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/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/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.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/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/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/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] + ] + } } 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"} ] } } diff --git a/__pycache__/simError.cpython-38.pyc b/__pycache__/simError.cpython-38.pyc new file mode 100644 index 0000000..2599603 Binary files /dev/null and b/__pycache__/simError.cpython-38.pyc differ diff --git a/__pycache__/simWrap.cpython-38.pyc b/__pycache__/simWrap.cpython-38.pyc new file mode 100644 index 0000000..e514d4a Binary files /dev/null and b/__pycache__/simWrap.cpython-38.pyc differ diff --git a/__pycache__/simWrapHillTau.cpython-38.pyc b/__pycache__/simWrapHillTau.cpython-38.pyc new file mode 100644 index 0000000..0904c6c Binary files /dev/null and b/__pycache__/simWrapHillTau.cpython-38.pyc differ diff --git a/__pycache__/simWrapMoose.cpython-38.pyc b/__pycache__/simWrapMoose.cpython-38.pyc new file mode 100644 index 0000000..1e24616 Binary files /dev/null and b/__pycache__/simWrapMoose.cpython-38.pyc differ diff --git a/findSim.py b/findSim.py index 3bf40d1..6c2f53a 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 ) @@ -510,9 +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: @@ -615,7 +617,7 @@ 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 +858,13 @@ 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 +922,7 @@ 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 +1023,7 @@ 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 +1068,12 @@ 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 +1185,18 @@ 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 +1223,17 @@ 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 +1267,7 @@ 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 +1327,7 @@ 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 +1400,7 @@ 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 +1558,7 @@ 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 +1578,10 @@ 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] diff --git a/models/synSynth7_map.json b/models/synSynth7_map.json index 511e29f..aa385d7 100644 --- a/models/synSynth7_map.json +++ b/models/synSynth7_map.json @@ -1,372 +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"], - "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"], - "SHCp":["SHC_p"], - "SHC":["SHC"], - "G_GDP":["G_GDP"], - "EGFR":["EGFR/EGFR"], - "EGFRp":["L.EGFR"], - "act_surface_EGFR":["L.EGFR"], - "EGFR_act_SHC":["L.EGFR/SHC_phospho"], - "PLCg":["PLC_g/PLC_g"], - "Ca_act_PLCg":["Ca_act_PLC_g"], - "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"], - "DHPG":["Glutamate"], - "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"], - "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"], - "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"], - "S6p":["_40S/_40S"], - "S6_phos":["S6_phos"], - "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"], - "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_bind_Gq":["Rec_Glu_bind_Gq"], - "Glu_bind_Rec_Gq":["Glu_bind_Rec_Gq"], - "mGluR_Gq":["Rec_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"], - "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"], - "S6Kp_act_CaMKIII":["S6K_thr_252/CaMKIII_phospho"], - "bS6K_act_CaMKIII":["S6K_basal/CaMKIII_basal"], - "bS6K_act":["basal_S6K"], - "bCaMKIII":["CaMKIII/CaMKIII_basal"], - "MAPKpp_feedback":["MAPK_p_p_feedback"], - "MAPKKthr":["MAPKKthr"], - "MAPKKtyr":["MAPKKtyr"], - "MKP1":["MKP_1"], - "MAPK_4EBPpp":["MAPK_4E_BP_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"], - 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"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/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..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) @@ -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]