Delete BioModelsRAG

BioModelsRAG/2data/BIOMD0000000001.txt

@@ -1,224 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000001()
-
-  // Compartments and Species:
-  compartment comp1;
-  species BLL in comp1, IL in comp1, AL in comp1, A in comp1, BL in comp1;
-  species B in comp1, DLL in comp1, D in comp1, ILL in comp1, DL in comp1;
-  species I in comp1, ALL in comp1;
-
-  // Reactions:
-  React0: B -> BL; comp1*(kf_0*B - kr_0*BL);
-  React1: BL -> BLL; comp1*(kf_1*BL - kr_1*BLL);
-  React2: BLL -> ALL; comp1*(kf_2*BLL - kr_2*ALL);
-  React3: A -> AL; comp1*(kf_3*A - kr_3*AL);
-  React4: AL -> ALL; comp1*(kf_4*AL - kr_4*ALL);
-  React5: B -> A; comp1*(kf_5*B - kr_5*A);
-  React6: BL -> AL; comp1*(kf_6*BL - kr_6*AL);
-  React7: I -> IL; comp1*(kf_7*I - kr_7*IL);
-  React8: IL -> ILL; comp1*(kf_8*IL - kr_8*ILL);
-  React9: A -> I; comp1*(kf_9*A - kr_9*I);
-  React10: AL -> IL; comp1*(kf_10*AL - kr_10*IL);
-  React11: ALL -> ILL; comp1*(kf_11*ALL - kr_11*ILL);
-  React12: D -> DL; comp1*(kf_12*D - kr_12*DL);
-  React13: DL -> DLL; comp1*(kf_13*DL - kr_13*DLL);
-  React14: I -> D; comp1*(kf_14*I - kr_14*D);
-  React15: IL -> DL; comp1*(kf_15*IL - kr_15*DL);
-  React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL);
-
-  // Events:
-  RemovalACh: at time > t2: kf_13 = 0, kf_8 = 0, kf_4 = 0, kf_1 = 0, kf_12 = 0, kf_7 = 0, kf_3 = 0, kf_0 = 0;
-
-  // Species initializations:
-  BLL = 0;
-  IL = 0;
-  AL = 0;
-  A = 0;
-  BL = 0;
-  B = 1.66057788110262e-21/comp1;
-  DLL = 0;
-  D = 0;
-  ILL = 0;
-  DL = 0;
-  I = 0;
-  ALL = 0;
-
-  // Compartment initializations:
-  comp1 = 1e-16;
-
-  // Variable initializations:
-  t2 = 20;
-  kf_0 = 3000;
-  kf_3 = 3000;
-  kf_7 = 3000;
-  kf_12 = 3000;
-  kf_1 = 1500;
-  kf_4 = 1500;
-  kf_8 = 1500;
-  kf_13 = 1500;
-  kr_0 = 8000;
-  kr_1 = 16000;
-  kf_2 = 30000;
-  kr_2 = 700;
-  kr_3 = 8.64;
-  kr_4 = 17.28;
-  kf_5 = 0.54;
-  kr_5 = 10800;
-  kf_6 = 130;
-  kr_6 = 2740;
-  kr_7 = 4;
-  kr_8 = 8;
-  kf_9 = 19.7;
-  kr_9 = 3.74;
-  kf_10 = 19.85;
-  kr_10 = 1.74;
-  kf_11 = 20;
-  kr_11 = 0.81;
-  kr_12 = 4;
-  kr_13 = 8;
-  kf_14 = 0.05;
-  kr_14 = 0.0012;
-  kf_15 = 0.05;
-  kr_15 = 0.0012;
-  kf_16 = 0.05;
-  kr_16 = 0.0012;
-
-  // Other declarations:
-  var kf_0, kf_3, kf_7, kf_12, kf_1, kf_4, kf_8, kf_13;
-  const comp1, t2, kr_0, kr_1, kf_2, kr_2, kr_3, kr_4, kf_5, kr_5, kf_6, kr_6;
-  const kr_7, kr_8, kf_9, kr_9, kf_10, kr_10, kf_11, kr_11, kr_12, kr_13;
-  const kf_14, kr_14, kf_15, kr_15, kf_16, kr_16;
-
-  // Display Names:
-  comp1 is "compartment1";
-  BLL is "BasalACh2";
-  IL is "IntermediateACh";
-  AL is "ActiveACh";
-  A is "Active";
-  BL is "BasalACh";
-  B is "Basal";
-  DLL is "DesensitisedACh2";
-  D is "Desensitised";
-  ILL is "IntermediateACh2";
-  DL is "DesensitisedACh";
-  I is "Intermediate";
-  ALL is "ActiveACh2";
-  RemovalACh is "removal of ACh";
-
-  // SBO terms:
-  comp1.sboTerm = 290
-  BLL.sboTerm = 297
-  IL.sboTerm = 297
-  AL.sboTerm = 297
-  A.sboTerm = 420
-  BL.sboTerm = 297
-  B.sboTerm = 420
-  DLL.sboTerm = 297
-  D.sboTerm = 420
-  ILL.sboTerm = 297
-  DL.sboTerm = 297
-  I.sboTerm = 420
-  ALL.sboTerm = 297
-  kf_0.sboTerm = 35
-  kf_3.sboTerm = 35
-  kf_7.sboTerm = 35
-  kf_12.sboTerm = 35
-  kf_1.sboTerm = 35
-  kf_4.sboTerm = 35
-  kf_8.sboTerm = 35
-  kf_13.sboTerm = 35
-  kr_0.sboTerm = 38
-  kr_1.sboTerm = 38
-  kf_2.sboTerm = 35
-  kr_2.sboTerm = 38
-  kr_3.sboTerm = 38
-  kr_4.sboTerm = 38
-  kf_5.sboTerm = 35
-  kr_5.sboTerm = 38
-  kf_6.sboTerm = 35
-  kr_6.sboTerm = 38
-  kr_7.sboTerm = 38
-  kr_8.sboTerm = 38
-  kf_9.sboTerm = 35
-  kr_9.sboTerm = 38
-  kf_10.sboTerm = 35
-  kr_10.sboTerm = 38
-  kf_11.sboTerm = 35
-  kr_11.sboTerm = 38
-  kr_12.sboTerm = 38
-  kr_13.sboTerm = 38
-  kf_14.sboTerm = 35
-  kr_14.sboTerm = 38
-  kf_15.sboTerm = 35
-  kr_15.sboTerm = 38
-  kf_16.sboTerm = 35
-  kr_16.sboTerm = 38
-  React0.sboTerm = 177
-  React1.sboTerm = 177
-  React2.sboTerm = 181
-  React3.sboTerm = 177
-  React4.sboTerm = 177
-  React5.sboTerm = 181
-  React6.sboTerm = 181
-  React7.sboTerm = 177
-  React8.sboTerm = 177
-  React9.sboTerm = 181
-  React10.sboTerm = 181
-  React11.sboTerm = 181
-  React12.sboTerm = 177
-  React13.sboTerm = 177
-  React14.sboTerm = 181
-  React15.sboTerm = 181
-  React16.sboTerm = 181
-
-  // CV terms:
-  comp1 identity "http://identifiers.org/go/GO:0031594"
-  BLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  IL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  AL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  A hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  BL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  B hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  DLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  D hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ILL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  DL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  I hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ALL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  React0 identity "http://identifiers.org/go/GO:0042166"
-  React1 identity "http://identifiers.org/go/GO:0042166"
-  React2 identity "http://identifiers.org/go/GO:0004889"
-  React3 identity "http://identifiers.org/go/GO:0042166"
-  React4 identity "http://identifiers.org/go/GO:0042166"
-  React5 identity "http://identifiers.org/go/GO:0004889"
-  React6 identity "http://identifiers.org/go/GO:0004889"
-  React7 identity "http://identifiers.org/go/GO:0042166"
-  React8 identity "http://identifiers.org/go/GO:0042166"
-  React9 identity "http://identifiers.org/go/GO:0004889"
-  React10 identity "http://identifiers.org/go/GO:0004889"
-  React11 identity "http://identifiers.org/go/GO:0004889"
-  React12 identity "http://identifiers.org/go/GO:0042166"
-  React13 identity "http://identifiers.org/go/GO:0042166"
-end
-
-BIOMD0000000001 is "Edelstein1996 - EPSP ACh event"
-
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6613849442"
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000001"
-BIOMD0000000001 description "http://identifiers.org/pubmed/8983160"
-BIOMD0000000001 hypernym "http://identifiers.org/go/GO:0007274",
-                         "http://identifiers.org/go/GO:0007166",
-                         "http://identifiers.org/go/GO:0019226"
-BIOMD0000000001 taxon "http://identifiers.org/taxonomy/7787"

