus": [ - "Ca", - "DAG" - ], + "stimulus": ["Ca","DAG"], "value": 17.0, "stderr": 0 }, { - "stimulus": [ - "Ca", - "DAG", - "AA" - ], + "stimulus": ["Ca","DAG","AA"], "value": 19.5, "stderr": 0 } @@ -122,52 +113,50 @@ }, "Modifications": { "subset": [ - "Ca", - "AA", - "PKC_g", - "DAG" + {"name":"Ca","alias":"Ca"},{"name":"AA","alias":"AA"},{"name":"PKC_g","alias":"PKC_g"},{"name":"DAG","alias":"DAG"} ], "itemsToDelete": [ - "PKC_act_raf", - "PKC_inact_GAP", - "PKC_act_GEF", - "PKC_phosph_neurogranin", - "PKC_phosph_ng_CaM", - "phosph_AC2" + {"name":"ePKC+craf","alias":"PKC_act_raf"},{"name":"PKC_inact_GAP","alias":"PKC_inact_GAP"},{"name":"PKC_act_GEF","alias":"PKC_act_GEF"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"phosph_AC2","alias":"phosph_AC2"} ], "parameterChange": [ { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "concInit", "value": 0.0001, "units": "mM" }, { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "isBuffered", "value": 1, "units": "none" diff --git a/TestJson/dp.json b/TestJson/dp.json index 5e6549b..5d7482e 100644 --- a/TestJson/dp.json +++ b/TestJson/dp.json @@ -23,28 +23,40 @@ "Readouts": { "paramdata": [ { - "entity": "MAPKpp_act_PLA2", + "entity" : { + "name": "eMAPK+PLA2", + "alias": "MAPKpp_act_PLA2" + }, "field": "kcat", "units": "1/sec", "value": 20, "stderr": 50 }, { - "entity": "MAPK_4EBP_phospho", + "entity" : { + "name": "eMAPK+eIF4EBPpq", + "alias": "MAPK_4EBP_phospho" + }, "field": "kcat", "units": "1/sec", "value": 0.1, "stderr": 0.05 }, { - "entity": "MAPKpp_act_PLA2", + "entity" : { + "name": "eMAPK+PLA2", + "alias": "MAPKpp_act_PLA2" + }, "field": "Km", "units": "uM", "value": 27, "stderr": 5 }, { - "entity": "MAPK_4EBP_phospho", + "entity" : { + "name": "eMAPK+eIF4EBPpq", + "alias": "MAPK_4EBP_phospho" + }, "field": "Km", "units": "uM", "value": 20, @@ -54,7 +66,7 @@ }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/TestJson/dp_Kd_tau.json b/TestJson/dp_Kd_tau.json index 0489684..650aac0 100644 --- a/TestJson/dp_Kd_tau.json +++ b/TestJson/dp_Kd_tau.json @@ -23,28 +23,40 @@ "Readouts": { "paramdata": [ { - "entity": "RecLigandBinding", + "entity" : { + "name": "RecLigandBinding", + "alias": "RecLigandBinding" + }, "field": "tau", "units": "sec", "value": 0.04, "stderr": 0.01 }, { - "entity": "makeTernary", + "entity" : { + "name": "makeTernary", + "alias": "makeTernary" + }, "field": "tau", "units": "sec", "value": 160, "stderr": 50 }, { - "entity": "RecLigandBinding", + "entity" : { + "name": "RecLigandBinding", + "alias": "RecLigandBinding" + }, "field": "Kd", "units": "uM", "value": 0.6, "stderr": 0.1 }, { - "entity": "makeTernary", + "entity" : { + "name": "makeTernary", + "alias": "makeTernary" + }, "field": "Kd", "units": "uM", "value": 0.015, @@ -54,11 +66,10 @@ }, "Modifications": { "subset": [ - "mGluR_g", - "G_GDP" + {"name":"mGluR_g","alias":"mGluR_g"},{"name":"Gq_GDP","alias":"G_GDP"} ], "itemsToDelete": [ - "Activate_Gq" + {"name":"Activate_Gq","alias":"Activate_Gq"} ] } } diff --git a/TestJson/dr_ratio_b2c.json b/TestJson/dr_ratio_b2c.json index 022e987..05234a2 100644 --- a/TestJson/dr_ratio_b2c.json +++ b/TestJson/dr_ratio_b2c.json @@ -24,7 +24,10 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Ca", + "entity" : { + "name": "Ca", + "alias": "Ca" + }, "field": "conc" } ], @@ -32,15 +35,16 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "ratio", - "entities": [ - "CaPLCgp" - ], + "entity" : { + "name": "aPLCg", + "alias": "CaPLCgp" + }, "field": "conc", "normalization": { - "time": 300, - "entities": [ - "CaPLCgp" - ], + "entity" : { + "name": "aPLCg", + "alias": "CaPLCgp" + }, "dose": 100, "sampling": "dose" }, @@ -49,75 +53,41 @@ "useYlog": false }, "data": [ - [ - 0, - 0, - 0 - ], - [ - 0.032, - 0.15, - 0 - ], - [ - 0.065, - 0.2, - 0 - ], - [ - 0.1, - 0.25, - 0 - ], - [ - 0.21, - 0.35, - 0 - ], - [ - 0.43, - 0.6, - 0 - ], - [ - 1, - 0.9, - 0 - ], - [ - 100, - 1, - 0 - ] + [0, 0, 0], + [0.032, 0.15, 0], + [0.065, 0.2, 0], + [0.1, 0.25, 0], + [0.21, 0.35, 0], + [0.43, 0.6, 0], + [1, 0.9, 0], + [100, 1, 0] ] }, "Modifications": { "subset": [ - "Ca_g", - "PLCg_g", - "EGFR_g" + {"name":"Ca_g","alias":"Ca_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"EGFR_g","alias":"EGFR_g"} ], "itemsToDelete": [ - "PLCgp_deph", - "EGFR_act_SHC", - "CaPLCg_PIP2hydr", - "EGF_act_PLCg" + {"name":"PLCgp_deph","alias":"PLCgp_deph"},{"name":"eEGFR+SHC","alias":"EGFR_act_SHC"},{"name":"eCaPLCg+PIP2","alias":"CaPLCg_PIP2hydr"},{"name":"EGF_act_PLCg","alias":"EGF_act_PLCg"} ], "parameterChange": [ { - "entity": "EGF", + "name": "EGF", + "alias": "EGF", "field": "concInit", "value": 0.0001, "units": "mM" }, { - "entity": "PLCg", + "name": "PLCg", + "alias": "PLCg", "field": "concInit", "value": 0.00082, "units": "mM" }, { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "isBuffered", "value": 1, "units": "none" diff --git a/TestJson/epsc.json b/TestJson/epsc.json index bd97526..991ae90 100644 --- a/TestJson/epsc.json +++ b/TestJson/epsc.json @@ -4,14 +4,14 @@ "organization": "NCBS", "email": "bhalla@ncbs.res.in", "source": { - "sourceType": "inhouse", - "PMID": 0, + "sourceType": "other", + "doi": "0", "authors": "None", "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim", "year": 0, "figure": "" }, - "testModel": "models/plastic8.py", + "testModel": "models/plastic8.py", "testMap": "models/plastic8.json" }, "Experiment": { @@ -24,85 +24,61 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity": "synInput", + "entity" : { + "name": "synInput", + "alias": "synInput" + }, "field": "rate", "data": [ - [ - 0, - 0 - ] + [0,0] ] }, { "timeUnits": "sec", "quantityUnits": "ratio", - "entity": "synapse", + "entity" : { + "name": "synapse", + "alias": "synapse" + }, "field": "weight", "data": [ - [ - 0, - 1 - ], - [ - 12, - 0.2 - ] + [0,1], + [12,0.2] ] }, { "timeUnits": "sec", "quantityUnits": "mV", - "entity": "soma", + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "Vclamp", "data": [ - [ - 0, - -65.0 - ], - [ - 10, - 0 - ], - [ - 11, - -65.0 - ] + [0,-65.0], + [10,0], + [11,-65.0] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "pA", - "entities": [ - "vclamp" - ], + "entity" : { + "name": "vclamp", + "alias": "vclamp" + }, "field": "EPSC_peak", "data": [ - [ - 4, - 40, - 0 - ], - [ - 8, - 50, - 0 - ], - [ - 15, - 65, - 0 - ], - [ - 20, - 130, - 0 - ] + [4, 40, 0], + [8, 50, 0], + [15, 65, 0], + [20, 130, 0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/TestJson/epsc_ratio.json b/TestJson/epsc_ratio.json index 7cac5fc..1cbb8a1 100644 --- a/TestJson/epsc_ratio.json +++ b/TestJson/epsc_ratio.json @@ -1,58 +1,66 @@ { - "Metadata": { - "transcriber": "Upinder S. Bhalla", - "organization": "NCBS", - "email": "bhalla@ncbs.res.in", - "source": { - "sourceType": "other", - "authors": "None", - "year": 2019, - "PMID": 0, - "figure": "synthetic" - }, - "testModel": "models/plastic8.py", - "testMap": "models/plastic8.json" - }, - "Experiment": { - "design": "TimeSeries", - "species": "rat", - "cellType": "hippocampal CA1 pyramidal neuron", - "temperature": 30, - "notes": "Synthetic dataset for testing purposes" - }, - "Stimuli": [ - { - "timeUnits": "sec", - "quantityUnits": "Hz", - "entity": "synInput", - "field": "rate", - "data": [ - [0, 0] - ] - }, - { - "timeUnits": "sec", - "quantityUnits": "ratio", - "entity": "synapse", - "field": "weight", - "data": [ - [0, 0.4], - [10, 1], - [11, 0.4] - ] - } - ], - - "Readouts": { - "timeUnits": "sec", - "quantityUnits": "mV", - "entities": ["soma"], - "field": "EPSP_peak", - "data": [ - [4, 2], - [8, 2], - [15, 11], - [20, 19] - ] - } + "Metadata": { + "transcriber": "Upinder S. Bhalla", + "organization": "NCBS", + "email": "bhalla@ncbs.res.in", + "source": { + "sourceType": "other", + "authors": "Bhalla", + "year": 2019, + "doi": "0", + "figure": "synthetic" + }, + "testModel": "models/plastic8.py", + "testMap": "models/plastic8.json" + }, + "Experiment": { + "design": "TimeSeries", + "species": "rat", + "cellType": "hippocampal CA1 pyramidal neuron", + "temperature": 30, + "notes": "Synthetic dataset for testing purposes" + }, + "Stimuli": [ + { + "timeUnits": "sec", + "quantityUnits": "Hz", + "entity" : { + "name": "synInput", + "alias": "synInput" + }, + "field": "rate", + "data": [ + [0,0] + ] + }, + { + "timeUnits": "sec", + "quantityUnits": "ratio", + "entity" : { + "name": "synapse", + "alias": "synapse" + }, + "field": "weight", + "data": [ + [0,0.4], + [10,1], + [11,0.4] + ] + } + ], + "Readouts": { + "timeUnits": "sec", + "quantityUnits": "mV", + "entity" : { + "name": "soma", + "alias": "soma" + }, + "field": "EPSP_peak", + "data": [ + [4, 2], + [8, 2], + [15, 11], + [20, 19] + ] + } } diff --git a/TestJson/fepsp.json b/TestJson/fepsp.json index b1a9720..2dded6c 100644 --- a/TestJson/fepsp.json +++ b/TestJson/fepsp.json @@ -5,7 +5,7 @@ "email": "bhalla@ncbs.res.in", "source": { "sourceType": "inhouse", - "PMID": 0, + "url": "www.ncbs.res.in", "authors": "None", "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim", "year": 0, @@ -24,92 +24,53 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity": "synInput", + "entity" : { + "name": "synInput", + "alias": "synInput" + }, "field": "rate", "data": [ - [ - 0, - 0 - ], - [ - 10, - 100 - ], - [ - 11, - 0 - ] + [0,0], + [10,100], + [11,0] ] }, { "timeUnits": "sec", "quantityUnits": "ratio", - "entity": "synapse", + "entity" : { + "name": "synapse", + "alias": "synapse" + }, "field": "weight", "data": [ - [ - 0, - 1 - ], - [ - 10, - 1 - ], - [ - 11, - 0.4 - ] + [0,1], + [10,1], + [11,0.4] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "mV", - "entities": [ - "soma" - ], + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "fEPSP_peak", "data": [ - [ - 6, - 0.15, - 0 - ], - [ - 8, - 0.15, - 0 - ], - [ - 15, - 0.4, - 0 - ], - [ - 16, - 0.45, - 0 - ], - [ - 17, - 0.5, - 0 - ], - [ - 18, - 0.55, - 0 - ], - [ - 20, - 0.6, - 0 - ] + [6, 0.15, 0], + [8, 0.15, 0], + [15, 0.4, 0], + [16, 0.45, 0], + [17, 0.5, 0], + [18, 0.55, 0], + [20, 0.6, 0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/TestJson/iclamp_hh13.json b/TestJson/iclamp_hh13.json index 6f428db..e7c07b2 100644 --- a/TestJson/iclamp_hh13.json +++ b/TestJson/iclamp_hh13.json @@ -24,65 +24,39 @@ { "timeUnits": "msec", "quantityUnits": "nA", - "entity": "soma", + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "inject", "data": [ - [ - 0, - 2000 - ], - [ - 0.1, - 0 - ] + [0,2000], + [0.1,0] ] } ], "Readouts": { "timeUnits": "msec", "quantityUnits": "mV", - "entities": [ - "soma" - ], + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "Vm", "data": [ - [ - 0, - -45.0 - ], - [ - 1, - 25 - ], - [ - 2, - -20.0 - ], - [ - 3, - -75.0 - ], - [ - 4, - -74.0 - ], - [ - 5, - -73.0 - ], - [ - 10, - -66.0 - ], - [ - 15, - -65.0 - ] + [0, -45.0], + [1, 25], + [2, -20.0], + [3, -75.0], + [4, -74.0], + [5, -73.0], + [10, -66.0], + [15, -65.0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/TestJson/ts_j4d.json b/TestJson/ts_j4d.json index e5a72b5..a991fba 100644 --- a/TestJson/ts_j4d.json +++ b/TestJson/ts_j4d.json @@ -24,90 +24,56 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity":"eEF2p", + "entity" : { + "name": "eEF2p", + "alias": "eEF2p" + }, "field": "conc" } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entities": [ - "eEF2" - ], + "entity" : { + "name": "eEF2", + "alias": "eEF2" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 300, - 0.24, - 0 - ], - [ - 600, - 0.44, - 0 - ], - [ - 900, - 0.62, - 0 - ], - [ - 1000, - 0.7, - 0 - ], - [ - 1200, - 0.82, - 0 - ], - [ - 1500, - 0.92, - 0 - ] + [0, 0, 0], + [300, 0.24, 0], + [600, 0.44, 0], + [900, 0.62, 0], + [1000, 0.7, 0], + [1200, 0.82, 0], + [1500, 0.92, 0] ] }, "Modifications": { "subset": [ - "PP2A", - "eEF2", - "eEF2p" + {"name":"PP2A","alias":"PP2A"},{"name":"eEF2","alias":"eEF2"},{"name":"eEF2p","alias":"eEF2p"} ], "itemsToDelete": [ - "PP2A_dephospho_I1", - "PP2A_dephospho_PP1_I_p", - "clus_S6K_deph", - "S6K_dephosp", - "S6K_deph", - "AKTpS473_deph", - "AKTpT308_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "mGluR_deph" + {"name":"PP2A_dephospho_I1","alias":"PP2A_dephospho_I1"},{"name":"PP2A_dephospho_PP1_I_p","alias":"PP2A_dephospho_PP1_I_p"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"mGluR_deph","alias":"mGluR_deph"} ], "parameterChange": [ { - "entity": "PP2A", + "name": "PP2A", + "alias": "PP2A", "field": "concInit", "value": 6.5e-07, "units": "mM" }, { - "entity": "eEF2", + "name": "eEF2", + "alias": "eEF2", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "eEF2p", + "name": "eEF2p", + "alias": "eEF2p", "field": "concInit", "value": 2.2e-05, "units": "mM" diff --git a/TestJson/ts_norm_m3b.json b/TestJson/ts_norm_m3b.json index 7ad9112..66f6f78 100644 --- a/TestJson/ts_norm_m3b.json +++ b/TestJson/ts_norm_m3b.json @@ -24,84 +24,45 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Glutamate", + "entity" : { + "name": "Glutamate", + "alias": "Glutamate" + }, "field": "conc", "data": [ - [ - 0, - 100.0 - ] + [0,100.0] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "tot_surface_mGluR_with_barr2" - ], + "entity" : { + "name": "tot_surface_mGluR_with_barr2", + "alias": "tot_surface_mGluR_with_barr2" + }, "field": "conc", "normalization": { - "time": 0, - "entities": [ - "tot_surface_mGluR_with_barr2" - ], - "dose": 0, + "entity" : { + "name": "tot_surface_mGluR_with_barr2", + "alias": "tot_surface_mGluR_with_barr2" + }, "sampling": "start" }, "data": [ - [ - 0, - 1, - 0 - ], - [ - 300, - 0.43, - 0 - ], - [ - 600, - 0.38, - 0 - ], - [ - 900, - 0.32, - 0 - ], - [ - 1800, - 0.34, - 0 - ] + [0, 1, 0], + [300, 0.43, 0], + [600, 0.38, 0], + [900, 0.32, 0], + [1800, 0.34, 0] ] }, "Modifications": { "subset": [ - "mGluR_g", - "barr2_g", - "PP2A" + {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"} ], "itemsToDelete": [ - "mGluR_Gq", - "Glu_mGluR_Gq", - "Glu_mGluR_bind_Gq", - "Glu_bind_mGluR_Gq", - "Act_Gq", - "mGluR_bind_Gq", - "clus_S6K_deph", - "S6K_dephosp", - "S6K_deph", - "AKTpS473_deph", - "AKTpT308_deph", - "eEF2p_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "PP2A_dephos_I1", - "PP2A_dephos_PP1_Ip" + {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"} ] } } diff --git a/TestJson/ts_ratio_t2a.json b/TestJson/ts_ratio_t2a.json index 0c3f773..5d85bf0 100644 --- a/TestJson/ts_ratio_t2a.json +++ b/TestJson/ts_ratio_t2a.json @@ -24,111 +24,53 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Glutamate", + "entity" : { + "name": "Glutamate", + "alias": "Glutamate" + }, "field": "conc", "data": [ - [ - 300, - 0.0 - ] + [300,0.0] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "beta2ARp" - ], + "entity" : { + "name": "beta2ARp", + "alias": "beta2ARp" + }, "field": "conc", "normalization": { - "time": 300, - "entities": [ - "beta2ARp" - ], - "dose": 0, + "entity" : { + "name": "beta2ARp", + "alias": "beta2ARp" + }, "sampling": "start" }, "data": [ - [ - 300, - 1, - 0 - ], - [ - 600, - 0.95, - 0 - ], - [ - 900, - 0.82, - 0 - ], - [ - 1200, - 0.65, - 0 - ], - [ - 1500, - 0.52, - 0 - ], - [ - 2100, - 0.32, - 0 - ], - [ - 3900, - 0.09, - 0 - ], - [ - 5700, - 0.01, - 0 - ] + [300, 1, 0], + [600, 0.95, 0], + [900, 0.82, 0], + [1200, 0.65, 0], + [1500, 0.52, 0], + [2100, 0.32, 0], + [3900, 0.09, 0], + [5700, 0.01, 0] ] }, "Modifications": { "subset": [ - "mGluR_g", - "barr2_g", - "PP2A", - "MAPK_g" + {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"},{"name":"MAPK_g","alias":"MAPK_g"} ], "itemsToDelete": [ - "mGluR_Gq", - "Glu_mGluR_Gq", - "Glu_mGluR_bind_Gq", - "Glu_bind_mGluR_Gq", - "Act_Gq", - "mGluR_bind_Gq", - "clus_S6K_deph", - "S6K_dephosp", - "S6K_deph", - "AKTpS473_deph", - "AKTpT308_deph", - "eEF2p_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "PP2A_dephos_I1", - "PP2A_dephos_PP1_Ip", - "clus_S6K_phospho", - "MAPKpp_feedback", - "MAPKpp_act_PLA2", - "Sos_phospho", - "MAPK_4EBPpp", - "MAPK_4EBP_phospho" - + {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+crafp","alias":"MAPKpp_feedback"},{"name":"eMAPK+PLA2","alias":"MAPKpp_act_PLA2"},{"name":"Sos_phospho","alias":"Sos_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"} ], "parameterChange": [ { - "entity": "Glutamate", + "name": "Glutamate", + "alias": "Glutamate", "field": "concInit", "value": 0.1, "units": "mM" diff --git a/TestJson/vclamp_hh.json b/TestJson/vclamp_hh.json index 085d87d..4b43ee3 100644 --- a/TestJson/vclamp_hh.json +++ b/TestJson/vclamp_hh.json @@ -24,111 +24,47 @@ { "timeUnits": "msec", "quantityUnits": "mV", - "entity": "soma", + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "Vclamp", "data": [ - [ - 0, - -65.0 - ], - [ - 10, - -25.0 - ], - [ - 60, - -65.0 - ], - [ - 100, - -65.0 - ] + [0,-65.0], + [10,-25.0], + [60,-65.0], + [100,-65.0] ] } ], "Readouts": { "timeUnits": "msec", "quantityUnits": "uA", - "entities": [ - "vclamp" - ], + "entity" : { + "name": "vclamp", + "alias": "vclamp" + }, "field": "current", "data": [ - [ - 0, - 0, - 0 - ], - [ - 10, - 0, - 0 - ], - [ - 11, - -7.0, - 0 - ], - [ - 12, - -2.0, - 0 - ], - [ - 13, - 1.5, - 0 - ], - [ - 14, - 3.2, - 0 - ], - [ - 16, - 6, - 0 - ], - [ - 20, - 6.9, - 0 - ], - [ - 60, - 6.9, - 0 - ], - [ - 61, - 1.2, - 0 - ], - [ - 62, - 0.8, - 0 - ], - [ - 63, - 0.6, - 0 - ], - [ - 64, - 0.4, - 0 - ], - [ - 100, - 0, - 0 - ] + [0, 0, 0], + [10, 0, 0], + [11, -7.0, 0], + [12, -2.0, 0], + [13, 1.5, 0], + [14, 3.2, 0], + [16, 6, 0], + [20, 6.9, 0], + [60, 6.9, 0], + [61, 1.2, 0], + [62, 0.8, 0], + [63, 0.6, 0], + [64, 0.4, 0], + [100, 0, 0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } From fd348174576abb59f7852f9282396b4e468dfffb Mon Sep 17 00:00:00 2001 From: hrani Date: Fri, 5 Apr 2024 21:38:42 +0530 Subject: [PATCH 7/8] Further clean up in TestJson files --- TestJson/epsp.json | 77 +++++++--------------- TestJson/epsp_ratio.json | 136 +++++++++++++++++++++------------------ 2 files changed, 99 insertions(+), 114 deletions(-) diff --git a/TestJson/epsp.json b/TestJson/epsp.json index 8a413e1..809058b 100644 --- a/TestJson/epsp.json +++ b/TestJson/epsp.json @@ -5,13 +5,13 @@ "email": "bhalla@ncbs.res.in", "source": { "sourceType": "inhouse", - "PMID": 0, + "url": "www.ncbs.res.in", "authors": "None", "journal": "None. This is a purely fictional _experiment_ for the purposes of testing findSim", "year": 0, "figure": "" }, - "testModel": "models/plastic8.py", + "testModel": "models/plastic8.py", "testMap": "models/plastic8.json" }, "Experiment": { @@ -24,77 +24,50 @@ { "timeUnits": "sec", "quantityUnits": "Hz", - "entity": "synInput", + "entity" : { + "name": "synInput", + "alias": "synInput" + }, "field": "rate", "data": [ - [ - 0, - 0 - ], - [ - 10, - 100 - ], - [ - 11, - 0 - ] + [0,0], + [10,100], + [11,0] ] }, { "timeUnits": "sec", "quantityUnits": "ratio", - "entity": "synapse", + "entity" : { + "name": "synapse", + "alias": "synapse" + }, "field": "weight", "data": [ - [ - 0, - 0.4 - ], - [ - 10, - 1 - ], - [ - 11, - 0.4 - ] + [0,0.4], + [10,1], + [11,0.4] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "mV", - "entities": [ - "soma" - ], + "entity" : { + "name": "soma", + "alias": "soma" + }, "field": "EPSP_peak", "data": [ - [ - 4, - 2, - 0 - ], - [ - 8, - 2, - 0 - ], - [ - 15, - 11, - 0 - ], - [ - 20, - 19, - 0 - ] + [4, 2, 0], + [8, 2, 0], + [15, 11, 0], + [20, 19, 0] ] }, "Modifications": { "subset": [ - "all" + {"name":"all"} ] } } diff --git a/TestJson/epsp_ratio.json b/TestJson/epsp_ratio.json index fd4f489..298be39 100644 --- a/TestJson/epsp_ratio.json +++ b/TestJson/epsp_ratio.json @@ -1,64 +1,76 @@ { - "Metadata": { - "transcriber": "Upinder S. Bhalla", - "organization": "NCBS", - "email": "bhalla@ncbs.res.in", - "source": { - "sourceType": "other", - "authors": "None", - "year": 2019, - "PMID": 0, - "figure": "synthetic" - }, - "testModel": "models/plastic8.py", - "testMap": "models/plastic8.json" - }, - "Experiment": { - "design": "TimeSeries", - "species": "rat", - "cellType": "hippocampal CA1 pyramidal neuron", - "temperature": 30, - "notes": "Synthetic dataset for testing purposes" - }, - "Stimuli": [ - { - "timeUnits": "sec", - "quantityUnits": "Hz", - "entity": "synInput", - "field": "rate", - "data": [ - [0, 0], - [10, 100], - [11, 0] - ] - }, - { - "timeUnits": "sec", - "quantityUnits": "ratio", - "entity": "synapse", - "field": "weight", - "data": [ - [0, 0.4], - [10, 1], - [11, 0.4] - ] - } - ], - - "Readouts": { - "timeUnits": "sec", - "quantityUnits": "ratio", - "entities": ["soma"], - "field": "EPSP_peak", - "normalization": { - "sampling": "start", - "entities": ["soma"] - }, - "data": [ - [4, 1], - [8, 1], - [15, 5.5], - [20, 8.5] - ] - } + "Metadata": { + "transcriber": "Upinder S. Bhalla", + "organization": "NCBS", + "email": "bhalla@ncbs.res.in", + "source": { + "sourceType": "other", + "doi": "www.ncbs.res.in", + "authors": "None", + "year": 2019, + "PMID": 0, + "figure": "synthetic" + }, + "testModel": "models/plastic8.py", + "testMap": "models/plastic8.json" + }, + "Experiment": { + "design": "TimeSeries", + "species": "rat", + "cellType": "hippocampal CA1 pyramidal neuron", + "temperature": 30, + "notes": "Synthetic dataset for testing purposes" + }, + "Stimuli": [ + { + "timeUnits": "sec", + "quantityUnits": "Hz", + "entity" : { + "name": "synInput", + "alias": "synInput" + }, + "field": "rate", + "data": [ + [0,0], + [10,100], + [11,0] + ] + }, + { + "timeUnits": "sec", + "quantityUnits": "ratio", + "entity" : { + "name": "synapse", + "alias": "synapse" + }, + "field": "weight", + "data": [ + [0,0.4], + [10,1], + [11,0.4] + ] + } + ], + "Readouts": { + "timeUnits": "sec", + "quantityUnits": "ratio", + "entity" : { + "name": "soma", + "alias": "soma" + }, + "field": "EPSP_peak", + "normalization": { + "sampling": "start", + "entity" : { + "name": "soma", + "alias": "soma" + } + }, + "data": [ + [4, 1], + [8, 1], + [15, 5.5], + [20, 8.5] + ] + } } From e8ad517eb9655b831e18b1edb14ecfd1003b0ecc Mon Sep 17 00:00:00 2001 From: hrani Date: Tue, 9 Apr 2024 17:27:16 +0530 Subject: [PATCH 8/8] Converted all Json experiment file to support newschema,update map file for the new naming and small chages in findsim.py and simWrapMoose.py to accodomate the changes --- Curated/Bhalla1999_Fig2B.json | 260 +++-- Curated/Bhalla1999_Fig4C.json | 538 +++------- Curated/Gu2004_fig3B.json | 145 +-- Curated/Jain2009_Fig2B.json | 53 +- Curated/Jain2009_Fig2F.json | 78 +- Curated/Jain2009_Fig3F.json | 80 +- Curated/Jain2009_Fig4C.json | 65 +- Curated/Jain2009_Fig4D.json | 80 +- Curated/Jain2009_Fig4F.json | 54 +- Curated/Jain2009_Fig5B.json | 78 +- Curated/Ji2010_fig1C_ERK_acute.json | 188 ++-- Curated/Mundell2001_Fig3B.json | 79 +- Curated/Tran2007_Fig2A.json | 107 +- Non-Curated/Jain2009_Fig2D.json | 58 +- findSim.py | 5 +- models/synSynth7_map.json | 1508 +++++++++++++++++++-------- simWrapMoose.py | 2 +- 17 files changed, 1704 insertions(+), 1674 deletions(-) diff --git a/Curated/Bhalla1999_Fig2B.json b/Curated/Bhalla1999_Fig2B.json index 7891375..94d1d6e 100644 --- a/Curated/Bhalla1999_Fig2B.json +++ b/Curated/Bhalla1999_Fig2B.json @@ -25,158 +25,154 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity": "EGF", + "entity" : { + "name": "EGF", + "alias": "EGF" + }, "field": "conc", "data": [ - [ - 2100, - 0.0001 - ] + [2100,0.0001] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "aMAPK" - ], + "entity" : { + "name": "aMAPK", + "alias": "aMAPK" + }, "field": "conc", "normalization": { - "time": 2400, - "entities": [ - "aMAPK" - ], + "entity" : { + "name": "aMAPK", + "alias": "aMAPK" + }, "dose": 0, - "sampling": "presetTime" + "sampling": "presetTime", + "sampTime": 2400 }, "data": [ - [ - 2100, - 0.02, - 0.06 - ], - [ - 2400, - 1, - 0 - ], - [ - 3900, - 0.12, - 0.17 - ], - [ - 5700, - 0.1, - 0.1 - ], - [ - 9300, - 0.08, - 0.08 - ] + [2100, 0.02, 0.06], + [2400, 1, 0], + [3900, 0.12, 0.17], + [5700, 0.1, 0.1], + [9300, 0.08, 0.08] ] }, "Modifications": { "subset": [ - "EGFR_g", - "Sos_g", - "Ras_g", - "MAPK_g", - "Ca_g", - "PKC_g", - "Phosphatase_g", - "PLCg_g", - "PLCb_g", - "PLA2_g", - "PC", - "IP3", - "PIP2" + {"name":"EGFR_g","alias":"EGFR_g"},{"name":"Sos_g","alias":"Sos_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"Ca_g","alias":"Ca_g"},{"name":"PKC_g","alias":"PKC_g"},{"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"PLCb_g","alias":"PLCb_g"},{"name":"PLA2_g","alias":"PLA2_g"},{"name":"PC","alias":"PC"},{"name":"IP3","alias":"IP3"},{"name":"PIP2","alias":"PIP2"} ], "itemsToDelete": [ - "PP2A", - "phospho_AC2", - "GEF_Gprot_bg", - "bg_act_GEF", - "MEK_phospho", - "MEKp_phospho", - "mGluR_barr2_Raf", - "clus_S6K_phospho", - "MAPK_4EBPpp", - "MAPK_4EBP_phospho", - "Act_PLC_by_Gq", - "Inact_PLC_Gq", - "PLC_bind_Gq", - "PKC_phospho_ng", - "PKC_phospho_ng_CaM", - "PIP2_PLA2_act", - "PIP2_Ca_PLA2_act", - "CaM_bind_GEF", - "PI3K_bind_RasGTP", - "PIP2_phospho_Ras_GTP" + {"name":"PP2A","alias":"PP2A"},{"name":"phospho_AC2","alias":"phospho_AC2"},{"name":"GEF_Gprot_bg","alias":"GEF_Gprot_bg"},{"name":"bg_act_GEF","alias":"bg_act_GEF"},{"name":"ecraf+MAPKK","alias":"MEK_phospho"},{"name":"ecraf+MAPKKp","alias":"MEKp_phospho"},{"name":"craf1+barr2","alias":"mGluR_barr2_Raf"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"},{"name":"PLC_Ca+Gq","alias":"Act_PLC_by_Gq"},{"name":"Inact_PLC_Gq","alias":"Inact_PLC_Gq"},{"name":"PLC_bind_Gq","alias":"PLC_bind_Gq"},{"name":"PKC_phospho_ng","alias":"PKC_phospho_ng"},{"name":"PKC_phospho_ng_CaM","alias":"PKC_phospho_ng_CaM"},{"name":"PIP2_PLA2_act","alias":"PIP2_PLA2_act"},{"name":"PIP2_Ca_PLA2_act","alias":"PIP2_Ca_PLA2_act"},{"name":"CaMCa4+GEF","alias":"CaM_bind_GEF"},{"name":"PI3K+RasGTP","alias":"PI3K_bind_RasGTP"},{"name":"PIP2_phospho_Ras_GTP","alias":"PIP2_phospho_Ras_GTP"} ], - "parameterChange" : - [{"entity": "bPKCp", - "field": "concInit", - "value" :2.00E-05, - "units" :"mM"}, - {"entity": "GAP", - "field": "concInit", - "value" :2.0E-5, - "units" :"mM"}, - {"entity": "PIP2", - "field": "concInit", - "value" :0.007, - "units" :"mM"}, - {"entity": "RasGDP", - "field": "concInit", - "value" :0.0005, - "units" :"mM"}, - {"entity": "SHCp_deph", - "field": "Kf", - "value" :0.2, - "units" :"none"}, - {"entity": "Ras_act_craf", - "field": "Kf", - "value" :9999.2668, - "units" :"none"}, - {"entity": "PKC_act_raf", - "field": "Km", - "value" :0.02098, - "units" :"none"}, - {"entity": "MKP1pY421_deph", - "field": "Km", - "value" :0.00734, - "units" :"none"}, - {"entity": "MKP1pT424_deph", - "field": "Km", - "value" :0.00734, - "units" :"none"}, - {"entity": "MKP1pT424_deph", - "field": "kcat", - "value" :4, - "units" :"none"}, - {"entity": "MKP1pY421_deph", - "field": "kcat", - "value" :4, - "units" :"none"}, - {"entity": "Rafp_RasGTP1", - "field": "kcat", - "value" :0.3, - "units" :"none"}, - {"entity": "Rafp_RasGTP2", - "field": "kcat", - "value" :0.3, - "units" :"none"}, - {"entity": "CaMGEF_actRas", - "field": "kcat", - "value" :0.02, - "units" :"none"}, - {"entity": "Sos_Ras_GEF", - "field": "kcat", - "value" :0.2, - "units" :"none"} + "parameterChange": [ + { + "name": "bPKC", + "alias": "bPKCp", + "field": "concInit", + "value": 2e-05, + "units": "mM" + }, + { + "name": "GAP", + "alias": "GAP", + "field": "concInit", + "value": 2e-05, + "units": "mM" + }, + { + "name": "PIP2", + "alias": "PIP2", + "field": "concInit", + "value": 0.007, + "units": "mM" + }, + { + "name": "RasGDP", + "alias": "RasGDP", + "field": "concInit", + "value": 0.0005, + "units": "mM" + }, + { + "name": "SHCp_deph", + "alias": "SHCp_deph", + "field": "Kf", + "value": 0.2, + "units": "none" + }, + { + "name": "Ras+craf", + "alias": "Ras_act_craf", + "field": "Kf", + "value": 9999.2668, + "units": "none" + }, + { + "name": "ePKC+craf", + "alias": "PKC_act_raf", + "field": "Km", + "value": 0.02098, + "units": "none" + }, + { + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", + "field": "Km", + "value": 0.00734, + "units": "none" + }, + { + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", + "field": "Km", + "value": 0.00734, + "units": "none" + }, + { + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", + "field": "kcat", + "value": 4, + "units": "none" + }, + { + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", + "field": "kcat", + "value": 4, + "units": "none" + }, + { + "name": "eRas+MAPKK1", + "alias": "Rafp_RasGTP1", + "field": "kcat", + "value": 0.3, + "units": "none" + }, + { + "name": "eRas+MAPKK2", + "alias": "Rafp_RasGTP2", + "field": "kcat", + "value": 0.3, + "units": "none" + }, + { + "name": "eCaMGEF+Ras", + "alias": "CaMGEF_actRas", + "field": "kcat", + "value": 0.02, + "units": "none" + }, + { + "name": "eSHCpSosGrb2+Ras", + "alias": "Sos_Ras_GEF", + "field": "kcat", + "value": 0.2, + "units": "none" + } ], "notes": "Bhalla1999_Fig2B" } diff --git a/Curated/Bhalla1999_Fig4C.json b/Curated/Bhalla1999_Fig4C.json index c0198eb..b542c15 100644 --- a/Curated/Bhalla1999_Fig4C.json +++ b/Curated/Bhalla1999_Fig4C.json @@ -24,572 +24,326 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Ca", + "entity" : { + "name": "Ca", + "alias": "Ca" + }, "field": "conc", "data": [ - [ - 1000, - 10 - ], - [ - 1000.2, - 9 - ], - [ - 1000.4, - 8 - ], - [ - 1000.8, - 7 - ], - [ - 1001, - 4 - ], - [ - 1002, - 1 - ], - [ - 1003, - 0.92 - ], - [ - 1004, - 0.8 - ], - [ - 1005, - 0.7 - ], - [ - 1006, - 0.6 - ], - [ - 1007, - 0.5 - ], - [ - 1008, - 0.48 - ], - [ - 1010, - 0.42 - ], - [ - 1012, - 0.38 - ], - [ - 1014, - 0.32 - ], - [ - 1016, - 0.28 - ], - [ - 1018, - 0.22 - ], - [ - 1020, - 0.18 - ], - [ - 1022, - 0.12 - ], - [ - 1032, - 0.1 - ], - [ - 1036, - 0.08 - ], - [ - 1600, - 10 - ], - [ - 1600.2, - 9 - ], - [ - 1600.4, - 8 - ], - [ - 1600.8, - 7 - ], - [ - 1601, - 4 - ], - [ - 1602, - 1 - ], - [ - 1603, - 0.92 - ], - [ - 1604, - 0.8 - ], - [ - 1605, - 0.7 - ], - [ - 1606, - 0.6 - ], - [ - 1607, - 0.5 - ], - [ - 1608, - 0.48 - ], - [ - 1610, - 0.42 - ], - [ - 1612, - 0.38 - ], - [ - 1614, - 0.32 - ], - [ - 1616, - 0.28 - ], - [ - 1618, - 0.22 - ], - [ - 1620, - 0.18 - ], - [ - 1622, - 0.12 - ], - [ - 1632, - 0.1 - ], - [ - 1636, - 0.08 - ], - [ - 2200, - 10 - ], - [ - 2200.2, - 9 - ], - [ - 2200.4, - 8 - ], - [ - 2200.8, - 7 - ], - [ - 2201, - 4 - ], - [ - 2202, - 1 - ], - [ - 2203, - 0.92 - ], - [ - 2204, - 0.8 - ], - [ - 2205, - 0.7 - ], - [ - 2206, - 0.6 - ], - [ - 2207, - 0.5 - ], - [ - 2208, - 0.48 - ], - [ - 2210, - 0.42 - ], - [ - 2212, - 0.38 - ], - [ - 2214, - 0.32 - ], - [ - 2216, - 0.28 - ], - [ - 2218, - 0.22 - ], - [ - 2220, - 0.18 - ], - [ - 2222, - 0.12 - ], - [ - 2232, - 0.1 - ], - [ - 2236, - 0.08 - ] + [1000,10], + [1000.2,9], + [1000.4,8], + [1000.8,7], + [1001,4], + [1002,1], + [1003,0.92], + [1004,0.8], + [1005,0.7], + [1006,0.6], + [1007,0.5], + [1008,0.48], + [1010,0.42], + [1012,0.38], + [1014,0.32], + [1016,0.28], + [1018,0.22], + [1020,0.18], + [1022,0.12], + [1032,0.1], + [1036,0.08], + [1600,10], + [1600.2,9], + [1600.4,8], + [1600.8,7], + [1601,4], + [1602,1], + [1603,0.92], + [1604,0.8], + [1605,0.7], + [1606,0.6], + [1607,0.5], + [1608,0.48], + [1610,0.42], + [1612,0.38], + [1614,0.32], + [1616,0.28], + [1618,0.22], + [1620,0.18], + [1622,0.12], + [1632,0.1], + [1636,0.08], + [2200,10], + [2200.2,9], + [2200.4,8], + [2200.8,7], + [2201,4], + [2202,1], + [2203,0.92], + [2204,0.8], + [2205,0.7], + [2206,0.6], + [2207,0.5], + [2208,0.48], + [2210,0.42], + [2212,0.38], + [2214,0.32], + [2216,0.28], + [2218,0.22], + [2220,0.18], + [2222,0.12], + [2232,0.1], + [2236,0.08] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "uM", - "entities": [ - "MAPKpp" - ], + "entity" : { + "name": "MAPKpq", + "alias": "MAPKpp" + }, "field": "conc", "data": [ - [ - 600, - 0.0001, - 0 - ], - [ - 1000, - 0.0002, - 0 - ], - [ - 1200, - 0.0005, - 0 - ], - [ - 1800, - 0.01, - 0 - ], - [ - 2400, - 0.03, - 0 - ], - [ - 3000, - 0.13, - 0 - ], - [ - 3600, - 0.18, - 0 - ], - [ - 4200, - 0.21, - 0 - ], - [ - 4800, - 0.22, - 0 - ] + [600, 0.0001, 0], + [1000, 0.0002, 0], + [1200, 0.0005, 0], + [1800, 0.01, 0], + [2400, 0.03, 0], + [3000, 0.13, 0], + [3600, 0.18, 0], + [4200, 0.21, 0], + [4800, 0.22, 0] ] }, "Modifications": { "subset": [ - "Ca_g", - "Phosphatase_g", - "Gprotein_g", - "mGluR_g", - "AC_g", - "PKA_g", - "PP2B_g", - "PLCg_g", - "Ras_g", - "MAPK_g", - "PP1_g", - "CaM_g", - "CaMKII_g", - "mGluRAntag_g", - "PLCb_g", - "PLA2_g", - "PKC_g", - "PIP2", - "temp_PIP2", - "IP3", - "EGFR_g", - "Sos_g" + {"name":"Ca_g","alias":"Ca_g"},{"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"Gprotein_g","alias":"Gprotein_g"},{"name":"mGluR_g","alias":"mGluR_g"},{"name":"AC_g","alias":"AC_g"},{"name":"PKA_g","alias":"PKA_g"},{"name":"PP2B_g","alias":"PP2B_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"PP1_g","alias":"PP1_g"},{"name":"CaM_g","alias":"CaM_g"},{"name":"CaMKII_g","alias":"CaMKII_g"},{"name":"mGluRAntag_g","alias":"mGluRAntag_g"},{"name":"PLCb_g","alias":"PLCb_g"},{"name":"PLA2_g","alias":"PLA2_g"},{"name":"PKC_g","alias":"PKC_g"},{"name":"PIP2","alias":"PIP2"},{"name":"temp_PIP2","alias":"temp_PIP2"},{"name":"IP3","alias":"IP3"},{"name":"EGFR_g","alias":"EGFR_g"},{"name":"Sos_g","alias":"Sos_g"} ], "itemsToDelete": [ - "clus_S6K_deph", - "S6K_dephosp", - "Gab1", - "bPI3K", - "PI3K", - "PIP3", - "PTEN", - "SHCpGrb2Gab1_PI3K", - "bPLCg", - "bGEF_act", - "RasGTP_PI3K", - "S6K_deph", - "SHCpGrb2_Gab1", - "PI3K_act", - "bPI3K_act", - "PI3K_bind_RasGTP", - "AKTpS473_deph", - "AKTpT308_deph", - "eEF2p_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "aCaMKIII", - "PLCgp_deph", - "Grb2_bind_SHC", - "PDK1_act_S6K", - "phospho_AKTpT308", - "phospho_AKTpS473", - "clus_S6K_phospho", - "MAPK_4EBPpp", - "MAPK_4EBP_phospho", - "MEK_phospho", - "MEKp_phospho", - "AKTpT308S473", - "mGluR_barr2_Raf", - "mGluR_deph" + {"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"Gab1","alias":"Gab1"},{"name":"bPI3K","alias":"bPI3K"},{"name":"PI3K","alias":"PI3K"},{"name":"PIP3","alias":"PIP3"},{"name":"PTEN","alias":"PTEN"},{"name":"SHCpGrb2Gab1_PI3K","alias":"SHCpGrb2Gab1_PI3K"},{"name":"bPLCg","alias":"bPLCg"},{"name":"ebGEF+Ras","alias":"bGEF_act"},{"name":"RasGTP_PI3K","alias":"RasGTP_PI3K"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"SHCpGrb2_Gab1","alias":"SHCpGrb2_Gab1"},{"name":"SHCpGrb2Gab1+PI3K","alias":"PI3K_act"},{"name":"bPI3K_act","alias":"bPI3K_act"},{"name":"PI3K+RasGTP","alias":"PI3K_bind_RasGTP"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"aCaMKIII","alias":"aCaMKIII"},{"name":"PLCgp_deph","alias":"PLCgp_deph"},{"name":"SHCp+Grb2","alias":"Grb2_bind_SHC"},{"name":"PDK1_act_S6K","alias":"PDK1_act_S6K"},{"name":"ePI3K+AKT","alias":"phospho_AKTpT308"},{"name":"ePDK2+AKTp","alias":"phospho_AKTpS473"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"},{"name":"ecraf+MAPKK","alias":"MEK_phospho"},{"name":"ecraf+MAPKKp","alias":"MEKp_phospho"},{"name":"aAKT","alias":"AKTpT308S473"},{"name":"craf1+barr2","alias":"mGluR_barr2_Raf"},{"name":"mGluR_deph","alias":"mGluR_deph"} ], "parameterChange": [ { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "concInit", "value": 8e-05, "units": "mM" }, { - "entity": "Ca", + "name": "Ca", + "alias": "Ca", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "MKP1", + "name": "MKP1", + "alias": "MKP1", "field": "concInit", "value": 2e-06, "units": "mM" }, { - "entity": "Ras_act_craf", + "name": "Ras+craf", + "alias": "Ras_act_craf", "field": "Kf", "value": 24000, "units": "none" }, { - "entity": "CaM_bind_GEF", + "name": "CaMCa4+GEF", + "alias": "CaM_bind_GEF", "field": "Kf", "value": 60000, "units": "none" }, { - "entity": "MAPK", + "name": "MAPK", + "alias": "MAPK", "field": "concInit", "value": 0.00036, "units": "mM" }, { - "entity": "MAPKKthr", + "name": "eMAPKK+MAPKp", + "alias": "MAPKKthr", "field": "kcat", "value": 0.15, "units": "none" }, { - "entity": "MAPKKtyr", + "name": "eMAPKK+MAPK", + "alias": "MAPKKtyr", "field": "kcat", "value": 0.15, "units": "none" }, { - "entity": "Rafp_RasGTP1", + "name": "eRas+MAPKK1", + "alias": "Rafp_RasGTP1", "field": "kcat", "value": 0.105, "units": "none" }, { - "entity": "Rafp_RasGTP2", + "name": "eRas+MAPKK2", + "alias": "Rafp_RasGTP2", "field": "kcat", "value": 0.105, "units": "none" }, { - "entity": "MKP1pT424_deph", + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", "field": "kcat", "value": 1, "units": "none" }, { - "entity": "MKP1pY421_deph", + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", "field": "kcat", "value": 1, "units": "none" }, { - "entity": "MKP1pT424_deph", + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", "field": "Km", "value": 6.97e-05, "units": "none" }, { - "entity": "MKP1pY421_deph", + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", "field": "Km", "value": 6.97e-05, "units": "none" }, { - "entity": "EGFR_act_SHC", + "name": "eEGFR+SHC", + "alias": "EGFR_act_SHC", "field": "Km", "value": 0.000871, "units": "none" }, { - "entity": "SHCp_deph", + "name": "SHCp_deph", + "alias": "SHCp_deph", "field": "Kf", "value": 