From e8ad517eb9655b831e18b1edb14ecfd1003b0ecc Mon Sep 17 00:00:00 2001 From: hrani Date: Tue, 9 Apr 2024 17:27:16 +0530 Subject: [PATCH] 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"], 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+ "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)