BioModelsRAG/__init__.py

@@ -1,19 +0,0 @@
-__version__ = "0.1.0"
-__author__ = "Bhavyahshree Navaneetha Krishnan"
-
-from langchain_text_splitters import CharacterTextSplitter
-import os
-import chromadb
-from chromadb.utils import embedding_functions
-import ollama
-
-import splitBioModels
-import createVectorDB
-import createDocuments
-# Import functions from other modules
-from splitBioModels import splitBioModels
-from createVectorDB import createVectorDB
-from createDocuments import createDocuments
-
-# Define __all__ to specify which names are publicly accessible
-__all__ = ['splitBioModels', 'createVectorDB', 'createDocuments']

BioModelsRAG/data/BIOMD0000000001.txt

@@ -1,224 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000001()
-
-  // Compartments and Species:
-  compartment comp1;
-  species BLL in comp1, IL in comp1, AL in comp1, A in comp1, BL in comp1;
-  species B in comp1, DLL in comp1, D in comp1, ILL in comp1, DL in comp1;
-  species I in comp1, ALL in comp1;
-
-  // Reactions:
-  React0: B -> BL; comp1*(kf_0*B - kr_0*BL);
-  React1: BL -> BLL; comp1*(kf_1*BL - kr_1*BLL);
-  React2: BLL -> ALL; comp1*(kf_2*BLL - kr_2*ALL);
-  React3: A -> AL; comp1*(kf_3*A - kr_3*AL);
-  React4: AL -> ALL; comp1*(kf_4*AL - kr_4*ALL);
-  React5: B -> A; comp1*(kf_5*B - kr_5*A);
-  React6: BL -> AL; comp1*(kf_6*BL - kr_6*AL);
-  React7: I -> IL; comp1*(kf_7*I - kr_7*IL);
-  React8: IL -> ILL; comp1*(kf_8*IL - kr_8*ILL);
-  React9: A -> I; comp1*(kf_9*A - kr_9*I);
-  React10: AL -> IL; comp1*(kf_10*AL - kr_10*IL);
-  React11: ALL -> ILL; comp1*(kf_11*ALL - kr_11*ILL);
-  React12: D -> DL; comp1*(kf_12*D - kr_12*DL);
-  React13: DL -> DLL; comp1*(kf_13*DL - kr_13*DLL);
-  React14: I -> D; comp1*(kf_14*I - kr_14*D);
-  React15: IL -> DL; comp1*(kf_15*IL - kr_15*DL);
-  React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL);
-
-  // Events:
-  RemovalACh: at time > t2: kf_13 = 0, kf_8 = 0, kf_4 = 0, kf_1 = 0, kf_12 = 0, kf_7 = 0, kf_3 = 0, kf_0 = 0;
-
-  // Species initializations:
-  BLL = 0;
-  IL = 0;
-  AL = 0;
-  A = 0;
-  BL = 0;
-  B = 1.66057788110262e-21/comp1;
-  DLL = 0;
-  D = 0;
-  ILL = 0;
-  DL = 0;
-  I = 0;
-  ALL = 0;
-
-  // Compartment initializations:
-  comp1 = 1e-16;
-
-  // Variable initializations:
-  t2 = 20;
-  kf_0 = 3000;
-  kf_3 = 3000;
-  kf_7 = 3000;
-  kf_12 = 3000;
-  kf_1 = 1500;
-  kf_4 = 1500;
-  kf_8 = 1500;
-  kf_13 = 1500;
-  kr_0 = 8000;
-  kr_1 = 16000;
-  kf_2 = 30000;
-  kr_2 = 700;
-  kr_3 = 8.64;
-  kr_4 = 17.28;
-  kf_5 = 0.54;
-  kr_5 = 10800;
-  kf_6 = 130;
-  kr_6 = 2740;
-  kr_7 = 4;
-  kr_8 = 8;
-  kf_9 = 19.7;
-  kr_9 = 3.74;
-  kf_10 = 19.85;
-  kr_10 = 1.74;
-  kf_11 = 20;
-  kr_11 = 0.81;
-  kr_12 = 4;
-  kr_13 = 8;
-  kf_14 = 0.05;
-  kr_14 = 0.0012;
-  kf_15 = 0.05;
-  kr_15 = 0.0012;
-  kf_16 = 0.05;
-  kr_16 = 0.0012;
-
-  // Other declarations:
-  var kf_0, kf_3, kf_7, kf_12, kf_1, kf_4, kf_8, kf_13;
-  const comp1, t2, kr_0, kr_1, kf_2, kr_2, kr_3, kr_4, kf_5, kr_5, kf_6, kr_6;
-  const kr_7, kr_8, kf_9, kr_9, kf_10, kr_10, kf_11, kr_11, kr_12, kr_13;
-  const kf_14, kr_14, kf_15, kr_15, kf_16, kr_16;
-
-  // Display Names:
-  comp1 is "compartment1";
-  BLL is "BasalACh2";
-  IL is "IntermediateACh";
-  AL is "ActiveACh";
-  A is "Active";
-  BL is "BasalACh";
-  B is "Basal";
-  DLL is "DesensitisedACh2";
-  D is "Desensitised";
-  ILL is "IntermediateACh2";
-  DL is "DesensitisedACh";
-  I is "Intermediate";
-  ALL is "ActiveACh2";
-  RemovalACh is "removal of ACh";
-
-  // SBO terms:
-  comp1.sboTerm = 290
-  BLL.sboTerm = 297
-  IL.sboTerm = 297
-  AL.sboTerm = 297
-  A.sboTerm = 420
-  BL.sboTerm = 297
-  B.sboTerm = 420
-  DLL.sboTerm = 297
-  D.sboTerm = 420
-  ILL.sboTerm = 297
-  DL.sboTerm = 297
-  I.sboTerm = 420
-  ALL.sboTerm = 297
-  kf_0.sboTerm = 35
-  kf_3.sboTerm = 35
-  kf_7.sboTerm = 35
-  kf_12.sboTerm = 35
-  kf_1.sboTerm = 35
-  kf_4.sboTerm = 35
-  kf_8.sboTerm = 35
-  kf_13.sboTerm = 35
-  kr_0.sboTerm = 38
-  kr_1.sboTerm = 38
-  kf_2.sboTerm = 35
-  kr_2.sboTerm = 38
-  kr_3.sboTerm = 38
-  kr_4.sboTerm = 38
-  kf_5.sboTerm = 35
-  kr_5.sboTerm = 38
-  kf_6.sboTerm = 35
-  kr_6.sboTerm = 38
-  kr_7.sboTerm = 38
-  kr_8.sboTerm = 38
-  kf_9.sboTerm = 35
-  kr_9.sboTerm = 38
-  kf_10.sboTerm = 35
-  kr_10.sboTerm = 38
-  kf_11.sboTerm = 35
-  kr_11.sboTerm = 38
-  kr_12.sboTerm = 38
-  kr_13.sboTerm = 38
-  kf_14.sboTerm = 35
-  kr_14.sboTerm = 38
-  kf_15.sboTerm = 35
-  kr_15.sboTerm = 38
-  kf_16.sboTerm = 35
-  kr_16.sboTerm = 38
-  React0.sboTerm = 177
-  React1.sboTerm = 177
-  React2.sboTerm = 181
-  React3.sboTerm = 177
-  React4.sboTerm = 177
-  React5.sboTerm = 181
-  React6.sboTerm = 181
-  React7.sboTerm = 177
-  React8.sboTerm = 177
-  React9.sboTerm = 181
-  React10.sboTerm = 181
-  React11.sboTerm = 181
-  React12.sboTerm = 177
-  React13.sboTerm = 177
-  React14.sboTerm = 181
-  React15.sboTerm = 181
-  React16.sboTerm = 181
-
-  // CV terms:
-  comp1 identity "http://identifiers.org/go/GO:0031594"
-  BLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  IL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  AL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  A hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  BL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  B hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  DLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  D hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ILL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  DL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  I hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ALL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  React0 identity "http://identifiers.org/go/GO:0042166"
-  React1 identity "http://identifiers.org/go/GO:0042166"
-  React2 identity "http://identifiers.org/go/GO:0004889"
-  React3 identity "http://identifiers.org/go/GO:0042166"
-  React4 identity "http://identifiers.org/go/GO:0042166"
-  React5 identity "http://identifiers.org/go/GO:0004889"
-  React6 identity "http://identifiers.org/go/GO:0004889"
-  React7 identity "http://identifiers.org/go/GO:0042166"
-  React8 identity "http://identifiers.org/go/GO:0042166"
-  React9 identity "http://identifiers.org/go/GO:0004889"
-  React10 identity "http://identifiers.org/go/GO:0004889"
-  React11 identity "http://identifiers.org/go/GO:0004889"
-  React12 identity "http://identifiers.org/go/GO:0042166"
-  React13 identity "http://identifiers.org/go/GO:0042166"
-end
-
-BIOMD0000000001 is "Edelstein1996 - EPSP ACh event"
-
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6613849442"
-BIOMD0000000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000001"
-BIOMD0000000001 description "http://identifiers.org/pubmed/8983160"
-BIOMD0000000001 hypernym "http://identifiers.org/go/GO:0007274",
-                         "http://identifiers.org/go/GO:0007166",
-                         "http://identifiers.org/go/GO:0019226"
-BIOMD0000000001 taxon "http://identifiers.org/taxonomy/7787"