0.00167, "units": "none" }, { - "entity": "Sos_Ras_GEF", + "name": "eSHCpSosGrb2+Ras", + "alias": "Sos_Ras_GEF", "field": "kcat", "value": 0.02, "units": "none" }, { - "entity": "PKC_act_raf", + "name": "ePKC+craf", + "alias": "PKC_act_raf", "field": "Km", "value": 0.0697, "units": "none" }, { - "entity": "CaMGEF_actRas", + "name": "eCaMGEF+Ras", + "alias": "CaMGEF_actRas", "field": "kcat", "value": 0.02, "units": "none" }, { - "entity": "bPKCp", + "name": "bPKC", + "alias": "bPKCp", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "craf1", + "name": "craf1", + "alias": "craf1", "field": "concInit", "value": 0.0002, "units": "mM" }, { - "entity": "MAPKK", + "name": "MAPKK", + "alias": "MAPKK", "field": "concInit", "value": 0.00018, "units": "mM" }, { - "entity": "PP2A", + "name": "PP2A", + "alias": "PP2A", "field": "concInit", "value": 0.00012, "units": "mM" }, { - "entity": "PPhosphatase2A", + "name": "PPhosphatase2A", + "alias": "PPhosphatase2A", "field": "concInit", "value": 0.000224, "units": "mM" }, { - "entity": "PIP2", + "name": "PIP2", + "alias": "PIP2", "field": "concInit", "value": 0.01, "units": "mM" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "isBuffered", "value": 0, "units": "none" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "isBuffered", "value": 0, "units": "none" }, { - "entity": "AA", + "name": "AA", + "alias": "AA", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "DAG", + "name": "DAG", + "alias": "DAG", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "PLCg", + "name": "PLCg", + "alias": "PLCg", "field": "concInit", "value": 0.00082, "units": "mM" }, { - "entity": "GAP", + "name": "GAP", + "alias": "GAP", "field": "concInit", "value": 2e-06, "units": "mM" }, { - "entity": "RasGDP", + "name": "RasGDP", + "alias": "RasGDP", "field": "concInit", "value": 0.0002, "units": "mM" diff --git a/Curated/Gu2004_fig3B.json b/Curated/Gu2004_fig3B.json index 6561f60..524f8c7 100644 --- a/Curated/Gu2004_fig3B.json +++ b/Curated/Gu2004_fig3B.json @@ -24,195 +24,156 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "EGF", + "entity" : { + "name": "EGF", + "alias": "EGF" + }, "field": "conc", "data": [ - [ - 3600, - 1.0 - ] + [3600,1.0] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "aMAPK" - ], + "entity" : { + "name": "aMAPK", + "alias": "aMAPK" + }, "field": "conc", "normalization": { - "time": 3600, - "entities": [ - "aMAPK" - ], - "dose": 0, + "entity" : { + "name": "aMAPK", + "alias": "aMAPK" + }, "sampling": "start" }, "data": [ - [ - 3600, - 1, - 0 - ], - [ - 3900, - 2.5, - 1 - ], - [ - 5400, - 1.5, - 0.3 - ], - [ - 7200, - 1.3, - 0.6 - ], - [ - 14400, - 1.2, - 0.5 - ], - [ - 36000, - 1, - 0.5 - ] + [3600, 1, 0], + [3900, 2.5, 1], + [5400, 1.5, 0.3], + [7200, 1.3, 0.6], + [14400, 1.2, 0.5], + [36000, 1, 0.5] ] }, "Modifications": { "subset": [ - "EGFR_g", - "Sos_g", - "Ras_g", - "MAPK_g", - "Ca_g", - "PKC_g", - "Phosphatase_g", - "PLCg_g", - "PLCb_g", - "PLA2_g", - "PC", - "IP3", - "PIP2" + {"name":"EGFR_g","alias":"EGFR_g"},{"name":"Sos_g","alias":"Sos_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"Ca_g","alias":"Ca_g"},{"name":"PKC_g","alias":"PKC_g"},{"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"PLCb_g","alias":"PLCb_g"},{"name":"PLA2_g","alias":"PLA2_g"},{"name":"PC","alias":"PC"},{"name":"IP3","alias":"IP3"},{"name":"PIP2","alias":"PIP2"} ], "itemsToDelete": [ - "PP2A", - "phosph_AC2", - "GEF_Gprot_bg", - "bg_act_GEF", - "MEK_phospho", - "MEKp_phospho", - "mGluR_barr2_Raf_scaffolding", - "MAPK_p_p/cluster_phospho_S6K", - "MAPK_p_p/MAPK_4E_BP_p_p", - "MAPK_p_p/MAPK_4E_BP_phospho", - "Act_PLC_by_Gq", - "Inact_PLC_Gq", - "PLC_bind_Gq", - "PKC_phosph_neurogranin", - "PKC_phosph_ng_CaM", - "PIP2_PLA2_act", - "PIP2_Ca_PLA2_act", - "CaM_bind_GEF", - "PI3K_bind_Ras_GTP", - "PIP2_phospho_Ras_GTP" + {"name":"PP2A","alias":"PP2A"},{"name":"phosph_AC2","alias":"phosph_AC2"},{"name":"GEF_Gprot_bg","alias":"GEF_Gprot_bg"},{"name":"bg_act_GEF","alias":"bg_act_GEF"},{"name":"ecraf+MAPKK","alias":"MEK_phospho"},{"name":"ecraf+MAPKKp","alias":"MEKp_phospho"},{"name":"mGluR_barr2_Raf_scaffolding","alias":"mGluR_barr2_Raf_scaffolding"},{"name":"MAPK_p_p/cluster_phospho_S6K","alias":"MAPK_p_p/cluster_phospho_S6K"},{"name":"MAPK_p_p/MAPK_4E_BP_p_p","alias":"MAPK_p_p/MAPK_4E_BP_p_p"},{"name":"MAPK_p_p/MAPK_4E_BP_phospho","alias":"MAPK_p_p/MAPK_4E_BP_phospho"},{"name":"PLC_Ca+Gq","alias":"Act_PLC_by_Gq"},{"name":"Inact_PLC_Gq","alias":"Inact_PLC_Gq"},{"name":"PLC_bind_Gq","alias":"PLC_bind_Gq"},{"name":"PKC_phosph_neurogranin","alias":"PKC_phosph_neurogranin"},{"name":"PKC_phosph_ng_CaM","alias":"PKC_phosph_ng_CaM"},{"name":"PIP2_PLA2_act","alias":"PIP2_PLA2_act"},{"name":"PIP2_Ca_PLA2_act","alias":"PIP2_Ca_PLA2_act"},{"name":"CaMCa4+GEF","alias":"CaM_bind_GEF"},{"name":"PI3K_bind_Ras_GTP","alias":"PI3K_bind_Ras_GTP"},{"name":"PIP2_phospho_Ras_GTP","alias":"PIP2_phospho_Ras_GTP"} ], "parameterChange": [ { - "entity": "EGF", + "name": "EGF", + "alias": "EGF", "field": "concInit", "value": 0.0, "units": "mM" }, { - "entity": "bPKCp", + "name": "bPKC", + "alias": "bPKCp", "field": "concInit", "value": 2e-05, "units": "mM" }, { - "entity": "GAP", + "name": "GAP", + "alias": "GAP", "field": "concInit", "value": 2e-05, "units": "mM" }, { - "entity": "PIP2", + "name": "PIP2", + "alias": "PIP2", "field": "concInit", "value": 0.007, "units": "mM" }, { - "entity": "enolase", + "name": "enolase", + "alias": "enolase", "field": "concInit", "value": 0.0005, "units": "mM" }, { - "entity": "SHCp_deph", + "name": "SHCp_deph", + "alias": "SHCp_deph", "field": "Kf", "value": 0.2, "units": "none" }, { - "entity": "Ras_act_craf", + "name": "Ras+craf", + "alias": "Ras_act_craf", "field": "Kf", "value": 9999.26668, "units": "none" }, { - "entity": "PKC_act_raf", + "name": "ePKC+craf", + "alias": "PKC_act_raf", "field": "Km", "value": 0.02098, "units": "none" }, { - "entity": "MKP1pY421_deph", + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", "field": "Km", "value": 0.00734, "units": "none" }, { - "entity": "MKP1pT424_deph", + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", "field": "Km", "value": 0.00734, "units": "none" }, { - "entity": "MKP1pT424_deph", + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", "field": "kcat", "value": 4, "units": "none" }, { - "entity": "MKP1pY421_deph", + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", "field": "kcat", "value": 4, "units": "none" }, { - "entity": "Rafp_RasGTP1", + "name": "eRas+MAPKK1", + "alias": "Rafp_RasGTP1", "field": "kcat", "value": 0.3, "units": "none" }, { - "entity": "Rafp_RasGTP2", + "name": "eRas+MAPKK2", + "alias": "Rafp_RasGTP2", "field": "kcat", "value": 0.3, "units": "none" }, { - "entity": "CaMGEF_actRas", + "name": "eCaMGEF+Ras", + "alias": "CaMGEF_actRas", "field": "kcat", "value": 0.2, "units": "none" }, { - "entity": "Sos_Ras_GEF", + "name": "eSHCpSosGrb2+Ras", + "alias": "Sos_Ras_GEF", "field": "kcat", "value": 0.2, "units": "none" diff --git a/Curated/Jain2009_Fig2B.json b/Curated/Jain2009_Fig2B.json index cec3c3d..fdc339d 100644 --- a/Curated/Jain2009_Fig2B.json +++ b/Curated/Jain2009_Fig2B.json @@ -25,59 +25,38 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "BDNF", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, "field": "conc", "data": [ - [ - 0, - 7.3 - ] + [0,7.3] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entities": [ - "BDNF_act_TrKB" - ], + "entity" : { + "name": "BDNF_act_TrKB", + "alias": "BDNF_act_TrKB" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 30, - 1, - 0 - ], - [ - 300, - 14.5, - 0 - ], - [ - 900, - 9.5, - 0 - ], - [ - 1800, - 7.5, - 0 - ] + [0, 0, 0], + [30, 1, 0], + [300, 14.5, 0], + [900, 9.5, 0], + [1800, 7.5, 0] ] }, "Modifications": { "subset": [ - "BDNF_g", - "TrKB_g" + {"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"} ], "itemsToDelete": [ - "TrKB_act_PLCg", - "TrKB_act_SHC" + {"name":"eTrKB+PLCg","alias":"TrKB_act_PLCg"},{"name":"eTrKB+SHC","alias":"TrKB_act_SHC"} ], "notes": "Jain2009_Fig2B" } diff --git a/Curated/Jain2009_Fig2F.json b/Curated/Jain2009_Fig2F.json index f69f0a7..124b3d5 100644 --- a/Curated/Jain2009_Fig2F.json +++ b/Curated/Jain2009_Fig2F.json @@ -25,87 +25,51 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "PDK1", + "entity" : { + "name": "PDK1", + "alias": "PDK1" + }, "field": "conc", "data": [ - [ - 0, - 3.5 - ] + [0,3.5] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entities": [ - "AKTpT308" - ], + "entity" : { + "name": "AKTp", + "alias": "AKTpT308" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 300, - 18, - 0 - ], - [ - 600, - 25, - 0 - ], - [ - 1200, - 40, - 0 - ], - [ - 2400, - 70, - 0 - ], - [ - 4800, - 110, - 0 - ] + [0, 0, 0], + [300, 18, 0], + [600, 25, 0], + [1200, 40, 0], + [2400, 70, 0], + [4800, 110, 0] ] }, "Modifications": { "subset": [ - "AKT_g", - "PI3K_g" + {"name":"AKT_g","alias":"AKT_g"},{"name":"PI3K_g","alias":"PI3K_g"} ], "itemsToDelete": [ - "PTEN", - "RasGTP_PI3K", - "bind_Gab1", - "temp_PIP2", - "SHCpGrb2Gab1_PI3K", - "PI3K", - "Gab1", - "bPI3K", - "SHCpGrb2_Gab1", - "PI3K_act", - "bPI3K_act", - "PI3K_bind_RasGTP", - "PIP3_PDK2", - "AKTpT308S473", - "PDK1_act_S6K" + {"name":"PTEN","alias":"PTEN"},{"name":"RasGTP_PI3K","alias":"RasGTP_PI3K"},{"name":"SHCp_Grb2+Gab1","alias":"bind_Gab1"},{"name":"temp_PIP2","alias":"temp_PIP2"},{"name":"SHCpGrb2Gab1_PI3K","alias":"SHCpGrb2Gab1_PI3K"},{"name":"PI3K","alias":"PI3K"},{"name":"Gab1","alias":"Gab1"},{"name":"bPI3K","alias":"bPI3K"},{"name":"SHCpGrb2_Gab1","alias":"SHCpGrb2_Gab1"},{"name":"SHCpGrb2Gab1+PI3K","alias":"PI3K_act"},{"name":"bPI3K_act","alias":"bPI3K_act"},{"name":"PI3K+RasGTP","alias":"PI3K_bind_RasGTP"},{"name":"PIP3_PDK2","alias":"PIP3_PDK2"},{"name":"aAKT","alias":"AKTpT308S473"},{"name":"PDK1_act_S6K","alias":"PDK1_act_S6K"} ], "parameterChange": [ { - "entity": "PIP3", + "name": "PIP3", + "alias": "PIP3", "field": "concInit", "value": 0.00025, "units": "mM" }, { - "entity": "AKT", + "name": "AKT", + "alias": "AKT", "field": "concInit", "value": 0.0005, "units": "mM" diff --git a/Curated/Jain2009_Fig3F.json b/Curated/Jain2009_Fig3F.json index 8f7ba94..f65dfbd 100644 --- a/Curated/Jain2009_Fig3F.json +++ b/Curated/Jain2009_Fig3F.json @@ -25,94 +25,68 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity": "eIF4E", + "entity" : { + "name": "eIF4E", + "alias": "eIF4E" + }, "field": "conc" } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "uM", - "entities": [ - "eIF4E_4EBP" - ], + "entity" : { + "name": "eIF4E_4EBP", + "alias": "eIF4E_4EBP" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 13, - 50, - 0 - ], - [ - 20, - 80, - 0 - ], - [ - 25, - 95, - 0 - ], - [ - 35, - 115, - 0 - ], - [ - 50, - 123, - 0 - ], - [ - 80, - 131, - 0 - ], - [ - 100, - 132, - 0 - ] + [0, 0, 0], + [13, 50, 0], + [20, 80, 0], + [25, 95, 0], + [35, 115, 0], + [50, 123, 0], + [80, 131, 0], + [100, 132, 0] ] }, "Modifications": { "subset": [ - "eIF4E_4EBP", - "eIF4E_bind_BP2", - "4EBP", - "eIF4E" + {"name":"eIF4E_4EBP","alias":"eIF4E_4EBP"},{"name":"eIF4E+4EBP","alias":"eIF4E_bind_BP2"},{"name":"4EBP","alias":"4EBP"},{"name":"eIF4E","alias":"eIF4E"} ], "parameterChange": [ { - "entity": "eIF4E", + "name": "eIF4E", + "alias": "eIF4E", "field": "concInit", "value": 0.0016, "units": "mM" }, { - "entity": "eIF4E", + "name": "eIF4E", + "alias": "eIF4E", "field": "isBuffered", "value": 1, "units": "none" }, { - "entity": "eIF4E_4EBP", + "name": "eIF4E_4EBP", + "alias": "eIF4E_4EBP", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "4EBP", + "name": "4EBP", + "alias": "4EBP", "field": "concInit", "value": 0.00027, "units": "mM" }, { - "entity": "4EBP", + "name": "4EBP", + "alias": "4EBP", "field": "isBuffered", "value": 1, "units": "none" diff --git a/Curated/Jain2009_Fig4C.json b/Curated/Jain2009_Fig4C.json index 2fb6644..9e7d9b8 100644 --- a/Curated/Jain2009_Fig4C.json +++ b/Curated/Jain2009_Fig4C.json @@ -24,78 +24,57 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity": "S6KpT229", + "entity" : { + "name": "S6Kpqrs", + "alias": "S6KpT229" + }, "field": "conc", "data": [ - [ - 0, - 1.67e-06 - ] + [0,1.67e-06] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entities": [ - "CaMKIIIp" - ], + "entity" : { + "name": "bCaMKIII", + "alias": "CaMKIIIp" + }, "field": "conc", "data": [ - [ - 