BioModelsRAG/data/BIOMD0000000002.txt

@@ -1,155 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000002()
-
-  // Compartments and Species:
-  compartment comp1;
-  species BLL in comp1, IL in comp1, AL in comp1, A in comp1, BL in comp1;
-  species B in comp1, DLL in comp1, D in comp1, ILL in comp1, DL in comp1;
-  species I in comp1, ALL in comp1, L in comp1;
-
-  // Reactions:
-  React0: B + L -> BL; comp1*(kf_0*B*L - kr_0*BL);
-  React1: BL + L -> BLL; comp1*(kf_1*BL*L - kr_1*BLL);
-  React2: BLL -> ALL; comp1*(kf_2*BLL - kr_2*ALL);
-  React3: A + L -> AL; comp1*(kf_3*A*L - kr_3*AL);
-  React4: AL + L -> ALL; comp1*(kf_4*AL*L - kr_4*ALL);
-  React5: B -> A; comp1*(kf_5*B - kr_5*A);
-  React6: BL -> AL; comp1*(kf_6*BL - kr_6*AL);
-  React7: I + L -> IL; comp1*(kf_7*I*L - kr_7*IL);
-  React8: IL + L -> ILL; comp1*(kf_8*IL*L - kr_8*ILL);
-  React9: A -> I; comp1*(kf_9*A - kr_9*I);
-  React10: AL -> IL; comp1*(kf_10*AL - kr_10*IL);
-  React11: ALL -> ILL; comp1*(kf_11*ALL - kr_11*ILL);
-  React12: D + L -> DL; comp1*(kf_12*D*L - kr_12*DL);
-  React13: DL + L -> DLL; comp1*(kf_13*DL*L - kr_13*DLL);
-  React14: I -> D; comp1*(kf_14*I - kr_14*D);
-  React15: IL -> DL; comp1*(kf_15*IL - kr_15*DL);
-  React16: ILL -> DLL; comp1*(kf_16*ILL - kr_16*DLL);
-
-  // Species initializations:
-  BLL = 0;
-  IL = 0;
-  AL = 0;
-  A = 0;
-  BL = 0;
-  B = 1e-22/comp1;
-  DLL = 0;
-  D = 0;
-  ILL = 0;
-  DL = 0;
-  I = 0;
-  ALL = 0;
-  L = 1e-21/comp1;
-
-  // Compartment initializations:
-  comp1 = 1e-16;
-
-  // Variable initializations:
-  kf_0 = 300000000;
-  kr_0 = 8000;
-  kf_1 = 150000000;
-  kr_1 = 16000;
-  kf_2 = 30000;
-  kr_2 = 700;
-  kf_3 = 300000000;
-  kr_3 = 8.64;
-  kf_4 = 150000000;
-  kr_4 = 17.28;
-  kf_5 = 0.54;
-  kr_5 = 10800;
-  kf_6 = 130;
-  kr_6 = 2740;
-  kf_7 = 300000000;
-  kr_7 = 4;
-  kf_8 = 150000000;
-  kr_8 = 8;
-  kf_9 = 19.7;
-  kr_9 = 3.74;
-  kf_10 = 19.85;
-  kr_10 = 1.74;
-  kf_11 = 20;
-  kr_11 = 0.81;
-  kf_12 = 300000000;
-  kr_12 = 4;
-  kf_13 = 150000000;
-  kr_13 = 8;
-  kf_14 = 0.05;
-  kr_14 = 0.0012;
-  kf_15 = 0.05;
-  kr_15 = 0.0012;
-  kf_16 = 0.05;
-  kr_16 = 0.0012;
-
-  // Other declarations:
-  const comp1, kf_0, kr_0, kf_1, kr_1, kf_2, kr_2, kf_3, kr_3, kf_4, kr_4;
-  const kf_5, kr_5, kf_6, kr_6, kf_7, kr_7, kf_8, kr_8, kf_9, kr_9, kf_10;
-  const kr_10, kf_11, kr_11, kf_12, kr_12, kf_13, kr_13, kf_14, kr_14, kf_15;
-  const kr_15, kf_16, kr_16;
-
-  // Display Names:
-  comp1 is "compartment1";
-  BLL is "BasalACh2";
-  IL is "IntermediateACh";
-  AL is "ActiveACh";
-  A is "Active";
-  BL is "BasalACh";
-  B is "Basal";
-  DLL is "DesensitisedACh2";
-  D is "Desensitised";
-  ILL is "IntermediateACh2";
-  DL is "DesensitisedACh";
-  I is "Intermediate";
-  ALL is "ActiveACh2";
-  L is "ACh";
-
-  // CV terms:
-  comp1 identity "http://identifiers.org/go/GO:0031594"
-  BLL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  IL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  AL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  A hypernym "http://identifiers.org/go/GO:0005892"
-  BL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  B hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  DLL hypernym "http://identifiers.org/go/GO:0005892"
-  D hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ILL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  DL hypernym "http://identifiers.org/interpro/IPR002394",
-              "http://identifiers.org/go/GO:0005892"
-  I hypernym "http://identifiers.org/interpro/IPR002394",
-             "http://identifiers.org/go/GO:0005892"
-  ALL hypernym "http://identifiers.org/interpro/IPR002394",
-               "http://identifiers.org/go/GO:0005892"
-  L identity "http://identifiers.org/chebi/CHEBI:15355",
-             "http://identifiers.org/kegg.compound/C01996"
-  React0 identity "http://identifiers.org/go/GO:0042166"
-  React1 identity "http://identifiers.org/go/GO:0042166"
-  React2 identity "http://identifiers.org/go/GO:0004889"
-  React3 identity "http://identifiers.org/go/GO:0042166"
-  React4 identity "http://identifiers.org/go/GO:0042166"
-  React5 identity "http://identifiers.org/go/GO:0004889"
-  React6 identity "http://identifiers.org/go/GO:0004889"
-  React7 identity "http://identifiers.org/go/GO:0042166"
-  React8 identity "http://identifiers.org/go/GO:0042166"
-  React9 identity "http://identifiers.org/go/GO:0004889"
-  React10 identity "http://identifiers.org/go/GO:0004889"
-  React11 identity "http://identifiers.org/go/GO:0004889"
-  React12 identity "http://identifiers.org/go/GO:0042166"
-  React13 identity "http://identifiers.org/go/GO:0042166"
-end
-
-BIOMD0000000002 is "Edelstein1996 - EPSP ACh species"
-
-BIOMD0000000002 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614086398"
-BIOMD0000000002 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000002"
-BIOMD0000000002 description "http://identifiers.org/pubmed/8983160"
-BIOMD0000000002 taxon "http://identifiers.org/taxonomy/7787"
-BIOMD0000000002 hypernym "http://identifiers.org/go/GO:0007166",
-                         "http://identifiers.org/go/GO:0007274",
-                         "http://identifiers.org/go/GO:0019226"

BioModelsRAG/data/BIOMD0000000003.txt

@@ -1,124 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000003()
-
-  // Compartments and Species:
-  compartment cell;
-  species C in cell, M in cell, X in cell;
-
-  // Assignment Rules:
-  V1 := C*VM1*(C + Kc)^-1;
-  V3 := M*VM3;
-
-  // Reactions:
-  reaction1:  => C; cell*reaction1_vi;
-  reaction2: C => ; C*cell*reaction2_kd;
-  reaction3: C => ; C*cell*reaction3_vd*X*(C + reaction3_Kd)^-1;
-  reaction4:  => M; cell*(1 + -1*M)*V1*(reaction4_K1 + -1*M + 1)^-1;
-  reaction5: M => ; cell*M*reaction5_V2*(reaction5_K2 + M)^-1;
-  reaction6:  => X; cell*V3*(1 + -1*X)*(reaction6_K3 + -1*X + 1)^-1;
-  reaction7: X => ; cell*reaction7_V4*X*(reaction7_K4 + X)^-1;
-
-  // Species initializations:
-  C = 0.01;
-  C has substance_per_volume;
-  M = 0.01;
-  M has substance_per_volume;
-  X = 0.01;
-  X has substance_per_volume;
-
-  // Compartment initializations:
-  cell = 1;
-  cell has volume;
-
-  // Variable initializations:
-  VM1 = 3;
-  Kc = 0.5;
-  VM3 = 1;
-  reaction1_vi = 0.025;
-  reaction2_kd = 0.01;
-  reaction3_vd = 0.25;
-  reaction3_Kd = 0.02;
-  reaction4_K1 = 0.005;
-  reaction5_V2 = 1.5;
-  reaction5_K2 = 0.005;
-  reaction6_K3 = 0.005;
-  reaction7_K4 = 0.005;
-  reaction7_V4 = 0.5;
-
-  // Other declarations:
-  var V1, V3;
-  const cell, VM1, Kc, VM3;
-
-  // Unit definitions:
-  unit volume = litre;
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  C is "Cyclin";
-  M is "CDC-2 Kinase";
-  X is "Cyclin Protease";
-  reaction1 is "creation of cyclin";
-  reaction2 is "default degradation of cyclin";
-  reaction3 is "cdc2 kinase triggered degration of cyclin";
-  reaction4 is "activation of cdc2 kinase";
-  reaction5 is "deactivation of cdc2 kinase";
-  reaction6 is "activation of cyclin protease";
-  reaction7 is "deactivation of cyclin protease";
-
-  // SBO terms:
-  cell.sboTerm = 290
-  C.sboTerm = 252
-  M.sboTerm = 252
-  X.sboTerm = 297
-  V1.sboTerm = 186
-  VM1.sboTerm = 25
-  Kc.sboTerm = 27
-  V3.sboTerm = 186
-  VM3.sboTerm = 186
-  reaction1.sboTerm = 393
-  reaction1_vi.sboTerm = 48
-  reaction2.sboTerm = 179
-  reaction2_kd.sboTerm = 22
-  reaction3.sboTerm = 179
-  reaction3_vd.sboTerm = 186
-  reaction3_Kd.sboTerm = 27
-  reaction4.sboTerm = 330
-  reaction4_K1.sboTerm = 27
-  reaction5.sboTerm = 216
-  reaction5_V2.sboTerm = 186
-  reaction5_K2.sboTerm = 27
-  reaction6.sboTerm = 216
-  reaction6_K3.sboTerm = 27
-  reaction7.sboTerm = 330
-  reaction7_K4.sboTerm = 27
-  reaction7_V4.sboTerm = 186
-
-  // CV terms:
-  cell identity "http://identifiers.org/go/GO:0005623"
-  C hypernym "http://identifiers.org/uniprot/Q4KLA0",
-             "http://identifiers.org/interpro/IPR006670"
-  M version "http://identifiers.org/uniprot/P24033",
-            "http://identifiers.org/uniprot/P35567"
-  X hypernym "http://identifiers.org/go/GO:0005680"
-  X version "http://identifiers.org/reactome/REACT_7165.1"
-  reaction1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction2 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction3 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/go/GO:0045737",
-                     "http://identifiers.org/go/GO:0006470"
-  reaction5 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                     "http://identifiers.org/go/GO:0045736",
-                     "http://identifiers.org/go/GO:0006468"
-end
-
-BIOMD0000000003 is "Goldbeter1991 - Min Mit Oscil"
-
-BIOMD0000000003 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614271263"
-BIOMD0000000003 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000003"
-BIOMD0000000003 description "http://identifiers.org/pubmed/1833774"
-BIOMD0000000003 homolog "http://identifiers.org/reactome/REACT_152"
-BIOMD0000000003 hypernym "http://identifiers.org/kegg.pathway/hsa04110",
-                         "http://identifiers.org/go/GO:0000278"
-BIOMD0000000003 taxon "http://identifiers.org/taxonomy/8292"