60, - 8, - 0 - ], - [ - 180, - 12, - 0 - ], - [ - 300, - 26, - 0 - ], - [ - 600, - 25, - 0 - ], - [ - 900, - 50, - 0 - ] + [60, 8, 0], + [180, 12, 0], + [300, 26, 0], + [600, 25, 0], + [900, 50, 0] ] }, "Modifications": { "subset": [ - "CaMKIII_g", - "S6K_g" + {"name":"CaMKIII_g","alias":"CaMKIII_g"},{"name":"S6K_g","alias":"S6K_g"} ], "itemsToDelete": [ - "S6_phos", - "S6_phospho", - "S6_dephosph", - "CaMKIII_CaM_Ca4[0]/phospho", - "eEF2thr56_basal" + {"name":"eS6Kpqr+40S","alias":"S6_phos"},{"name":"eS6Kpqrs+40S","alias":"S6_phospho"},{"name":"CaMKIII_CaM_Ca4[0]/phospho","alias":"CaMKIII_CaM_Ca4[0]/phospho"},{"name":"eEF2thr56_basal","alias":"eEF2thr56_basal"} ], "parameterChange": [ { - "entity": "bS6K", + "name": "bS6K", + "alias": "bS6K", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "CaMKIII", + "name": "CaMKIII", + "alias": "CaMKIII", "field": "concInit", "value": 6.8e-05, "units": "mM" }, { - "entity": "CaMKIII_deph", + "name": "CaMKIIIp_deph", + "alias": "CaMKIII_deph", "field": "Kf", "value": 0, "units": "none" diff --git a/Curated/Jain2009_Fig4D.json b/Curated/Jain2009_Fig4D.json index bc55ad9..659a9aa 100644 --- a/Curated/Jain2009_Fig4D.json +++ b/Curated/Jain2009_Fig4D.json @@ -25,90 +25,56 @@ { "timeUnits": "sec", "quantityUnits": "mM", - "entity": "eEF2p", + "entity" : { + "name": "eEF2p", + "alias": "eEF2p" + }, "field": "conc" } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "nM", - "entities": [ - "eEF2" - ], + "entity" : { + "name": "eEF2", + "alias": "eEF2" + }, "field": "conc", "data": [ - [ - 0, - 0, - 0 - ], - [ - 300, - 0.24, - 0 - ], - [ - 600, - 0.44, - 0 - ], - [ - 900, - 0.62, - 0 - ], - [ - 1000, - 0.7, - 0 - ], - [ - 1200, - 0.82, - 0 - ], - [ - 1500, - 0.92, - 0 - ] + [0, 0, 0], + [300, 0.24, 0], + [600, 0.44, 0], + [900, 0.62, 0], + [1000, 0.7, 0], + [1200, 0.82, 0], + [1500, 0.92, 0] ] }, "Modifications": { "subset": [ - "PP2A", - "eEF2", - "eEF2p" + {"name":"PP2A","alias":"PP2A"},{"name":"eEF2","alias":"eEF2"},{"name":"eEF2p","alias":"eEF2p"} ], "itemsToDelete": [ - "PP2A_dephospho_I1", - "PP2A_dephospho_PP1_I_p", - "clus_S6K_deph", - "S6K_dephosp", - "S6K_deph", - "AKTpS473_deph", - "AKTpT308_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "mGluR_deph" + {"name":"PP2A_dephospho_I1","alias":"PP2A_dephospho_I1"},{"name":"PP2A_dephospho_PP1_I_p","alias":"PP2A_dephospho_PP1_I_p"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"mGluR_deph","alias":"mGluR_deph"} ], "parameterChange": [ { - "entity": "PP2A", + "name": "PP2A", + "alias": "PP2A", "field": "concInit", "value": 6.5e-07, "units": "mM" }, { - "entity": "eEF2", + "name": "eEF2", + "alias": "eEF2", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "eEF2p", + "name": "eEF2p", + "alias": "eEF2p", "field": "concInit", "value": 2.2e-05, "units": "mM" diff --git a/Curated/Jain2009_Fig4F.json b/Curated/Jain2009_Fig4F.json index a01b5de..b86502b 100644 --- a/Curated/Jain2009_Fig4F.json +++ b/Curated/Jain2009_Fig4F.json @@ -24,62 +24,46 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "S6p", + "entity" : { + "name": "aS6", + "alias": "S6p" + }, "field": "conc", - "isBuffered": 0 + "isBuffered": 0 } ], "Readouts": { "timeUnits": "sec", "settleTime": 2400, "quantityUnits": "nM", - "entities": [ - "43S" - ], + "entity" : { + "name": "43S", + "alias": "43S" + }, "field": "conc", "data": [ - [ - 6.8, - 3.61, - 0 - ], - [ - 20.4, - 15.3, - 0 - ], - [ - 68, - 30.7, - 0 - ], - [ - 204, - 42.4, - 0 - ], - [ - 612, - 45.3, - 0 - ] + [6.8, 3.61, 0], + [20.4, 15.3, 0], + [68, 30.7, 0], + [204, 42.4, 0], + [612, 45.3, 0] ] }, "Modifications": { "subset": [ - "Transl_init_g", - "40S_g", - "43S_g" + {"name":"Transl_init_g","alias":"Transl_init_g"},{"name":"_40S_g","alias":"40S_g"},{"name":"_43S_g","alias":"43S_g"} ], "parameterChange": [ { - "entity": "M_clx", + "name": "M_clx", + "alias": "M_clx", "field": "concInit", "value": 0.0015, "units": "mM" }, { - "entity": "Q_clx", + "name": "Q_clx", + "alias": "Q_clx", "field": "concInit", "value": 4.97e-05, "units": "mM" diff --git a/Curated/Jain2009_Fig5B.json b/Curated/Jain2009_Fig5B.json index 5e6a0a6..0d537d1 100644 --- a/Curated/Jain2009_Fig5B.json +++ b/Curated/Jain2009_Fig5B.json @@ -25,87 +25,55 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "BDNF", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, "field": "conc", "data": [ - [ - 900, - 2 - ] + [900,2] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "uM", - "entities": [ - "aAKT" - ], + "entity" : { + "name": "aAKT", + "alias": "aAKT" + }, "field": "conc", "data": [ - [ - 900, - 0.005, - 0 - ], - [ - 930, - 0.01, - 0 - ], - [ - 1020, - 0.082, - 0 - ], - [ - 1200, - 0.078, - 0 - ], - [ - 1500, - 0.072, - 0 - ], - [ - 2700, - 0.069, - 0 - ] + [900, 0.005, 0], + [930, 0.01, 0], + [1020, 0.082, 0], + [1200, 0.078, 0], + [1500, 0.072, 0], + [2700, 0.069, 0] ] }, "Modifications": { "subset": [ - "Phosphatase_g", - "Ca_g", - "PLCg_g", - "Sos_g", - "BDNF_g", - "TrKB_g", - "AKT_g", - "PI3K_g", - "PIP2", - "PIP3", - "MAPK_g", - "Ras_g", - "PKC_g" + {"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"Ca_g","alias":"Ca_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"Sos_g","alias":"Sos_g"},{"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"AKT_g","alias":"AKT_g"},{"name":"PI3K_g","alias":"PI3K_g"},{"name":"PIP2","alias":"PIP2"},{"name":"PIP3","alias":"PIP3"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"PKC_g","alias":"PKC_g"} ], "parameterChange": [ { - "entity": "AKT", + "name": "AKT", + "alias": "AKT", "field": "concInit", "value": 0.00017, "units": "mM" - }, + }, { - "entity": "BDNF", + "name": "BDNF", + "alias": "BDNF", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "SHCp_deph", + "name": "SHCp_deph", + "alias": "SHCp_deph", "field": "Kf", "value": 0.2, "units": "none" diff --git a/Curated/Ji2010_fig1C_ERK_acute.json b/Curated/Ji2010_fig1C_ERK_acute.json index 2a8aed3..6d30d44 100644 --- a/Curated/Ji2010_fig1C_ERK_acute.json +++ b/Curated/Ji2010_fig1C_ERK_acute.json @@ -24,237 +24,165 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "BDNF", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, "field": "conc", "data": [ - [ - 1800, - 1 - ] + [1800,1] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "pERK" - ], + "entity" : { + "name": "pERK", + "alias": "pERK" + }, "field": "conc", "normalization": { - "time": 1800, - "entities": [ - "pERK" - ], - "dose": 0, - "sampling": "presetTime" + "entity" : { + "name": "pERK", + "alias": "pERK" + }, + "sampling": "presetTime", + "sampTime": 1800 }, "data": [ - [ - 1800, - 1, - 0 - ], - [ - 2700, - 5.6, - 0.55 - ], - [ - 3600, - 3.9, - 0.4 - ], - [ - 5400, - 4, - 0.8 - ], - [ - 9000, - 3, - 0.5 - ], - [ - 16200, - 2.2, - 0.7 - ], - [ - 30600, - 2.2, - 0.2 - ] + [1800, 1, 0], + [2700, 5.6, 0.55], + [3600, 3.9, 0.4], + [5400, 4, 0.8], + [9000, 3, 0.5], + [16200, 2.2, 0.7], + [30600, 2.2, 0.2] ] }, "Modifications": { "subset": [ - "Ca_g", - "Phosphatase_g", - "Sos_g", - "Ras_g", - "MAPK_g", - "CaM_g", - "PKC_g", - "PI3K_g", - "BDNF_g", - "TrKB_g", - "PLA2_g", - "PLCb_g", - "PLCg_g", - "PC" + {"name":"Ca_g","alias":"Ca_g"},{"name":"Phosphatase_g","alias":"Phosphatase_g"},{"name":"Sos_g","alias":"Sos_g"},{"name":"Ras_g","alias":"Ras_g"},{"name":"MAPK_g","alias":"MAPK_g"},{"name":"CaM_g","alias":"CaM_g"},{"name":"PKC_g","alias":"PKC_g"},{"name":"PI3K_g","alias":"PI3K_g"},{"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"PLA2_g","alias":"PLA2_g"},{"name":"PLCb_g","alias":"PLCb_g"},{"name":"PLCg_g","alias":"PLCg_g"},{"name":"PC","alias":"PC"} ], "itemsToDelete": [ - "MAPKpp_act_PLA2", - "dephosph_inhib1", - "MEK_phospho", - "MEKp_phospho", - "PIP3_AKT_t308_s473", - "phosph_AC2", - "bg_act_GEF", - "dephosph_inact_GEF_p", - "dephosph_PLC_g", - "ng_bind_CaM", - "CaM_ng_deph", - "PKC_phospho_ng", - "PKC_phospho_ng_CaM", - "GEF_Gprot_bg", - "tCaM_CaN", - "mGluR_barr2_Raf", - "CaN_deph_I1p", - "PP2A_dephospho_I1", - "mGluR_deph", - "CaMKIII_bind_CaMCa4", - "bS6K", - "S6Kp_act_CaMKIII", - "MAPK_4EBPpp", - "MAPK_4EBP_phospho", - "PP2A_dephospho_PP1_Ip", - "AKTpS473_deph", - "eEF2p_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_4EBP", - "SHCpGrb2Gab1PI3K_phospho", - "bPIP2_phospho", - "PIP3_deph", - "PIP2_phospho_RasGTP", - "phospho_AKTpS473", - "TOR_4EBP_phospho", - "TOR_4EBPp", - "S6_phos", - "S6_phospho", - "S6_deph", - "PLC_bind_Gq", - "Inact_PLC_Gq", - "Act_PLC_by_Gq", - "AKTpT308_deph", - "PDK1_act_S6K", - "S6K_dephosp", - "S6K_deph", - "clus_S6K_deph", - "clus_S6K_phospho" + {"name":"eMAPK+PLA2","alias":"MAPKpp_act_PLA2"},{"name":"dephosph_inhib1","alias":"dephosph_inhib1"},{"name":"ecraf+MAPKK","alias":"MEK_phospho"},{"name":"ecraf+MAPKKp","alias":"MEKp_phospho"},{"name":"PIP3_AKT_t308_s473","alias":"PIP3_AKT_t308_s473"},{"name":"phosph_AC2","alias":"phosph_AC2"},{"name":"bg_act_GEF","alias":"bg_act_GEF"},{"name":"dephosph_inact_GEF_p","alias":"dephosph_inact_GEF_p"},{"name":"dephosph_PLC_g","alias":"dephosph_PLC_g"},{"name":"ng+CaM","alias":"ng_bind_CaM"},{"name":"eCaM+ngp","alias":"CaM_ng_deph"},{"name":"PKC_phospho_ng","alias":"PKC_phospho_ng"},{"name":"PKC_phospho_ng_CaM","alias":"PKC_phospho_ng_CaM"},{"name":"GEF_Gprot_bg","alias":"GEF_Gprot_bg"},{"name":"aCaM_CaN","alias":"tCaM_CaN"},{"name":"craf1+barr2","alias":"mGluR_barr2_Raf"},{"name":"eCaN+I1p","alias":"CaN_deph_I1p"},{"name":"PP2A_dephospho_I1","alias":"PP2A_dephospho_I1"},{"name":"mGluR_deph","alias":"mGluR_deph"},{"name":"CaMCa4+CaMKIII","alias":"CaMKIII_bind_CaMCa4"},{"name":"bS6K","alias":"bS6K"},{"name":"eS6Kpqrs+CaMKIII","alias":"S6Kp_act_CaMKIII"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"},{"name":"PP2A_dephospho_PP1_Ip","alias":"PP2A_dephospho_PP1_Ip"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"PP2A_4EBP","alias":"PP2A_4EBP"},{"name":"SHCpGrb2Gab1PI3K_phospho","alias":"SHCpGrb2Gab1PI3K_phospho"},{"name":"ebPI3K+PIP2","alias":"bPIP2_phospho"},{"name":"ePTEN+PIP3","alias":"PIP3_deph"},{"name":"eRas+PIP2","alias":"PIP2_phospho_RasGTP"},{"name":"ePDK2+AKTp","alias":"phospho_AKTpS473"},{"name":"emTORC1+4EBP","alias":"TOR_4EBPp"},{"name":"eS6Kpqr+40S","alias":"S6_phos"},{"name":"eS6Kpqrs+40S","alias":"S6_phospho"},{"name":"S6_deph","alias":"S6_deph"},{"name":"PLC_bind_Gq","alias":"PLC_bind_Gq"},{"name":"Inact_PLC_Gq","alias":"Inact_PLC_Gq"},{"name":"PLC_Ca+Gq","alias":"Act_PLC_by_Gq"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"PDK1_act_S6K","alias":"PDK1_act_S6K"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"} ], "parameterChange": [ { - "entity": "BDNF", + "name": "BDNF", + "alias": "BDNF", "field": "concInit", "value": 0, "units": "mM" }, { - "entity": "bPKCp", + "name": "bPKC", + "alias": "bPKCp", "field": "concInit", "value": 2e-05, "units": "mM" }, { - "entity": "PPhosphatase2A", + "name": "PPhosphatase2A", + "alias": "PPhosphatase2A", "field": "concInit", "value": 0.001, "units": "mM" }, { - "entity": "Ras_act_craf", + "name": "Ras+craf", + "alias": "Ras_act_craf", "field": "Kf", "value": 9999.6668, "units": "none" }, { - "entity": "SHCp_deph", + "name": "SHCp_deph", + "alias": "SHCp_deph", "field": "Kf", "value": 0.2, "units": "none" }, { - "entity": "PKC_act_raf", + "name": "ePKC+craf", + "alias": "PKC_act_raf", "field": "Km", "value": 0.0209818384, "units": "none" }, { - "entity": "MAPKKtyr", + "name": "eMAPKK+MAPK", + "alias": "MAPKKtyr", "field": "kcat", "value": 0.3, "units": "none" }, { - "entity": "MAPKKthr", + "name": "eMAPKK+MAPKp", + "alias": "MAPKKthr", "field": "kcat", "value": 0.3, "units": "none" }, { - "entity": "Rafp_RasGTP1", + "name": "eRas+MAPKK1", + "alias": "Rafp_RasGTP1", "field": "kcat", "value": 0.3, "units": "none" }, { - "entity": "Rafp_RasGTP2", + "name": "eRas+MAPKK2", + "alias": "Rafp_RasGTP2", "field": "kcat", "value": 0.3, "units": "none" }, { - "entity": "Sos_Ras_GEF", + "name": "eSHCpSosGrb2+Ras", + "alias": "Sos_Ras_GEF", "field": "kcat", "value": 0.2, "units": "none" }, { - "entity": "MKP1pY421_deph", + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", "field": "kcat", "value": 4, "units": "none" }, { - "entity": "MKP1pT424_deph", + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", "field": "kcat", "value": 4, "units": "none" }, { - "entity": "MKP1pT424_deph", + "name": "eMKP1+MAPKpq", + "alias": "MKP1pT424_deph", "field": "Km", "value": 