BioModelsRAG/data/BIOMD0000000004.txt

@@ -1,102 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000004()
-
-  // Compartments and Species:
-  compartment cell;
-  species C in cell, M in cell, X in cell, MI in cell, XI in cell;
-
-  // Assignment Rules:
-  V1 := C*VM1*(C + Kc)^-1;
-  V3 := M*VM3;
-
-  // Reactions:
-  reaction1:  => C; cell*reaction1_vi;
-  reaction2: C => ; C*cell*reaction2_kd;
-  reaction3: C => ; C*cell*reaction3_vd*X*(C + reaction3_Kd)^-1;
-  reaction4: MI => M; cell*MI*V1*(reaction4_K1 + MI)^-1;
-  reaction5: M => MI; cell*M*reaction5_V2*(reaction5_K2 + M)^-1;
-  reaction6: XI => X; cell*V3*XI*(reaction6_K3 + XI)^-1;
-  reaction7: X => XI; cell*reaction7_V4*X*(reaction7_K4 + X)^-1;
-
-  // Species initializations:
-  C = 0.01;
-  C has substance_per_volume;
-  M = 0.01;
-  M has substance_per_volume;
-  X = 0.01;
-  X has substance_per_volume;
-  MI = 0.99;
-  MI has substance_per_volume;
-  XI = 0.99;
-  XI has substance_per_volume;
-
-  // Compartment initializations:
-  cell = 1;
-  cell has volume;
-
-  // Variable initializations:
-  VM1 = 3;
-  Kc = 0.5;
-  VM3 = 1;
-  reaction1_vi = 0.025;
-  reaction2_kd = 0.01;
-  reaction3_vd = 0.25;
-  reaction3_Kd = 0.02;
-  reaction4_K1 = 0.005;
-  reaction5_V2 = 1.5;
-  reaction5_K2 = 0.005;
-  reaction6_K3 = 0.005;
-  reaction7_K4 = 0.005;
-  reaction7_V4 = 0.5;
-
-  // Other declarations:
-  var V1, V3;
-  const cell, VM1, Kc, VM3;
-
-  // Unit definitions:
-  unit volume = litre;
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  C is "Cyclin";
-  M is "Active CDC-2 Kinase";
-  X is "Active Cyclin Protease";
-  MI is "Inactive CDC-2 Kinase";
-  XI is "Inactive Cyclin Protease";
-  reaction1 is "creation of cyclin";
-  reaction2 is "default degradation of cyclin";
-  reaction3 is "cdc2 kinase triggered degration of cyclin";
-  reaction4 is "activation of cdc2 kinase";
-  reaction5 is "deactivation of cdc2 kinase";
-  reaction6 is "activation of cyclin protease";
-  reaction7 is "deactivation of cyclin protease";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  C hypernym "http://identifiers.org/interpro/IPR006670"
-  M version "http://identifiers.org/uniprot/P24033",
-            "http://identifiers.org/uniprot/P35567"
-  MI version "http://identifiers.org/uniprot/P24033",
-             "http://identifiers.org/uniprot/P35567"
-  reaction1 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  reaction2 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  reaction3 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  reaction4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0045737",
-                     "http://identifiers.org/obo.go/GO:0006470"
-  reaction5 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                     "http://identifiers.org/obo.go/GO:0045736",
-                     "http://identifiers.org/obo.go/GO:0006468"
-end
-
-BIOMD0000000004 is "Goldbeter1991 - Min Mit Oscil, Expl Inact"
-
-BIOMD0000000004 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614389071"
-BIOMD0000000004 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000004"
-BIOMD0000000004 description "http://identifiers.org/pubmed/1833774"
-BIOMD0000000004 origin "http://identifiers.org/biomodels.db/BIOMD0000000003"
-BIOMD0000000004 hypernym "http://identifiers.org/kegg.pathway/hsa04110",
-                         "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000004 homolog "http://identifiers.org/reactome/REACT_152"
-BIOMD0000000004 taxon "http://identifiers.org/taxonomy/8292"

BioModelsRAG/data/BIOMD0000000005.txt

@@ -1,114 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000005()
-
-  // Compartments and Species:
-  compartment cell;
-  species $EmptySet in cell, C2 in cell, CP in cell, M in cell, pM in cell;
-  species Y in cell, YP in cell, $YT in cell, $CT in cell;
-
-  // Assignment Rules:
-  YT := Y + YP + M + pM;
-  CT := C2 + CP + M + pM;
-
-  // Reactions:
-  Reaction1: M => C2 + YP; cell*Reaction1_k6*M;
-  Reaction2: C2 => CP; cell*C2*Reaction2_k8notP;
-  Reaction3: CP => C2; cell*CP*Reaction3_k9;
-  Reaction4: CP + Y => pM; cell*CP*Reaction4_k3*Y;
-  Reaction5: M => pM; cell*Reaction5_k5notP*M;
-  Reaction6: $EmptySet => Y; cell*Reaction6_k1aa;
-  Reaction7: Y => $EmptySet; cell*Reaction7_k2*Y;
-  Reaction8: YP => $EmptySet; cell*Reaction8_k7*YP;
-  Reaction9: pM => M; cell*pM*(Reaction9_k4prime + Reaction9_k4*(M/CT)^2);
-
-  // Species initializations:
-  EmptySet = 0;
-  C2 = 0;
-  CP = 0.75/cell;
-  M = 0;
-  pM = 0.25/cell;
-  Y = 0;
-  YP = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  Reaction1_k6 = 1;
-  Reaction2_k8notP = 1000000;
-  Reaction3_k9 = 1000;
-  Reaction4_k3 = 200;
-  Reaction5_k5notP = 0;
-  Reaction6_k1aa = 0.015;
-  Reaction7_k2 = 0;
-  Reaction8_k7 = 0.6;
-  Reaction9_k4 = 180;
-  Reaction9_k4prime = 0.018;
-
-  // Other declarations:
-  const cell;
-
-  // Display Names:
-  C2 is "cdc2k";
-  CP is "cdc2k-P";
-  M is "p-cyclin_cdc2";
-  pM is "p-cyclin_cdc2-p";
-  Y is "cyclin";
-  YP is "p-cyclin";
-  YT is "total_cyclin";
-  CT is "total_cdc2";
-  Reaction1 is "cyclin_cdc2k dissociation";
-  Reaction2 is "cdc2k phosphorylation";
-  Reaction3 is "cdc2k dephosphorylation";
-  Reaction4 is "cyclin cdc2k-p association";
-  Reaction5 is "deactivation of cdc2 kinase";
-  Reaction6 is "cyclin biosynthesis";
-  Reaction7 is "default degradation of cyclin";
-  Reaction8 is "cdc2 kinase triggered degration of cyclin";
-  Reaction9 is "activation of cdc2 kinase";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  C2 hypernym "http://identifiers.org/uniprot/P04551"
-  CP hypernym "http://identifiers.org/uniprot/P04551"
-  M part "http://identifiers.org/uniprot/P04551",
-         "http://identifiers.org/interpro/IPR006670"
-  pM part "http://identifiers.org/uniprot/P04551",
-          "http://identifiers.org/interpro/IPR006670"
-  Y hypernym "http://identifiers.org/interpro/IPR006670"
-  YP hypernym "http://identifiers.org/interpro/IPR006670"
-  YT hypernym "http://identifiers.org/interpro/IPR006670"
-  CT hypernym "http://identifiers.org/uniprot/P04551"
-  Reaction1 version "http://identifiers.org/reactome/REACT_6308"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0000079"
-  Reaction2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                     "http://identifiers.org/obo.go/GO:0006468"
-  Reaction3 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0006470"
-  Reaction4 version "http://identifiers.org/reactome/REACT_6216",
-                    "http://identifiers.org/reactome/REACT_6308"
-  Reaction5 hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                     "http://identifiers.org/obo.go/GO:0006468",
-                     "http://identifiers.org/obo.go/GO:0045736"
-  Reaction5 version "http://identifiers.org/reactome/REACT_3178",
-                    "http://identifiers.org/reactome/REACT_6327"
-  Reaction6 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0008054"
-  Reaction9 version "http://identifiers.org/reactome/REACT_6257",
-                    "http://identifiers.org/reactome/REACT_6175",
-                    "http://identifiers.org/reactome/REACT_6294"
-  Reaction9 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0006470",
-                     "http://identifiers.org/obo.go/GO:0045737"
-end
-
-BIOMD0000000005 is "Tyson1991 - Cell Cycle 6 var"
-
-BIOMD0000000005 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614644188"
-BIOMD0000000005 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000005"
-BIOMD0000000005 description "http://identifiers.org/pubmed/1831270"
-BIOMD0000000005 taxon "http://identifiers.org/taxonomy/33154"
-BIOMD0000000005 hypernym "http://identifiers.org/kegg.pathway/sce04111",
-                         "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000005 version "http://identifiers.org/reactome/REACT_152"

BioModelsRAG/data/BIOMD0000000006.txt

@@ -1,66 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000006()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species $EmptySet in cell, $u in cell, $v in cell, $z in cell;
-
-  // Assignment Rules:
-  alpha := k4prime/k4;
-  z := v - u;
-
-  // Rate Rules:
-  u' = k4*(v - u)*(alpha + u^2) - k6*u;
-  v' = kappa - k6*u;
-
-  // Reactions:
-  Reaction1: $EmptySet => $z; kappa;
-  Reaction2: $u => $EmptySet; k6*u;
-  Reaction3: $z => $u; k4*z*(k4prime/k4 + u^2);
-
-  // Species initializations:
-  EmptySet = 1/cell;
-  u = 0;
-  v = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  k4 = 180;
-  k6 = 1;
-  kappa = 0.015;
-  k4prime = 0.018;
-
-  // Other declarations:
-  var alpha;
-  const cell, k4, k6, kappa, k4prime;
-
-  // SBO terms:
-  EmptySet.sboTerm = 291
-  u.sboTerm = 297
-  v.sboTerm = 297
-  z.sboTerm = 297
-  Reaction1.sboTerm = 205
-  Reaction2.sboTerm = 179
-  Reaction3.sboTerm = 176
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  u property "http://identifiers.org/obo.go/GO:0004693"
-  u hypernym "http://identifiers.org/obo.go/GO:0031387"
-  v version "http://identifiers.org/uniprot/P04551"
-  v version "http://identifiers.org/obo.go/GO:0031387"
-  v property "http://identifiers.org/obo.go/GO:0004693"
-  z version "http://identifiers.org/uniprot/P04551"
-end
-
-BIOMD0000000006 is "Tyson1991 - Cell Cycle 2 var"
-
-BIOMD0000000006 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614715255"
-BIOMD0000000006 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000006"
-BIOMD0000000006 description "http://identifiers.org/pubmed/1831270"
-BIOMD0000000006 taxon "http://identifiers.org/taxonomy/33154"
-BIOMD0000000006 identity "http://identifiers.org/kegg.pathway/sce04111"
-BIOMD0000000006 hypernym "http://identifiers.org/obo.go/GO:0000278"
-BIOMD0000000006 version "http://identifiers.org/reactome/REACT_152"