0.00734, "units": "none" }, { - "entity": "MKP1pY421_deph", + "name": "eMKP1+MAPKp", + "alias": "MKP1pY421_deph", "field": "Km", "value": 0.00734, "units": "none" }, { - "entity": "PI3K_bind_RasGTP", + "name": "PI3K+RasGTP", + "alias": "PI3K_bind_RasGTP", "field": "Kf", "value": 3600, "units": "none" }, { - "entity": "PI3K_bind_RasGTP", + "name": "PI3K+RasGTP", + "alias": "PI3K_bind_RasGTP", "field": "Kb", "value": 0.2, "units": "none" diff --git a/Curated/Mundell2001_Fig3B.json b/Curated/Mundell2001_Fig3B.json index fa7ad99..703ba67 100644 --- a/Curated/Mundell2001_Fig3B.json +++ b/Curated/Mundell2001_Fig3B.json @@ -25,84 +25,45 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Glutamate", + "entity" : { + "name": "Glutamate", + "alias": "Glutamate" + }, "field": "conc", "data": [ - [ - 0, - 100.0 - ] + [0,100.0] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "tot_surface_mGluR_with_barr2" - ], + "entity" : { + "name": "tot_surface_mGluR_with_barr2", + "alias": "tot_surface_mGluR_with_barr2" + }, "field": "conc", "normalization": { - "time": 0, - "entities": [ - "tot_surface_mGluR_with_barr2" - ], - "dose": 0, + "entity" : { + "name": "tot_surface_mGluR_with_barr2", + "alias": "tot_surface_mGluR_with_barr2" + }, "sampling": "start" }, "data": [ - [ - 0, - 1, - 0 - ], - [ - 300, - 0.43, - 0 - ], - [ - 600, - 0.38, - 0 - ], - [ - 900, - 0.32, - 0 - ], - [ - 1800, - 0.34, - 0 - ] + [0, 1, 0], + [300, 0.43, 0], + [600, 0.38, 0], + [900, 0.32, 0], + [1800, 0.34, 0] ] }, "Modifications": { "subset": [ - "mGluR_g", - "barr2_g", - "PP2A" + {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"} ], "itemsToDelete": [ - "mGluR_Gq", - "Glu_mGluR_Gq", - "Glu_mGluR_bind_Gq", - "Glu_bind_mGluR_Gq", - "Act_Gq", - "mGluR_bind_Gq", - "clus_S6K_deph", - "S6K_dephosp", - "S6K_deph", - "AKTpS473_deph", - "AKTpT308_deph", - "eEF2p_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "PP2A_dephos_I1", - "PP2A_dephos_PP1_Ip" + {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"} ] } } diff --git a/Curated/Tran2007_Fig2A.json b/Curated/Tran2007_Fig2A.json index 76ad6c0..d8ec792 100644 --- a/Curated/Tran2007_Fig2A.json +++ b/Curated/Tran2007_Fig2A.json @@ -25,110 +25,53 @@ { "timeUnits": "sec", "quantityUnits": "uM", - "entity": "Glutamate", + "entity" : { + "name": "Glutamate", + "alias": "Glutamate" + }, "field": "conc", "data": [ - [ - 300, - 0.0 - ] + [300,0.0] ] } ], "Readouts": { "timeUnits": "sec", "quantityUnits": "ratio", - "entities": [ - "beta2ARp" - ], + "entity" : { + "name": "beta2ARp", + "alias": "beta2ARp" + }, "field": "conc", "normalization": { - "time": 300, - "entities": [ - "beta2ARp" - ], - "dose": 0, + "entity" : { + "name": "beta2ARp", + "alias": "beta2ARp" + }, "sampling": "start" }, "data": [ - [ - 300, - 1, - 0 - ], - [ - 600, - 0.95, - 0 - ], - [ - 900, - 0.82, - 0 - ], - [ - 1200, - 0.65, - 0 - ], - [ - 1500, - 0.52, - 0 - ], - [ - 2100, - 0.32, - 0 - ], - [ - 3900, - 0.09, - 0 - ], - [ - 5700, - 0.01, - 0 - ] + [300, 1, 0], + [600, 0.95, 0], + [900, 0.82, 0], + [1200, 0.65, 0], + [1500, 0.52, 0], + [2100, 0.32, 0], + [3900, 0.09, 0], + [5700, 0.01, 0] ] }, "Modifications": { "subset": [ - "mGluR_g", - "barr2_g", - "PP2A", - "MAPK_g" + {"name":"mGluR_g","alias":"mGluR_g"},{"name":"barr2_g","alias":"barr2_g"},{"name":"PP2A","alias":"PP2A"},{"name":"MAPK_g","alias":"MAPK_g"} ], "itemsToDelete": [ - "mGluR_Gq", - "Glu_mGluR_Gq", - "Glu_mGluR_bind_Gq", - "Glu_bind_mGluR_Gq", - "Act_Gq", - "mGluR_bind_Gq", - "clus_S6K_deph", - "S6K_dephosp", - "S6K_deph", - "AKTpS473_deph", - "AKTpT308_deph", - "eEF2p_deph", - "PP2A_4EBPpp", - "PP2A_4EBPp", - "PP2A_eIF4EBPpp", - "PP2A_eIF4EBPp", - "PP2A_dephos_I1", - "PP2A_dephos_PP1_Ip", - "clus_S6K_phospho", - "MAPKpp_feedback", - "MAPKpp_act_PLA2", - "Sos_phospho", - "MAPK_4EBPpp", - "MAPK_4EBP_phospho" + {"name":"mGluR_Gq","alias":"mGluR_Gq"},{"name":"amGluR","alias":"Glu_mGluR_Gq"},{"name":"Glu_mGluR+Gq","alias":"Glu_mGluR_bind_Gq"},{"name":"Glu+mGluR_Gq","alias":"Glu_bind_mGluR_Gq"},{"name":"Act_Gq","alias":"Act_Gq"},{"name":"mGluR_bind_Gq","alias":"mGluR_bind_Gq"},{"name":"ePP2A+S6Kpq","alias":"clus_S6K_deph"},{"name":"ePP2A+S6Kpqrs","alias":"S6K_dephosp"},{"name":"ePP2A+S6Kpqr","alias":"S6K_deph"},{"name":"ePP2A+AKTpq","alias":"AKTpS473_deph"},{"name":"ePP2A+AKTp","alias":"AKTpT308_deph"},{"name":"ePP2A+eEF2p","alias":"eEF2p_deph"},{"name":"ePP2A+4EBPpqr","alias":"PP2A_4EBPpp"},{"name":"ePP2A+4EBPpq","alias":"PP2A_4EBPp"},{"name":"ePP2A+eIF4EBPpqr","alias":"PP2A_eIF4EBPpp"},{"name":"ePP2A+eIF4EBPpq","alias":"PP2A_eIF4EBPp"},{"name":"ePP2A+I1p","alias":"PP2A_dephos_I1"},{"name":"PP2A_dephos_PP1_Ip","alias":"PP2A_dephos_PP1_Ip"},{"name":"eMAPK+S6K","alias":"clus_S6K_phospho"},{"name":"eMAPK+crafp","alias":"MAPKpp_feedback"},{"name":"eMAPK+PLA2","alias":"MAPKpp_act_PLA2"},{"name":"Sos_phospho","alias":"Sos_phospho"},{"name":"eMAPK+4EBPpq","alias":"MAPK_4EBPpp"},{"name":"eMAPK+eIF4EBPpq","alias":"MAPK_4EBP_phospho"} ], "parameterChange": [ { - "entity": "Glutamate", + "name": "Glutamate", + "alias": "Glutamate", "field": "concInit", "value": 0.1, "units": "mM" diff --git a/Non-Curated/Jain2009_Fig2D.json b/Non-Curated/Jain2009_Fig2D.json index b68f2f4..538dc25 100644 --- a/Non-Curated/Jain2009_Fig2D.json +++ b/Non-Curated/Jain2009_Fig2D.json @@ -11,7 +11,7 @@ "year": 1999, "figure": "Fig3" }, - "testModel": "models/synSynth7.g", + "testModel": "models/synSynth7.g", "testMap": "models/synSynth7_map.json" }, "Experiment": { @@ -25,7 +25,10 @@ { "timeUnits": "sec", "quantityUnits": "nM", - "entity": "BDNF", + "entity" : { + "name": "BDNF", + "alias": "BDNF" + }, "field": "conc" } ], @@ -33,55 +36,30 @@ "timeUnits": "sec", "settleTime": 300, "quantityUnits": "nM", - "entities": [ - "PLCgp" - ], + "entity" : { + "name": "PLCgp", + "alias": "PLCgp" + }, "field": "conc", "data": [ - [ - 0, - 3, - 0 - ], - [ - 1, - 15, - 0 - ], - [ - 2, - 24, - 0 - ], - [ - 3.8, - 34, - 0 - ], - [ - 7.5, - 41, - 0 - ] + [0, 3, 0], + [1, 15, 0], + [2, 24, 0], + [3.8, 34, 0], + [7.5, 41, 0] ] }, "Modifications": { "subset": [ - "BDNF_g", - "TrKB_g", - "PLCg_g" + {"name":"BDNF_g","alias":"BDNF_g"},{"name":"TrKB_g","alias":"TrKB_g"},{"name":"PLCg_g","alias":"PLCg_g"} ], "itemsToDelete": [ - "TrKB_act_SHC", - "CaPLCg", - "CaPLCgp", - "Ca_act_PLCg", - "Ca_act_PLCgp", - "dephosph_PLC_g" + {"name":"eTrKB+SHC","alias":"TrKB_act_SHC"},{"name":"Ca_PLCg","alias":"CaPLCg"},{"name":"aPLCg","alias":"CaPLCgp"},{"name":"Ca+PLCg","alias":"Ca_act_PLCg"},{"name":"Ca+PLCgp","alias":"Ca_act_PLCgp"},{"name":"dephosph_PLC_g","alias":"dephosph_PLC_g"} ], "parameterChange": [ { - "entity": "PLCg", + "name": "PLCg", + "alias": "PLCg", "field": "concInit", "value": 0.0001, "units": "mM" diff --git a/findSim.py b/findSim.py index a571280..6c2f53a 100644 --- a/findSim.py +++ b/findSim.py @@ -511,9 +511,10 @@ def displayPlots( self, fname, modelLookup, stims, hideSubplots, exptType, bigFo ylabel = pp.ylabel if self.field in ( Readout.epspFields + Readout.epscFields ): if self.field in Readout.epspFields: - plt.ylabel( '{} Vm ({})'.format( self.entities[0], tsUnits ) ) + plt.ylabel( '{} Vm ({})'.format( self.entities['name'], tsUnits ) ) else: - plt.ylabel( '{} holding current ({})'.format( self.entities[0], tsUnits ) ) + print("516 ",self.entities['name']) + plt.ylabel( '{} holding current ({})'.format( self.entities['name'], tsUnits ) ) plt.figure( self.field ) # Do the EPSP in a new figure if self.useNormalization: diff --git a/models/synSynth7_map.json b/models/synSynth7_map.json index beb98cd..aa385d7 100644 --- a/models/synSynth7_map.json +++ b/models/synSynth7_map.json @@ -1,409 +1,1103 @@ { - "all":["all"], - "PKC_g":["PKC"], - "PLA2_g":["PLA2"], - "PLCb_g":["PLCbeta"], - "mGluRAntag_g":["kinetics/mGluRAntag"], - "MAPK_g":["kinetics/MAPK"], - "Ras_g":["Ras"], - "EGFR_g":["kinetics/EGFR"], - "Sos_g":["kinetics/Sos"], - "PLCg_g":["kinetics/PLC_g"], - "CaMKII_g":["kinetics/CaMKII"], - "CaM_g":["kinetics/CaM"], - "PP1_g":["PP1"], - "PP2B_g":["PP2B"], - "PKA_g":["PKA"], - "AC_g":["AC"], - "mGluR_g":["kinetics/mGluR"], - "Gprotein_g":["Gprotein"], - "Phosphatase_g":["Phosphatase"], - "Ca_g":["kinetics/Ca"], - "PI3K_g":["PI3K_activation"], - "AKT_g":["AKT_activation"], - "TrKB_g":["kinetics/TrKB"], - "mTORC1_g":["mTORC1"], - "S6K_g":["S6Kinase"], - "4EBP_g":["kinetics/_4E_BP"], - "43S_g":["_43S_complex"], - "_43S_g":["_43S_complex"], - "protein_g":["kinetics/protein"], - "BDNF_g":["kinetics/BDNF"], - "CaMKIII_g":["kinetics/CaMKIII"], - "Transl_init_g":["Translation_initiation"], - "Transl_elong_g":["Translation_elongation"], - "40S_g":["kinetics/_40S"], - "_40S_g":["kinetics/_40S"], - "TSC1_TSC2_g":["kinetics/TSC1_TSC2"], - "HomerPIKE_g":["HomerPIKE"], - "barr2_g":["barr2_signaling"], - "DHPG_mGluR_g":["DHPG_mGluR"], - "CaseinKinase_g":["CaseinKinase"], - "FMRP_g":["kinetics/FMRP"], - "RecLigandBinding":["RecLigandBinding"], - "makeTernary":["Rec_Glu_bind_Gq"], - "CaM":["CaM/CaM"], - "ERK":["MAPK/MAPK"], - "pERK":["MAPK/MAPK_p_p","MAPK/MAPK_p"], - "FMRP_synth":["FMRP_synth"], - "aSHC":["SHC_p"], - "SHCp":["SHC_p"], - "SHC":["SHC"], - "Gq_GDP":["G_GDP"], - "G_GDP":["G_GDP"], - "EGFR":["EGFR/EGFR"], - "EGFRp":["L.EGFR"], - "act_surface_EGFR":["L.EGFR"], - "eEGFR+SHC":["L.EGFR/SHC_phospho"], - "EGFR_act_SHC":["L.EGFR/SHC_phospho"], - "PLCg":["PLC_g/PLC_g"], - "Ca+PLCg":["Ca_act_PLC_g"], - "Ca_act_PLCg":["Ca_act_PLC_g"], - "Ca+PLCgp":["Ca_act_PLC_g_p"], - "Ca_act_PLCgp":["Ca_act_PLC_g_p"], - "enolase":["GDP_Ras"], - "enolase_p":["GTP_Ras"], - "AA":["Arachidonic_Acid"], - "Ca":["Ca/Ca"], - "DAG":["DAG"], - "PIP3_PDK2":["PIP3_PDK2"], - "PIP2phospho_HomerPIKE":["PIP2phospho_HomerPIKE"], - "PIP2":["PIP2"], - "PIP3":["PIP3"], - "IP3":["IP3"], - "temp_PIP2":["temp_PIP2"], - "Degrade_AA":["Degrade_AA"], - "PC":["PC"], - "PD098059":["MAPKK"], - "Wortmannin":["PI3K"], - "PP2A":["PP2A"], - "PPhosphatase2A":["PPhosphatase2A"], - "aPP1":["PP1_active"], - "Inact_PP1":["Inact_PP1"], - "SHCp_deph":["SHC_p_dephospho"], - "MAPKpp":["MAPK/MAPK_p_p"], - "MAPKp":["MAPK/MAPK_p"], - "EGF":["EGF"], - "Glutamate":["Glutamate"], - "CaMKIII":["CaMKIII/CaMKIII"], - "CaMKIII_deph":["CaMKIII_dephospho"], - "CaMKIIIp":["CaMKIII_p"], - "AKT":["AKT"], - "PIP3_deph":["PIP3_dephosp"], - "PIP3_bind_AKT":["PIP3_bind_AKT"], - "PIP3_bind_PDK1":["PIP3_bind_PDK1"], - "PIP3_AKT":["PIP3_AKT"], - "AKTpT308S473":["PIP3_AKT_t308_s473"], - "aAKT":["PIP3_AKT_t308_s473"], - "43S":["_43Scomplex"], - "mTOR":["TOR_clx"], - "mTOR_KO":["TOR_clx"], - "mTORp":["TOR_Rheb_GTP_clx"], - "aMAPK":["MAPK/MAPK_p_p","MAPK_p"], - "40S_mRNA":["RM"], - "Q_clx":["Quaternary_clx"], - "M_clx":["eIF4F_mRNA_clx"], - "eIF4E_bind_eIF4G":["eIF4F_clx"], - "eIF4E":["eIF4E"], - "eIF4G":["eIF4G"], - "eIF4A":["eIF4A"], - "eIF4F":["eIF4F"], - "mRNA":["mRNA"], - "eIF4GA":["eIF4G_A_clx"], - "eIF4G_bind_A":["eIF4G_A_clx_formation"], - "eIF4E_G_bind_mRNA":["eIF4F_mRNA_clx_formation"], - "eIF4F_bind_mRNA":["eIF4F_mRNA_clx_formation"], - "eIF4E_bind_mRNA":["eIF4E_mRNA_clx_formation"], - "eIF4EmRNA_bind_GA":["eIF4EmRNA_eIF4GA_clx_formation"], - "TSC2_inact":["TSC2_phospho"], - "Rheb_inact":["TSC2phospho"], - "S6K":["S6K"], - "S6KpT389":["S6K_thr_412"], - "S6Kpqr":["S6K_thr_412"], - "S6KpT412":["S6K_thr_412"], - "S6KpT229":["S6K_thr_252"], - "S6KpT252":["S6K_thr_252"], - "bS6K":["S6K_basal"], - "BDNF":["BDNF/BDNF"], - "NGF":["BDNF/BDNF"], - "Inact_Gq":["Inact_Gq"], - "bTransl":["Basal_Translation"], - "Translation_clx":["Translation_clx"], - "pro_syn":["pro_syn"], - "rad_pro_syn":["rad_pro_syn"], - "basal_syn":["basal_syn"], - "rad_basal_syn":["rad_basal_syn"], - "Transl_act":["activation"], - "elongation":["elongation"], - "protein":["protein/protein"], - "Raf1_deph":["deph_raf_ser259"], - "inact_Raf":["craf_1_p_ser259"], - "AKT_inhib_Raf":["Raf_inhib"], - "PLCbCa_PIP2hydr":["PLC_Ca/PLC_Ca"], - "Act_PLC_by_Gq":["Act_PLC_by_Gq"], - "Act_PLC_Ca":["Act_PLC_Ca"], - "PLC_Gq_bind_Ca":["PLC_Gq_bind_Ca"], - "PLCb_Ca_Gq":["PLCb_Ca_Gq"], - "aPLCg":["Ca.PLC_g_p"], - "CaPLCgp":["Ca.PLC_g_p"], - "CaPLCg":["Ca.PLC_g"], - "bPLCg":["PLCg_basal"], - "RasGDP":["GDP_Ras"], - "RasGTP":["GTP_Ras"], - "TSC1_2":["TSC1_TSC2/TSC1_TSC2"], - "TSC1_KO":["TSC1_TSC2/TSC1_TSC2"], - "Rheb_GTP":["Rheb_GTP"], - "Rheb_GDP":["Rheb_GDP"], - "GDPtoGTP":["GDP_to_GTP"], - "MAPK":["MAPK/MAPK"], - "80S":["_80S_ribos_clx"], - "60S":["_60S_R"], - "AKTpT308":["PIP3_AKT_thr308"], - "4EBPpT37T46":["_4E_BP_t37_46"], - "4EBPpT37T46S65":["_4E_BP_t37_46_s65"], - "CaPLCg_phospho":["Ca.PLC_g_phospho"], - "EGFR_act_PLCg":["Ca.PLC_g_phospho"], - "tPLCgp":["PLC_g_p","Ca.PLC_g_p"], - "PLCgp":["PLC_g_p"], - "EGF_bind_EGFR":["act_EGFR"], - "eIF4E_bind_BP2":["eIF4E_bind_BP2"], - "4EBP":["_4E_BP/_4E_BP"], - "t4EBP":["_4E_BP/_4E_BP","eIF4E_BP"], - "a4EBP_tot":["_4E_BP_t37_46","_4E_BP_t37_46_s65","eIF4E_BP_thr37_46","eIF4E_BP_t37_46_s65"], - "eIF4EBPpT37T46":["eIF4E_BP_thr37_46"], - "eIF4EBPpT37T46S65":["eIF4E_BP_thr37_46_s65"], - "eIF4E_4EBP":["eIF4E_BP"], - "eIF4EBP2_disso":["eIF4E_BP2_disso"], - "eIF4EBP_disso":["eIF4E_BP_disso"], - "eIF4E":["eIF4E"], - "eIF4E_S209":["eIF4E"], - "S6":["_40S_inact"], - "aS6":["_40S/_40S"], - "S6p":["_40S/_40S"], - "eS6Kpqr+40S":["S6_phos"], - "S6_phos":["S6_phos"], - "eS6Kpqrs+40S":["S6_phospho"], - "S6_phospho":["S6_phospho"], - "Glu_mGluR":["RecLigandBinding"], - "Ligand_binding":["Ligand_binding"], - "aPKC":["PKC_active"], - "cPKC":["PKC_cytosolic"], - "cPLA2":["PLA2_cytosolic"], - "PLA2p":["PLA2_p"], - "Src_p416":["SHC_p"], - "Src":["SHC"], - "SHCpGrb2Gab1_PI3K":["SHC_p_Grb2_Gab1_PI3K_clx"], - "SHCpGrb2Gab1PI3K_phospho":["SHC_p_Grb2_Gab1_PI3K_clx/Phospho"], - "SHCpGrb2_Gab1":["SHC_p_Grb2_Gab1_clx"], - "Basal_Act_Gq":["Basal_Act_Gq"], - "PDK1":["PDK1"], - "APC":["APC"], - "CaPLCgp_PIP2hydr":["Ca.PLC_g_p/PIP2_hydrolysis"], - "eCaPLCg+PIP2":["Ca.PLC_g/PIP2_hydrolysis"], - "CaPLCg_PIP2hydr":["Ca.PLC_g/PIP2_hydrolysis"], - "EGF_act_PLCg":["Ca.PLC_g_p/PIP2_hydrolysis"], - "act_PLCg":["Ca.PLC_g/PIP2_hydrolysis"], - "bPKCp":["PKC_basal_p"], - "BDNF_act_TrKB":["BDNF_TrKB2_p_clx"], - "TrKB_internal":["Int_BDNF_TrKB2_p_clx"], - "EGFR_internal":["Internal_L.EGFR"], - "TrKBp":["Int_BDNF_TrKB2_p_clx","BDNF_TrKB2_p_clx"], - "GAP":["GAP"], - "GAP_inact_Ras":["GAP_inact_Ras"], - "Ras_intrinsic_GTPase":["Ras_intrinsic_GTPase"], - "mGluR_bind_Homer":["L.mGluR_HomerBinding"], - "mGluRpHomerPIKE_PI3K":["L.mGluR_p.Homer.PIKE_L.PI3K"], - "mGluRpHomerPIKE_bind_PI3K":["L.mGluR.Homer.PIKE_PI3K_Binding"], - "mGluR":["mGluR/mGluR"], - "tot_surface_mGluR":["mGluR/mGluR","Rec_Glu","L.mGluR_p"], - "tot_surface_mGluR_with_barr2":["mGluR/mGluR","Rec_Glu","L.mGluR_p","L.mGluR_p.barr2","mGluR_p.barr2"], - "beta2ARp":["Internal_mGluR_p","L.mGluR_p"], - "Rafp_RasGTP1":["Raf_p_GTP_Ras.1"], - "Rafp_RasGTP2":["Raf_p_GTP_Ras.2"], - "Rafp_RasGTP":["Raf_p_GTP_Ras"], - "CaMGEF_actRas":["CaM_GEF_act_Ras"], - "Ras_act_craf":["Ras_act_craf"], - "PKC_act_raf":["PKC_act_raf"], - "MKP1pY421_deph":["MKP1_tyr_deph"], - "MKP1pT424_deph":["MKP1_thr_deph"], - "Sos_Ras_GEF":["Sos.Ras_GEF"], - "Sos_deph":["dephosph_Sos"], - "40S_bind_mRNA":["R_binds_M"], - "Q_bind_40S":["Q_binds_R"], - "QR_bind_mRNA":["QR_binds_M"], - "40SmRNA_bind_Q":["RM_binds_Q"], - "QR":["Q.R"], - "Rec_bind_Gq":["Rec_bind_Gq"], - "Glu_mGluR+Gq":["Rec_Glu_bind_Gq"], - "Glu_mGluR_bind_Gq":["Rec_Glu_bind_Gq"], - "Glu_bind_Rec_Gq":["Glu_bind_Rec_Gq"], - "mGluR_Gq":["Rec_Gq"], - "amGluR":["Rec_Glu_Gq"], - "Glu_mGluR_Gq":["Rec_Glu_Gq"], - "eEF2":["eEF2"], - "eEF2p":["eEFthr_56"], - "S6KpT421S424":["S6K_p"], - "CaMCa4":["CaM_Ca4"], - "CaMKII":["CaMKII/CaMKII"], - "CaMKII_bind_CaM":["CaMKII_bind_CaM"], - "CaMKIIT286_bind_CaM":["CaMKII_thr286_bind_CaM"], - "CaMCaMKII_act_T286":["CaM_act_286"], - "CaMCaMKII_act_T305":["CaM_act_305"], - "CaMCa4+CaMKIII":["CaMKIII_bind_CaM_Ca4"], - "CaMKIII_bind_CaMCa4":["CaMKIII_bind_CaM_Ca4"], - "aCaMKIII":["CaMKIII_CaM_Ca4"], - "PP1_deph_T286":["Deph_thr286"], - "PP1_deph_T305":["Deph_thr305"], - "PP1_deph_T306":["Deph_thr306"], - "PP1_deph_T286b":["Deph_thr286b"], - "PP1_deph_T286c":["Deph_thr286c"], - "Ca_bound":["CaM_Ca4","CaM_Ca3","CaM_Ca2","CaM_Ca"], - "tot_Ca_on_CaM":["CaM_Ca4","CaM_Ca4","CaM_Ca4","CaM_Ca4","CaM_Ca3","CaM_Ca3","CaM_Ca3","CaM_Ca2","CaM_Ca2","CaM_Ca"], - "eEF2_phospho":["CaMKIII_CaM_Ca4/phospho"], - "eS6Kpqrs+CaMKIII":["S6K_thr_252/CaMKIII_phospho"], - "S6Kp_act_CaMKIII":["S6K_thr_252/CaMKIII_phospho"], - "bS6K_act_CaMKIII":["S6K_basal/CaMKIII_basal"], - "bS6K_act":["basal_S6K"], - "bCaMKIII":["CaMKIII/CaMKIII_basal"], - "eMAPK+crafp":["MAPK_p_p_feedback"], - "MAPKpp_feedback":["MAPK_p_p_feedback"], - "MAPKKthr":["MAPKKthr"], - "MAPKKtyr":["MAPKKtyr"], - "MKP1":["MKP_1"], - "eMAPK+4EBPpq":["MAPK_4E_BP_p_p"], - "MAPK_4EBPpp":["MAPK_4E_BP_p_p"], - "eMAPK+PLA2":["MAPK_p_p/MAPK_p_p"], - "MAPKpp_act_PLA2":["MAPK_p_p/MAPK_p_p"], - "TrKB_cycling":["LR_cycling"], - "TrKB_Internalize":["LR_Internalize"], - "auto_TrKB":["Autophos_TrKB"], - "TrKB":["TrKB/TrKB"], - "CaMKIIT286_auto":["CaMKII_thr286"], - "CaMKIIT286_CaM":["CaMKII_thr286_p_CaM"], - "tCaMKIIT286":["CaMKII_thr286","CaMKII_thr286_p_CaM"], - "CaM_act_286":["CaM_act_286"], - "auton_286":["auton_286"], - "craf1":["craf_1"], - "craf1pp":["craf_1_p_p"], - "craf1p":["craf_1_p"], - "MAPKK":["MAPKK"], - "MAPKKp":["MAPKK_p"], - "MAPKKpp":["MAPKK_p_p"], - "GEFp_actRas":["GEF_p_act_Ras"], - "bGEF_act":["basal_GEF_activity"], - - "ePP2A+S6Kpq":["dephos_clus_S6K"], - "clus_S6K_deph":["dephos_clus_S6K"], - "ePP2A+S6Kpqr":["dephos_S6K"], - "S6K_deph":["dephos_S6K"], - "ePP2A+S6Kpqrs":["dephosp_S6K"], - "S6K_dephosp":["dephosp_S6K"], - "CaMCaN_deph_I1p":["dephosph_inhib1"], - "CaN_deph_I1p":["dephosph_inhib1_noCaM"], - "CaMCaN_deph_PP1_I1p":["dephosph_PP1_I_p"], - "ePP2A+I1p":["PP2A_dephospho_I1"], - "PP2A_dephos_I1":["PP2A_dephospho_I1"], - "PP2A_dephos_PP1_Ip":["PP2A_dephospho_PP1_I_p"], - "Gab1":["Gab1"], - "bPI3K":["PI3K_basal"], - "PI3K":["PI3K"], - "PTEN":["PTEN"], - "PIP2toPIP3":["SHC_p_Grb2_Gab1_PI3K_clx/Phospho"], - "SHC_p_Grb2_Gab1_PI3K_clx":["SHC_p_Grb2_Gab1_PI3K_clx"], - "PI3Kp_tot":["SHC_p_Grb2_Gab1_PI3K_clx","Ras_GTP_PI3K","PI3K_basal"], - "RasGTP_PI3K":["Ras_GTP_PI3K"], - "dephosp_S6K":["dephosp_S6K"], - "bind_Gab1":["bind_Gab1"], - "PI3K_act":["PI3K_act"], - "bPIP2_phospho":["basal_phosp"], - "bPI3K_act":["basal_PI3K_act"], - "PI3K_bind_RasGTP":["PI3K_bind_Ras_GTP"], - "phospho_AC2":["phosph_AC2"], - "GEF_Gprot_bg":["GEF_Gprot_bg"], - "GEFbg_act_Ras":["GEF_bg_act_Ras"], - "bg_act_GEF":["bg_act_GEF"], - "Inact_PLC_Gq":["Inact_PLC_Gq"], - "PLC_bind_Gq":["PLC_bind_Gq"], - "PKC_phospho_ng":["PKC_phosph_neurogranin"], - "PKC_phospho_ng_CaM":["PKC_phosph_ng_CaM"], - "PIP2_PLA2_act":["PIP2_PLA2_act"], - "PIP2_Ca_PLA2_act":["PIP2_Ca_PLA2_act"], - "CaM_bind_GEF":["CaM_bind_GEF"], - "PIP2_phospho_RasGTP":["PIP2_phospho_Ras_GTP"], - "ePP2A+AKTpq":["Dephos_AKTser473"], - "AKTpS473_deph":["Dephos_AKTser473"], - "ePP2A+AKTp":["Dephosph_AKTthr308"], - "AKTpT308_deph":["Dephosph_AKTthr308"], - "ePP2A+eEF2p":["eEF2thr_56_dephospho"], - "eEF2p_deph":["eEF2thr_56_dephospho"], - "beEF2p":["eEF2thr56_basal"], - "GST_PKBalpha":["AKT"], - "pGST_PKBalpha":["PIP3_AKT_thr308"], - "ePP2A+4EBPpqr":["PP2A_4E_BP_p_p"], - "PP2A_4EBPpp":["PP2A_4E_BP_p_p"], - "ePP2A+4EBPpq":["PP2A_4E_BP_p"], - "PP2A_4EBPp":["PP2A_4E_BP_p"], - "ePP2A+eIF4EBPpqr":["PP2A_4E_BP"], - "PP2A_eIF4EBPpp":["PP2A_4E_BP"], - "ePP2A+eIF4EBPpq":["PP2A_4EBP"], - "PP2A_eIF4EBPp":["PP2A_4EBP"], - "PLCgp_deph":["PLC_g_p_dephospho"], - "Grb2_bind_SHC":["Grb2_bind_SHC"], - "Grb2_bind_Sos":["Grb2_bind_Sos"], - "PDK1_act_S6K":["PDK1/S6K_phospho"], - "mTOR_act_S6K":["TOR_Rheb_GTP_clx/S6K_phospho"], - "phospho_AKTpT308":["phospho_thr308"], - "phospho_AKTpS473":["phosp_AKTser473"], - "eMAPK+S6K":["cluster_phospho_S6K"], - "clus_S6K_phospho":["cluster_phospho_S6K"], - "eMAPK+eIF4EBPpq" :["MAPK_4E_BP_phospho"], - "MAPK_4EBP_phospho":["MAPK_4E_BP_phospho"], - "MEK_phospho":["MEK_phospho"], - "MEKp_phospho":["MEKp_phospho"], - "mGluR_barr2_Raf":["mGluR_barr2_Raf_scaffolding"], - "mGluR_deph":["mGluR_dephosph"], - "FMRP_deph":["dephos_FMRP"], - "CaM_bind_CaNAB":["CaMCa4_bind_CaNAB"], - "tCaM_CaN":["CaM(Ca)n_CaNAB"], - "CaN":["CaNAB"], - "CaM_bind_PDE1":["CaM_bind_PDE1"], - "CaM_PDE1":["CaM.PDE1/CaM.PDE1"], - "Ca_bind_CaNCa2":["Ca_bind_CaNAB_Ca2"], - "Ca_bind_CaN":["Ca_bind_CaNAB"], - "CaMCa2_bind_CaN":["CaM_Ca2_bind_CaNAB"], - "CaMCa3_bind_CaN":["CaMCa3_bind_CaNAB"], - "CaMCa4_bind_CaN":["CaMCa4_bind_CaNAB"], - "CaM_bind_Ca":["CaM_bind_Ca"], - "CaMCa_bind_Ca":["CaM_Ca_bind_Ca"], - "CaMCa2_bind_Ca":["CaM_Ca2_bind_Ca"], - "CaMCa3_bind_Ca":["CaM_Ca3_bind_Ca"], - "CaN_Ca4":["CaNAB_Ca4"], - "ng":["neurogranin"], - "ng_CaM":["neurogranin_CaM"], - "ngp":["neurogranin_p"], - "ng_bind_CaM":["neurogranin_bind_CaM"], - "CaM_ng_deph":["CaM/dephosph_neurogranin"], - "CaN_ng_deph":["CaM(Ca)n_CaNAB/dephosph_neurogranin"], - "PKC_inact_GAP":["PKC_inact_GAP"], - "PKC_act_GEF":["PKC_act_GEF"], - "PKC_act_Ca_AA":["PKC_act_by_Ca_AA"], - "PKC_act_AA":["PKC_act_by_AA"], - "PKC_DAG_AA":["PKC_n_DAG_AA"], - "mGluR_barr2Raf":["mGluR_barr2_Raf"], - "PKC_act_DAG_AA":["PKC_act_by_DAG_AA"], - "eTrKB+PLCg":["BDNF_TrKB2_p_clx/PLC_g_phospho"], - "TrKB_act_PLCg":["BDNF_TrKB2_p_clx/PLC_g_phospho"], - "eTrKB+SHC":["BDNF_TrKB2_p_clx/SHC_phospho"], - "TrKB_act_SHC":["BDNF_TrKB2_p_clx/SHC_phospho"], - "Act_Gq":["Activate_Gq"], - "Sos_phospho":["phosph_Sos"], - "craf_deph" :["craf_dephospho"], - "MAPKK_deph":["MAPKK_dephospho"], - "MAPKKp_deph":["MAPKK_dephospho_ser"], - "crafpp_deph":["craf_p_p_dephospho"], - "S6_deph":["S6_dephosph"], - "emTORC1+4EBPhospho":["TOR_4E_BP_phospho"], - "TOR_4EBP_phospho":["TOR_4E_BP_phospho"], - "emTORC1+4EBP":["TOR_4E_BP_p"], - "TOR_4EBPp":["TOR_4E_BP_p"] + "all": [ + "all" + ], + "PKC_g": [ + "PKC" + ], + "PLA2_g": [ + "PLA2" + ], + "PLCb_g": [ + "PLCbeta" + ], + "mGluRAntag_g": [ + "kinetics/mGluRAntag" + ], + "MAPK_g": [ + "kinetics/MAPK" + ], + "Ras_g": [ + "Ras" + ], + "EGFR_g": [ + "kinetics/EGFR" + ], + "Sos_g": [ + "kinetics/Sos" + ], + "PLCg_g": [ + "kinetics/PLC_g" + ], + "CaMKII_g": [ + "kinetics/CaMKII" + ], + "CaM_g": [ + "kinetics/CaM" + ], + "PP1_g": [ + "PP1" + ], + "PP2B_g": [ + "PP2B" + ], + "PKA_g": [ + "PKA" + ], + "AC_g": [ + "AC" + ], + "mGluR_g": [ + "kinetics/mGluR" + ], + "Gprotein_g": [ + "Gprotein" + ], + "Phosphatase_g": [ + "Phosphatase" + ], + "Ca_g": [ + "kinetics/Ca" + ], + "PI3K_g": [ + "PI3K_activation" + ], + "AKT_g": [ + "AKT_activation" + ], + "TrKB_g": [ + "kinetics/TrKB" + ], + "mTORC1_g": [ + "mTORC1" + ], + "S6K_g": [ + "S6Kinase" + ], + "_4EBP_g": [ + "kinetics/_4E_BP" + ], + "_43S_g": [ + "_43S_complex" + ], + "protein_g": [ + "kinetics/protein" + ], + "BDNF_g": [ + "kinetics/BDNF" + ], + "CaMKIII_g": [ + "kinetics/CaMKIII" + ], + "Transl_init_g": [ + "Translation_initiation" + ], + "Transl_elong_g": [ + "Translation_elongation" + ], + "_40S_g": [ + "kinetics/_40S" + ], + "TSC1_TSC2_g": [ + "kinetics/TSC1_TSC2" + ], + "HomerPIKE_g": [ + "HomerPIKE" + ], + "barr2_g": [ + "barr2_signaling" + ], + "DHPG_mGluR_g": [ + "DHPG_mGluR" + ], + "CaseinKinase_g": [ + "CaseinKinase" + ], + "FMRP_g": [ + "kinetics/FMRP" + ], + "RecLigandBinding": [ + "RecLigandBinding" + ], + "makeTernary": [ + "Rec_Glu_bind_Gq" + ], + "CaM": [ + "CaM/CaM" + ], + "ERK": [ + "MAPK/MAPK" + ], + "pERK": [ + "MAPK/MAPK_p_p", + "MAPK/MAPK_p" + ], + "FMRP_synth": [ + "FMRP_synth" + ], + "aSHC": [ + "SHC_p" + ], + "SHC": [ + "SHC" + ], + "Gq_GDP": [ + "G_GDP" + ], + "EGFR": [ + "EGFR/EGFR" + ], + "aEGFR": [ + "L.EGFR" + ], + "act_surface_EGFR": [ + "L.EGFR" + ], + "eEGFR+SHC": [ + "L.EGFR/SHC_phospho" + ], + "PLCg": [ + "PLC_g/PLC_g" + ], + "Ca+PLCg": [ + "Ca_act_PLC_g" + ], + "Ca+PLCgp": [ + "Ca_act_PLC_g_p" + ], + "enolase": [ + "GDP_Ras" + ], + "RasGTP": [ + "GTP_Ras" + ], + "AA": [ + "Arachidonic_Acid" + ], + "Ca": [ + "Ca/Ca" + ], + "DAG": [ + "DAG" + ], + "PIP3_PDK2": [ + "PIP3_PDK2" + ], + "PIP2phospho_HomerPIKE": [ + "PIP2phospho_HomerPIKE" + ], + "PIP2": [ + "PIP2" + ], + "PIP3": [ + "PIP3" + ], + "IP3": [ + "IP3" + ], + "temp_PIP2": [ + "temp_PIP2" + ], + "Degrade_AA": [ + "Degrade_AA" + ], + "PC": [ + "PC" + ], + "PD098059": [ + "MAPKK" + ], + "Wortmannin": [ + "PI3K" + ], + "PP2A": [ + "PP2A" + ], + "PPhosphatase2A": [ + "PPhosphatase2A" + ], + "aPP1": [ + "PP1_active" + ], + "I1_PP1": [ + "Inact_PP1" + ], + "SHCp_deph": [ + "SHC_p_dephospho" + ], + "MAPKpq": [ + "MAPK/MAPK_p_p" + ], + "MAPKp": [ + "MAPK/MAPK_p" + ], + "EGF": [ + "EGF" + ], + "DHPG": [ + "Glutamate" + ], + "Glutamate": [ + "Glutamate" + ], + "CaMKIII": [ + "CaMKIII/CaMKIII" + ], + "CaMKIIIp_deph": [ + "CaMKIII_dephospho" + ], + "bCaMKIII": [ + "CaMKIII_p" + ], + "AKT": [ + "AKT" + ], + "ePTEN+PIP3": [ + "PIP3_dephosp" + ], + "PIP3+AKT": [ + "PIP3_bind_AKT" + ], + "PIP3+PDK1": [ + "PIP3_bind_PDK1" + ], + "PIP3_AKT": [ + "PIP3_AKT" + ], + "aAKT": [ + "PIP3_AKT_t308_s473" + ], + "43S": [ + "_43Scomplex" + ], + "mTOR": [ + "TOR_clx" + ], + "mTOR_KO": [ + "TOR_clx" + ], + "mTORp": [ + "TOR_Rheb_GTP_clx" + ], + "aMAPK": [ + "MAPK/MAPK_p_p", + "MAPK_p" + ], + "40S_mRNA": [ + "RM" + ], + "Q_clx": [ + "Quaternary_clx" + ], + "M_clx": [ + "eIF4F_mRNA_clx" + ], + "eIF4E+GA": [ + "eIF4F_clx" + ], + "eIF4E": [ + "eIF4E" + ], + "eIF4G": [ + "eIF4G" + ], + "eIF4A": [ + "eIF4A" + ], + "eIF4F": [ + "eIF4F" + ], + "mRNA": [ + "mRNA" + ], + "eIF4GA": [ + "eIF4G_A_clx" + ], + "eIF4G_bind_A": [ + "eIF4G_A_clx_formation" + ], + "eIF4F+mRNA": [ + "eIF4F_mRNA_clx_formation" + ], + "eIF4F_bind_mRNA": [ + "eIF4F_mRNA_clx_formation" + ], + "eIF4E+mRNA": [ + "eIF4E_mRNA_clx_formation" + ], + "eIF4EmRNA+F": [ + "eIF4EmRNA_eIF4GA_clx_formation" + ], + "TSC2_inact": [ + "TSC2_phospho" + ], + "Rheb_inact": [ + "TSC2phospho" + ], + "S6K": [ + "S6K" + ], + "S6Kpqr": [ + "S6K_thr_412" + ], + "S6Kpqrs": [ + "S6K_thr_252" + ], + "bS6K": [ + "S6K_basal" + ], + "BDNF": [ + "BDNF/BDNF" + ], + "Gq_deph": [ + "Inact_Gq" + ], + "bTranslation": [ + "Basal_Translation" + ], + "Translation_clx": [ + "Translation_clx" + ], + "eTrans+AA": [ + "pro_syn" + ], + "rad_pro_syn": [ + "rad_pro_syn" + ], + "ebTrans+AA": [ + "basal_syn" + ], + "rad_basal_syn": [ + "rad_basal_syn" + ], + "Transl_act": [ + "activation" + ], + "elongation": [ + "elongation" + ], + "protein": [ + "protein/protein" + ], + "Raf1_deph": [ + "deph_raf_ser259" + ], + "inact_Raf": [ + "craf_1_p_ser259" + ], + "eAKT+Raf": [ + "Raf_inhib" + ], + "eCaPLCb+PIP2": [ + "PLC_Ca/PLC_Ca" + ], + "PLC_Ca+Gq": [ + "Act_PLC_by_Gq" + ], + "Act_PLC_Ca": [ + "Act_PLC_Ca" + ], + "PLC_Gq_bind_Ca": [ + "PLC_Gq_bind_Ca" + ], + "ePLCb+PIP2": [ + "PLCb_Ca_Gq" + ], + "aPLCg": [ + "Ca.PLC_g_p" + ], + "Ca_PLCg": [ + "Ca.PLC_g" + ], + "bPLCg": [ + "PLCg_basal" + ], + "RasGDP": [ + "GDP_Ras" + ], + "TSC1_2": [ + "TSC1_TSC2/TSC1_TSC2" + ], + "TSC1_KO": [ + "TSC1_TSC2/TSC1_TSC2" + ], + "Rheb_GTP": [ + "Rheb_GTP" + ], + "Rheb_GDP": [ + "Rheb_GDP" + ], + "Rheb_act": [ + "GDP_to_GTP" + ], + "MAPK": [ + "MAPK/MAPK" + ], + "80S": [ + "_80S_ribos_clx" + ], + "60S": [ + "_60S_R" + ], + "AKTp": [ + "PIP3_AKT_thr308" + ], + "t4EBPpq": [ + "_4E_BP_t37_46" + ], + "t4EBPpqr": [ + "_4E_BP_t37_46_s65" + ], + "CaPLCg_phospho": [ + "Ca.PLC_g_phospho" + ], + "eEGFR+PLCg": [ + "Ca.PLC_g_phospho" + ], + "tPLCgp": [ + "PLC_g_p", + "Ca.PLC_g_p" + ], + "PLCgp": [ + "PLC_g_p" + ], + "EGF+EGFR": [ + "act_EGFR" + ], + "eIF4E+4EBP": [ + "eIF4E_bind_BP2" + ], + "4EBP": [ + "_4E_BP/_4E_BP" + ], + "t4EBP": [ + "_4E_BP/_4E_BP", + "eIF4E_BP" + ], + "a4EBP": [ + "_4E_BP_t37_46", + "_4E_BP_t37_46_s65", + "eIF4E_BP_thr37_46", + "eIF4E_BP_t37_46_s65" + ], + "eIF4EBPpT37T46": [ + "eIF4E_BP_thr37_46" + ], + "eIF4EBPpT37T46S65": [ + "eIF4E_BP_thr37_46_s65" + ], + "eIF4E_4EBP": [ + "eIF4E_BP" + ], + "eIF4EBPpqr_disso": [ + "eIF4E_BP2_disso" + ], + "eIF4EBPpq_disso": [ + "eIF4E_BP_disso" + ], + "S6": [ + "_40S_inact" + ], + "aS6": [ + "_40S/_40S" + ], + "eS6Kpqr+40S": [ + "S6_phos" + ], + "eS6Kpqrs+40S": [ + "S6_phospho" + ], + "Glu_mGluR": [ + "RecLigandBinding" + ], + "BDNF+TrKB": [ + "Ligand_binding" + ], + "aPKC": [ + "PKC_active" + ], + "cPKC": [ + "PKC_cytosolic" + ], + "cPLA2": [ + "PLA2_cytosolic" + ], + "PLA2p": [ + "PLA2_p" + ], + "Src": [ + "SHC" + ], + "SHCpGrb2Gab1_PI3K": [ + "SHC_p_Grb2_Gab1_PI3K_clx" + ], + "SHCpGrb2Gab1PI3K_phospho": [ + "SHC_p_Grb2_Gab1_PI3K_clx/Phospho" + ], + "SHCpGrb2_Gab1": [ + "SHC_p_Grb2_Gab1_clx" + ], + "bGq_act": [ + "Basal_Act_Gq" + ], + "PDK1": [ + "PDK1" + ], + "APC": [ + "APC" + ], + "eCaPLCgp+PIP2": [ + "Ca.PLC_g_p/PIP2_hydrolysis" + ], + "eCaPLCg+PIP2": [ + "Ca.PLC_g/PIP2_hydrolysis" + ], + "EGF_act_PLCg": [ + "Ca.PLC_g_p/PIP2_hydrolysis" + ], + "act_PLCg": [ + "Ca.PLC_g/PIP2_hydrolysis" + ], + "bPKC": [ + "PKC_basal_p" + ], + "BDNF_act_TrKB": [ + "BDNF_TrKB2_p_clx" + ], + "iTrKB": [ + "Int_BDNF_TrKB2_p_clx" + ], + "iEGFR": [ + "Internal_L.EGFR" + ], + "TrKBp": [ + "Int_BDNF_TrKB2_p_clx", + "BDNF_TrKB2_p_clx" + ], + "GAP": [ + "GAP" + ], + "GAP_inact_Ras": [ + "GAP_inact_Ras" + ], + "bRasGTP_deph": [ + "Ras_intrinsic_GTPase" + ], + "mGluR_bind_Homer": [ + "L.mGluR_HomerBinding" + ], + "mGluRpHomerPIKE_PI3K": [ + "L.mGluR_p.Homer.PIKE_L.PI3K" + ], + "mGluRpHomerPIKE_bind_PI3K": [ + "L.mGluR.Homer.PIKE_PI3K_Binding" + ], + "mGluR": [ + "mGluR/mGluR" + ], + "tot_surface_mGluR": [ + "mGluR/mGluR", + "Rec_Glu", + "L.mGluR_p" + ], + "tot_surface_mGluR_with_barr2": [ + "mGluR/mGluR", + "Rec_Glu", + "L.mGluR_p", + "L.mGluR_p.barr2", + "mGluR_p.barr2" + ], + "beta2ARp": [ + "Internal_mGluR_p", + "L.mGluR_p" + ], + "eRas+MAPKK1": [ + "Raf_p_GTP_Ras.1" + ], + "eRas+MAPKK2": [ + "Raf_p_GTP_Ras.2" + ], + "Rafp_RasGTP": [ + "Raf_p_GTP_Ras" + ], + "eCaMGEF+Ras": [ + "CaM_GEF_act_Ras" + ], + "Ras+craf": [ + "Ras_act_craf" + ], + "ePKC+craf": [ + "PKC_act_raf" + ], + "eMKP1+MAPKp": [ + "MKP1_tyr_deph" + ], + "eMKP1+MAPKpq": [ + "MKP1_thr_deph" + ], + "eSHCpSosGrb2+Ras": [ + "Sos.Ras_GEF" + ], + "Sosp_deph": [ + "dephosph_Sos" + ], + "R+M": [ + "R_binds_M" + ], + "Q_bind_40S": [ + "Q_binds_R" + ], + "QR_bind_mRNA": [ + "QR_binds_M" + ], + "RM+Q": [ + "RM_binds_Q" + ], + "QR": [ + "Q.R" + ], + "Rec_bind_Gq": [ + "Rec_bind_Gq" + ], + "Glu_mGluR+Gq": [ + "Rec_Glu_bind_Gq" + ], + "Glu_bind_Rec_Gq": [ + "Glu_bind_Rec_Gq" + ], + "mGluR_Gq": [ + "Rec_Gq" + ], + "amGluR": [ + "Rec_Glu_Gq" + ], + "eEF2": [ + "eEF2" + ], + "eEF2p": [ + "eEFthr_56" + ], + "S6Kpq": [ + "S6K_p" + ], + "CaMCa4": [ + "CaM_Ca4" + ], + "CaMKII": [ + "CaMKII/CaMKII" + ], + "CaMKII+CaMCa4": [ + "CaMKII_bind_CaM" + ], + "CaMCa4+CaMKIIp": [ + "CaMKII_thr286_bind_CaM" + ], + "CaMCaMKII_act_T286": [ + "CaM_act_286" + ], + "CaMCaMKII_act_T305": [ + "CaM_act_305" + ], + "CaMCa4+CaMKIII": [ + "CaMKIII_bind_CaM_Ca4" + ], + "aCaMKIII": [ + "CaMKIII_CaM_Ca4" + ], + "PP1_deph_T286": [ + "Deph_thr286" + ], + "PP1_deph_T305": [ + "Deph_thr305" + ], + "PP1_deph_T306": [ + "Deph_thr306" + ], + "PP1_deph_T286b": [ + "Deph_thr286b" + ], + "PP1_deph_T286c": [ + "Deph_thr286c" + ], + "Ca_bound": [ + "CaM_Ca4", + "CaM_Ca3", + "CaM_Ca2", + "CaM_Ca" + ], + "tCa_on_CaM": [ + "CaM_Ca4", + "CaM_Ca4", + "CaM_Ca4", + "CaM_Ca4", + "CaM_Ca3", + "CaM_Ca3", + "CaM_Ca3", + "CaM_Ca2", + "CaM_Ca2", + "CaM_Ca" + ], + "eCaMKIII+eEF2": [ + "CaMKIII_CaM_Ca4/phospho" + ], + "eS6Kpqrs+CaMKIII": [ + "S6K_thr_252/CaMKIII_phospho" + ], + "bS6K_act_CaMKIII": [ + "S6K_basal/CaMKIII_basal" + ], + "bS6K_act": [ + "basal_S6K" + ], + "eMAPK+crafp": [ + "MAPK_p_p_feedback" + ], + "eMAPKK+MAPKp": [ + "MAPKKthr" + ], + "eMAPKK+MAPK": [ + "MAPKKtyr" + ], + "MKP1": [ + "MKP_1" + ], + "eMAPK+4EBPpq": [ + "MAPK_4E_BP_p_p" + ], + "eMAPK+PLA2": [ + "MAPK_p_p/MAPK_p_p" + ], + "TrKB_cycling": [ + "LR_cycling" + ], + "TrKB_Internalize": [ + "LR_Internalize" + ], + "auto_TrKB": [ + "Autophos_TrKB" + ], + "TrKB": [ + "TrKB/TrKB" + ], + "CaMKIIT286_CaM": [ + "CaMKII_thr286_p_CaM" + ], + "tCaMKIIT286": [ + "CaMKII_thr286", + "CaMKII_thr286_p_CaM" + ], + "CaM_act_286": [ + "CaM_act_286" + ], + "eCaMKIIp+CaMKII": [ + "auton_286" + ], + "craf1": [ + "craf_1" + ], + "craf1pp": [ + "craf_1_p_p" + ], + "acraf1": [ + "craf_1_p" + ], + "MAPKK": [ + "MAPKK" + ], + "MAPKKp": [ + "MAPKK_p" + ], + "MAPKKpq": [ + "MAPKK_p_p" + ], + "GEFp_actRas": [ + "GEF_p_act_Ras" + ], + "ebGEF+Ras": [ + "basal_GEF_activity" + ], + "ePP2A+S6Kpq": [ + "dephos_clus_S6K" + ], + "ePP2A+S6Kpqr": [ + "dephos_S6K" + ], + "ePP2A+S6Kpqrs": [ + "dephosp_S6K" + ], + "eCaMCaN+I1p": [ + "dephosph_inhib1" + ], + "eCaN+I1p": [ + "dephosph_inhib1_noCaM" + ], + "eCaMCaN+PP1_I1p": [ + "dephosph_PP1_I_p" + ], + "ePP2A+I1p": [ + "PP2A_dephospho_I1" + ], + "PP2A_dephos_PP1_Ip": [ + "PP2A_dephospho_PP1_I_p" + ], + "Gab1": [ + "Gab1" + ], + "bPI3K": [ + "PI3K_basal" + ], + "PI3K": [ + "PI3K" + ], + "PTEN": [ + "PTEN" + ], + "PIP2toPIP3": [ + "SHC_p_Grb2_Gab1_PI3K_clx/Phospho" + ], + "SHC_p_Grb2_Gab1_PI3K_clx": [ + "SHC_p_Grb2_Gab1_PI3K_clx" + ], + "PI3Kp_tot": [ + "SHC_p_Grb2_Gab1_PI3K_clx", + "Ras_GTP_PI3K", + "PI3K_basal" + ], + "RasGTP_PI3K": [ + "Ras_GTP_PI3K" + ], + "dephosp_S6K": [ + "dephosp_S6K" + ], + "SHCp_Grb2+Gab1": [ + "bind_Gab1" + ], + "SHCpGrb2Gab1+PI3K": [ + "PI3K_act" + ], + "ebPI3K+PIP2": [ + "basal_phosp" + ], + "bPI3K_act": [ + "basal_PI3K_act" + ], + "PI3K+RasGTP": [ + "PI3K_bind_Ras_GTP" + ], + "phospho_AC2": [ + "phosph_AC2" + ], + "GEF_Gprot_bg": [ + "GEF_Gprot_bg" + ], + "eGbg+Ras": [ + "GEF_bg_act_Ras" + ], + "bg_act_GEF": [ + "bg_act_GEF" + ], + "Inact_PLC_Gq": [ + "Inact_PLC_Gq" + ], + "PLC_bind_Gq": [ + "PLC_bind_Gq" + ], + "PKC_phospho_ng": [ + "PKC_phosph_neurogranin" + ], + "PKC_phospho_ng_CaM": [ + "PKC_phosph_ng_CaM" + ], + "PIP2_PLA2_act": [ + "PIP2_PLA2_act" + ], + "PIP2_Ca_PLA2_act": [ + "PIP2_Ca_PLA2_act" + ], + "CaMCa4+GEF": [ + "CaM_bind_GEF" + ], + "eRas+PIP2": [ + "PIP2_phospho_Ras_GTP" + ], + "ePP2A+AKTpq": [ + "Dephos_AKTser473" + ], + "ePP2A+AKTp": [ + "Dephosph_AKTthr308" + ], + "ePP2A+eEF2p": [ + "eEF2thr_56_dephospho" + ], + "beEF2p": [ + "eEF2thr56_basal" + ], + "ePP2A+4EBPpqr": [ + "PP2A_4E_BP_p_p" + ], + "ePP2A+4EBPpq": [ + "PP2A_4E_BP_p" + ], + "ePP2A+eIF4EBPpqr": [ + "PP2A_4E_BP" + ], + "ePP2A+eIF4EBPpq": [ + "PP2A_4EBP" + ], + "PLCgp_deph": [ + "PLC_g_p_dephospho" + ], + "SHCp+Grb2": [ + "Grb2_bind_SHC" + ], + "Sos+Grb2": [ + "Grb2_bind_Sos" + ], + "PDK1_act_S6K": [ + "PDK1/S6K_phospho" + ], + "emTORC1+S6K": [ + "TOR_Rheb_GTP_clx/S6K_phospho" + ], + "ePI3K+AKT": [ + "phospho_thr308" + ], + "ePDK2+AKTp": [ + "phosp_AKTser473" + ], + "eMAPK+S6K": [ + "cluster_phospho_S6K" + ], + "eMAPK+eIF4EBPpq": [ + "MAPK_4E_BP_phospho" + ], + "ecraf+MAPKK": [ + "MEK_phospho" + ], + "ecraf+MAPKKp": [ + "MEKp_phospho" + ], + "craf1+barr2": [ + "mGluR_barr2_Raf_scaffolding" + ], + "mGluR_deph": [ + "mGluR_dephosph" + ], + "FMRP_deph": [ + "dephos_FMRP" + ], + "CaM_bind_CaNAB": [ + "CaMCa4_bind_CaNAB" + ], + "aCaM_CaN": [ + "CaM(Ca)n_CaNAB" + ], + "CaN": [ + "CaNAB" + ], + "CaMCa4+PDE1": [ + "CaM_bind_PDE1" + ], + "CaM_PDE1": [ + "CaM.PDE1/CaM.PDE1" + ], + "Ca_bind_CaNCa2": [ + "Ca_bind_CaNAB_Ca2" + ], + "Ca+CaN": [ + "Ca_bind_CaNAB" + ], + "CaMCa2_bind_CaN": [ + "CaM_Ca2_bind_CaNAB" + ], + "CaMCa3_bind_CaN": [ + "CaMCa3_bind_CaNAB" + ], + "CaN+CaMCa4": [ + "CaMCa4_bind_CaNAB" + ], + "CaM+Ca": [ + "CaM_bind_Ca" + ], + "CaMCa+Ca": [ + "CaM_Ca_bind_Ca" + ], + "CaMCa2+Ca": [ + "CaM_Ca2_bind_Ca" + ], + "CaMCa3+Ca": [ + "CaM_Ca3_bind_Ca" + ], + "aCaN": [ + "CaNAB_Ca4" + ], + "neurogranin": [ + "neurogranin" + ], + "neurogranin_CaM": [ + "neurogranin_CaM" + ], + "neurograninp": [ + "neurogranin_p" + ], + "ng+CaM": [ + "neurogranin_bind_CaM" + ], + "eCaM+ngp": [ + "CaM/dephosph_neurogranin" + ], + "eCaMCaN+ngp": [ + "CaM(Ca)n_CaNAB/dephosph_neurogranin" + ], + "PKC_inact_GAP": [ + "PKC_inact_GAP" + ], + "PKC_act_GEF": [ + "PKC_act_GEF" + ], + "PKC_act_Ca_AA": [ + "PKC_act_by_Ca_AA" + ], + "PKC_act_AA": [ + "PKC_act_by_AA" + ], + "PKC_DAG_AA": [ + "PKC_n_DAG_AA" + ], + "mGluR_barr2Raf": [ + "mGluR_barr2_Raf" + ], + "PKC_act_DAG_AA": [ + "PKC_act_by_DAG_AA" + ], + "eTrKB+PLCg": [ + "BDNF_TrKB2_p_clx/PLC_g_phospho" + ], + "eTrKB+SHC": [ + "BDNF_TrKB2_p_clx/SHC_phospho" + ], + "Act_Gq": [ + "Activate_Gq" + ], + "Sos_phospho": [ + "phosph_Sos" + ], + "craf_deph": [ + "craf_dephospho" + ], + "ePP2A+MAPKKpq": [ + "MAPKK_dephospho" + ], + "ePP2A+MAPKKp": [ + "MAPKK_dephospho_ser" + ], + "crafpp_deph": [ + "craf_p_p_dephospho" + ], + "S6_deph": [ + "S6_dephosph" + ], + "emTORC1+4EBP": [ + "TOR_4E_BP_p" + ] } diff --git a/simWrapMoose.py b/simWrapMoose.py index 88f3e94..41c4582 100644 --- a/simWrapMoose.py +++ b/simWrapMoose.py @@ -478,7 +478,7 @@ def buildSolver( self, solver, useVclamp = False, minInterval = 1.0 ): def buildVclamp( self, stim ): # Stim.entities should be the compartment name here. - comptPath = self.lookup( stim.entities[0] )[0] + comptPath = self.lookup( stim.entities[0]['name'] )[0] vclamp = moose.VClamp( comptPath + '/vclamp' ) self.modelLookup['vclamp'] = [vclamp.path,] compt = moose.element(comptPath)