BioModelsRAG/data/BIOMD0000000007.txt

@@ -1,266 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000007()
-
-  // Compartments and Species:
-  compartment Cell;
-  substanceOnly species UbE in Cell, UbE2 in Cell, Wee1 in Cell, Cdc25 in Cell;
-  substanceOnly species G2K in Cell, R in Cell, G1K in Cell, IE in Cell, PG2 in Cell;
-  substanceOnly species G1R in Cell, G2R in Cell, PG2R in Cell, $SPF in Cell;
-  substanceOnly species $MPF in Cell, $IEB in Cell, $UbEB in Cell, $UbE2B in Cell;
-  substanceOnly species $Wee1B in Cell, $Cdc25B in Cell, $Rum1Total in Cell;
-  substanceOnly species $Cdc13Total in Cell, $Cig2Total in Cell;
-
-  // Assignment Rules:
-  SPF := Cig1 + alpha*G1K + MPF;
-  MPF := G2K + beta*PG2;
-  IEB := 1 - IE;
-  UbEB := 1 - UbE;
-  UbE2B := 1 - UbE2;
-  Wee1B := 1 - Wee1;
-  Cdc25B := 1 - Cdc25;
-  Rum1Total := G1R + G2R + PG2R + R;
-  Cdc13Total := G2K + G2R + PG2 + PG2R;
-  Cig2Total := G1K + G1R;
-  k2 := UbE*V2 + (1 - UbE)*V2prime;
-  k6 := UbE2*V6 + (1 - UbE2)*V6prime;
-  kwee := Vwprime*(1 - Wee1) + Vw*Wee1;
-  k25 := Cdc25*V25 + (1 - Cdc25)*V25prime;
-
-  // Rate Rules:
-  Mass' = Mass*mu;
-
-  // Reactions:
-  G2K_Creation:  => G2K; k1;
-  G1K_Creation:  => G1K; k5;
-  Cdc2Phos: G2K -> PG2; G2K*kwee - k25*PG2;
-  G2R_Creation: G2K + R -> G2R; G2K*k7*R - G2R*k7r;
-  PG2R_Creation: PG2 + R -> PG2R; k7*PG2*R - k7r*PG2R;
-  Rum1DegInG2R: G2R => G2K; G2R*k4;
-  Rum1Deg: R => ; k4*R;
-  Rum1DegInPG2R: PG2R => PG2; k4*PG2R;
-  RumDegInG1R: G1R => G1K; G1R*k4;
-  G2K_dissoc: G2K => ; G2K*k2;
-  PG2_dissoc: PG2 => ; k2*PG2;
-  G1K_Dissociation: G1K => ; G1K*k6;
-  PG2R_Dissociation: PG2R => R; k2prime*PG2R;
-  G2R_Dissociation: G2R => R; G2R*k2prime;
-  G1R_Dissociation: G1R => R; G1R*k6prime;
-  G1R_Binding: G1K + R -> G1R; G1K*k8*R - G1R*k8r;
-  G2R_Dissociation_UbE: G2R => R; G2R*k2;
-  PG2R_Dissociation_UbE: PG2R => R; k2*PG2R;
-  Rum1_Production:  => R; k3;
-  Rum1_Deg_SPF: R => ; kp*Mass*R*SPF/(Kmp + R);
-  IE_Reaction: $IEB -> IE; IEB*ki*MPF/(IEB + Kmi) - IE*kir/(IE + Kmir);
-  UbE_Reaction: $UbEB -> UbE; IE*ku*UbEB/(Kmu + UbEB) - kur*UbE/(Kmur + UbE);
-  UbE2_Reaction: $UbE2B -> UbE2; ku2*MPF*UbE2B/(Kmu2 + UbE2B) - kur2*UbE2/(Kmur2 + UbE2);
-  Wee1_Reaction: $Wee1B -> Wee1; kwr*Wee1B/(Kmwr + Wee1B) - kw*MPF*Wee1/(Kmw + Wee1);
-  Cdc25_Reaction: $Cdc25B -> Cdc25; Cdc25B*kc*MPF/(Cdc25B + Kmc) - Cdc25*kcr/(Cdc25 + Kmcr);
-
-  // Events:
-  Start: at 60 after SPF >= 0.1: kp = kp/2;
-  Division: at UbE <= 0.1: Mass = Mass/2, kp = 2*kp;
-
-  // Species initializations:
-  UbE = 0.11/Cell;
-  UbE2 = 0;
-  Wee1 = 0;
-  Cdc25 = 0;
-  G2K = 0;
-  R = 0.4/Cell;
-  G1K = 0;
-  IE = 0;
-  PG2 = 0;
-  G1R = 0;
-  G2R = 0;
-  PG2R = 0;
-
-  // Compartment initializations:
-  Cell = 1;
-  Cell has volume;
-
-  // Variable initializations:
-  Cig1 = 0;
-  alpha = 0.25;
-  beta = 0.05;
-  kp = 3.25;
-  Mass = 0.49;
-  mu = 0.00495;
-  k1 = 0.015;
-  k2prime = 0.05;
-  k3 = 0.09375;
-  k4 = 0.1875;
-  k5 = 0.00175;
-  k6prime = 0;
-  k7 = 100;
-  k7r = 0.1;
-  k8 = 10;
-  k8r = 0.1;
-  kc = 1;
-  kcr = 0.25;
-  ki = 0.4;
-  kir = 0.1;
-  ku = 0.2;
-  kur = 0.1;
-  ku2 = 1;
-  kur2 = 0.3;
-  kw = 1;
-  kwr = 0.25;
-  V2 = 0.25;
-  V2prime = 0.0075;
-  V6 = 7.5;
-  V6prime = 0.0375;
-  V25 = 0.5;
-  V25prime = 0.025;
-  Vw = 0.35;
-  Vwprime = 0.035;
-  Kmc = 0.1;
-  Kmcr = 0.1;
-  Kmi = 0.01;
-  Kmir = 0.01;
-  Kmp = 0.001;
-  Kmu = 0.01;
-  Kmur = 0.01;
-  Kmu2 = 0.05;
-  Kmur2 = 0.05;
-  Kmw = 0.1;
-  Kmwr = 0.1;
-
-  // Other declarations:
-  var kp, Mass, k2, k6, kwee, k25;
-  const Cell, Cig1, alpha, beta, mu, k1, k2prime, k3, k4, k5, k6prime, k7;
-  const k7r, k8, k8r, kc, kcr, ki, kir, ku, kur, ku2, kur2, kw, kwr, V2, V2prime;
-  const V6, V6prime, V25, V25prime, Vw, Vwprime, Kmc, Kmcr, Kmi, Kmir, Kmp;
-  const Kmu, Kmur, Kmu2, Kmur2, Kmw, Kmwr;
-
-  // Unit definitions:
-  unit time_unit = 60 second;
-  unit volume = litre;
-
-  // Display Names:
-  time_unit is "minutes";
-  UbE is "ubiquitinProtease1";
-  UbE2 is "ubiquitinProtease2";
-  G2K is "Cdc13_Cdc2";
-  R is "FreeRum1";
-  G1K is "Cig2_Cdc2";
-  IE is "IntermediaryEnzyme";
-  PG2 is "Cdc13_P-Cdc2";
-  G1R is "Cig2_Cdc2_Rum1";
-  G2R is "Cdc13_Cdc2_Rum1";
-  PG2R is "Cdc13_P-Cdc2_Rum1";
-  SPF is "S-phasePromotingFactor";
-  MPF is "M-phasePromotingFactor";
-  IEB is "BoundIntermediaryEnzyme";
-  UbEB is "BoundUbiquitinProtease1";
-  UbE2B is "BoundUbiquitinProtease2";
-  Wee1B is "BoundWee1";
-  Cdc25B is "BoundCdc25";
-  Rum1Total is "TotalRum1";
-  Cdc13Total is "TotalCdc13";
-  Cig2Total is "TotalCig2";
-  Start is "S-Phase Start";
-  Division is "Cell Division";
-  k2prime is "k2'";
-  k6prime is "k6'";
-  V2prime is "V2'";
-  V6prime is "V6'";
-  V25prime is "V25'";
-  Vwprime is "Vw'";
-  G2K_Creation is "Cdc13_Cdc2 creation";
-  G1K_Creation is "Cig2_Cdc2 creation";
-  Cdc2Phos is "Cdc2 phosphorylation";
-  G2R_Creation is "binding of Rum1 with Cdc13_Cdc2";
-  PG2R_Creation is "binding of Rum1 with Cdc13_P-Cdc2";
-  Rum1DegInG2R is "Rum1 degradation in Rum1_Cdc13_Cdc2";
-  Rum1Deg is "Rum1 degradation in solution";
-  Rum1DegInPG2R is "Rum1 degradation in Rum1_Cdc13_P-Cdc2";
-  RumDegInG1R is "Rum1 degradation in Rum1_Cig2_Cdc2";
-  G2K_dissoc is "Cdc13 degradation in Cdc13_Cdc2";
-  PG2_dissoc is "Cdc13 degradation in Cdc13_P-Cdc2";
-  G1K_Dissociation is "Cig2 degradation in Cig2_Cdc2";
-  PG2R_Dissociation is "Cdc13 degradation in Rum1_Cdc13_P-Cdc2";
-  G2R_Dissociation is "Cdc13 degradation in Rum1_Cdc13_Cdc2";
-  G1R_Dissociation is "Cig2 degradation in Rum1_Cig2_Cdc2";
-  G1R_Binding is "Binding of Rum1 to Cig2_Cdc2";
-  G2R_Dissociation_UbE is "UbE mediated degradation of Cdc13_Cdc2 in Rum1_Cdc13_Cdc2";
-  PG2R_Dissociation_UbE is "UbE mediated degradation of Cdc13_Cdc2 in Rum1_Cdc13_P-Cdc2";
-  Rum1_Production is "Rum1 creation";
-  Rum1_Deg_SPF is "Rum1 degradation by SPF";
-  IE_Reaction is "IE production & degradation";
-  UbE_Reaction is "UbE production & degradation";
-  UbE2_Reaction is "UbE2 production & degradation";
-  Wee1_Reaction is "Wee1 production & degradation";
-  Cdc25_Reaction is "Cdc25 production & degradation";
-
-  // CV terms:
-  Cell identity "http://identifiers.org/go/GO:0005623"
-  UbE hypernym "http://identifiers.org/go/GO:0000502"
-  UbE2 hypernym "http://identifiers.org/go/GO:0000502"
-  Wee1 version "http://identifiers.org/uniprot/P30290",
-               "http://identifiers.org/uniprot/P07527"
-  Cdc25 identity "http://identifiers.org/uniprot/P06652"
-  G2K part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P10815"
-  R hypernym "http://identifiers.org/uniprot/P40380"
-  G1K part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P36630"
-  PG2 part "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P04551"
-  G1R part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P36630",
-           "http://identifiers.org/uniprot/P40380"
-  G2R part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P40380"
-  PG2R part "http://identifiers.org/uniprot/P10815",
-            "http://identifiers.org/uniprot/P04551",
-            "http://identifiers.org/uniprot/P40380"
-  SPF part "http://identifiers.org/uniprot/P04551",
-           "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P36630"
-  MPF part "http://identifiers.org/uniprot/P10815",
-           "http://identifiers.org/uniprot/P04551"
-  UbEB hypernym "http://identifiers.org/go/GO:0000502"
-  UbE2B hypernym "http://identifiers.org/go/GO:0000502"
-  Wee1B version "http://identifiers.org/uniprot/P07527",
-                "http://identifiers.org/uniprot/P30290"
-  Cdc25B hypernym "http://identifiers.org/uniprot/P06652"
-  Rum1Total identity "http://identifiers.org/uniprot/P40380"
-  Cdc13Total identity "http://identifiers.org/uniprot/P10815"
-  Cig2Total identity "http://identifiers.org/uniprot/P36630"
-  Cdc2Phos part "http://identifiers.org/reactome/REACT_6294",
-                "http://identifiers.org/reactome/REACT_6327"
-  Cdc2Phos part "http://identifiers.org/reactome/REACT_6257",
-                "http://identifiers.org/reactome/REACT_6178"
-  Cdc2Phos hypernym "http://identifiers.org/ec-code/2.7.10.2",
-                    "http://identifiers.org/go/GO:0006468"
-  G2R_Creation hypernym "http://identifiers.org/go/GO:0006461"
-  PG2R_Creation hypernym "http://identifiers.org/go/GO:0006461"
-  Rum1DegInG2R hypernym "http://identifiers.org/go/GO:0030163"
-  Rum1Deg hypernym "http://identifiers.org/go/GO:0030163"
-  Rum1DegInPG2R hypernym "http://identifiers.org/go/GO:0030163"
-  RumDegInG1R hypernym "http://identifiers.org/go/GO:0030163"
-  G2K_dissoc hypernym "http://identifiers.org/go/GO:0008054"
-  PG2_dissoc hypernym "http://identifiers.org/go/GO:0008054"
-  G1K_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  PG2R_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  G2R_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  G1R_Dissociation hypernym "http://identifiers.org/go/GO:0008054"
-  G1R_Binding hypernym "http://identifiers.org/go/GO:0006461"
-  G2R_Dissociation_UbE hypernym "http://identifiers.org/kegg.pathway/spo04120",
-                                "http://identifiers.org/go/GO:0030163"
-  PG2R_Dissociation_UbE hypernym "http://identifiers.org/kegg.pathway/spo04120",
-                                 "http://identifiers.org/go/GO:0030163"
-  Rum1_Deg_SPF hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-BIOMD0000000007 is "Novak1997 - Cell Cycle"
-
-BIOMD0000000007 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614787694"
-BIOMD0000000007 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000007"
-BIOMD0000000007 description "http://identifiers.org/pubmed/9256450"
-BIOMD0000000007 origin "http://identifiers.org/pubmed/10395816"
-BIOMD0000000007 taxon "http://identifiers.org/taxonomy/4896"
-BIOMD0000000007 hypernym "http://identifiers.org/kegg.pathway/ko04110",
-                         "http://identifiers.org/go/GO:0000278"
-BIOMD0000000007 homolog "http://identifiers.org/reactome/REACT_152"

BioModelsRAG/data/BIOMD0000000008.txt

@@ -1,121 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000008()
-
-  // Compartments and Species:
-  compartment Cell;
-  species C in Cell, X in Cell, M in Cell, Y in Cell, Z in Cell;
-
-  // Assignment Rules:
-  V1 := C*V1p*(C + K6)^-1;
-  V3 := M*V3p;
-
-  // Reactions:
-  reaction1:  => C; reaction1_vi;
-  reaction2: C => ; C*reaction2_k1*X*(C + reaction2_K5)^-1;
-  reaction3: C => ; C*reaction3_kd;
-  reaction4:  => M; (1 + -1*M)*V1*(reaction4_K1 + -1*M + 1)^-1;
-  reaction5: M => ; M*reaction5_V2*(reaction5_K2 + M)^-1;
-  reaction6:  => X; V3*(1 + -1*X)*(reaction6_K3 + -1*X + 1)^-1;
-  reaction7: X => ; reaction7_V4*X*(reaction7_K4 + X)^-1;
-  reaction8: C + Y => Z; reaction8_a1*C*Y;
-  reaction9: Z => C + Y; reaction9_a2*Z;
-  reaction10: Z => C; reaction10_alpha*reaction10_d1*Z;
-  reaction11: Z => Y; reaction11_alpha*reaction11_kd*Z;
-  reaction12:  => Y; reaction12_vs;
-  reaction13: Y => ; reaction13_d1*Y;
-
-  // Species initializations:
-  C = 0;
-  C has substance_per_volume;
-  X = 0;
-  X has substance_per_volume;
-  M = 0;
-  M has substance_per_volume;
-  Y = 1/Cell;
-  Y has substance_per_volume;
-  Z = 1/Cell;
-  Z has substance_per_volume;
-
-  // Compartment initializations:
-  Cell = 1;
-  Cell has volume;
-
-  // Variable initializations:
-  V1p = 0.75;
-  K6 = 0.3;
-  V3p = 0.3;
-  reaction1_vi = 0.1;
-  reaction2_k1 = 0.5;
-  reaction2_K5 = 0.02;
-  reaction3_kd = 0.02;
-  reaction4_K1 = 0.1;
-  reaction5_V2 = 0.25;
-  reaction5_K2 = 0.1;
-  reaction6_K3 = 0.2;
-  reaction7_K4 = 0.1;
-  reaction7_V4 = 0.1;
-  reaction8_a1 = 0.05;
-  reaction9_a2 = 0.05;
-  reaction10_alpha = 0.1;
-  reaction10_d1 = 0.05;
-  reaction11_kd = 0.02;
-  reaction11_alpha = 0.1;
-  reaction12_vs = 0.2;
-  reaction13_d1 = 0.05;
-
-  // Other declarations:
-  var V1, V3;
-  const Cell, V1p, K6, V3p;
-
-  // Unit definitions:
-  unit volume = litre;
-  unit substance = mole;
-  unit substance_per_volume = mole / litre;
-
-  // Display Names:
-  C is "cyclin";
-  X is "protease";
-  M is "cdc2k";
-  Y is "cyclin inhibitor";
-  Z is "complex inhibitor-cyclin";
-  reaction1 is "creation of cyclin";
-  reaction2 is "cdc2 kinase triggered degration of cyclin";
-  reaction3 is "default degradation of cyclin";
-  reaction4 is "activation of cdc2 kinase";
-  reaction5 is "deactivation of cdc2 kinase";
-  reaction6 is "activation of cyclin protease";
-  reaction7 is "deactivation of cyclin protease";
-  reaction10 is "desinhibition of cyclin";
-  reaction11 is "degradation of inhibited cyclin";
-  reaction12 is "creation of cyclin inhibitor";
-  reaction13 is "degradation of cyclin inhibitor";
-
-  // CV terms:
-  Cell identity "http://identifiers.org/go/GO:0005737"
-  C identity "http://identifiers.org/interpro/IPR006670"
-  X property "http://identifiers.org/go/GO:0008233"
-  M version "http://identifiers.org/uniprot/P35567",
-            "http://identifiers.org/uniprot/P24033"
-  Z part "http://identifiers.org/interpro/IPR006670"
-  reaction1 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction2 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction3 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction4 hypernym "http://identifiers.org/go/GO:0045737"
-  reaction5 hypernym "http://identifiers.org/go/GO:0045736"
-  reaction9 hypernym "http://identifiers.org/go/GO:0043241"
-  reaction10 hypernym "http://identifiers.org/go/GO:0044257"
-  reaction11 hypernym "http://identifiers.org/go/GO:0008054"
-  reaction12 hypernym "http://identifiers.org/go/GO:0006412"
-  reaction13 hypernym "http://identifiers.org/go/GO:0044257"
-end
-
-BIOMD0000000008 is "Gardner1998 - Cell Cycle Goldbeter"
-
-BIOMD0000000008 model_entity_is "http://identifiers.org/biomodels.db/MODEL6614879888"
-BIOMD0000000008 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000008"
-BIOMD0000000008 description "http://identifiers.org/pubmed/9826676"
-BIOMD0000000008 origin "http://identifiers.org/biomodels.db/BIOMD0000000003",
-                       "http://identifiers.org/biomodels.db/BIOMD0000000004"
-BIOMD0000000008 hypernym "http://identifiers.org/go/GO:0000278"
-BIOMD0000000008 taxon "http://identifiers.org/taxonomy/8292"
-BIOMD0000000008 homolog "http://identifiers.org/reactome/REACT_152"

BioModelsRAG/data/BIOMD0000000009.txt

@@ -1,250 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000009()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species E1 in compartment_, E2 in compartment_, KKK in compartment_, P_KKK in compartment_;
-  species KK in compartment_, P_KK in compartment_, PP_KK in compartment_;
-  species K in compartment_, P_K in compartment_, PP_K in compartment_, KPase in compartment_;
-  species KKPase in compartment_, E1_KKK in compartment_, E2_P_KKK in compartment_;
-  species P_KKK_KK in compartment_, P_KKK_P_KK in compartment_, PP_KK_K in compartment_;
-  species PP_KK_P_K in compartment_, KKPase_PP_KK in compartment_, KKPase_P_KK in compartment_;
-  species KPase_PP_K in compartment_, KPase_P_K in compartment_, $K_PP_norm in compartment_;
-  species $KK_PP_norm in compartment_, $KKK_P_norm in compartment_, $rel_K_PP_max in compartment_;
-
-  // Assignment Rules:
-  K_PP_norm := (PP_K + KPase_PP_K)/(PP_K + P_K + K + PP_KK_K + PP_KK_P_K + KPase_PP_K + KPase_P_K);
-  KK_PP_norm := (PP_KK + PP_KK_K + PP_KK_P_K + KKPase_PP_KK)/(PP_KK + P_KK + KK + PP_KK_K + PP_KK_P_K + P_KKK_KK + P_KKK_P_KK + KKPase_PP_KK + KKPase_P_KK);
-  KKK_P_norm := (P_KKK + P_KKK_KK + P_KKK_P_KK)/(KKK + P_KKK + P_KKK_KK + P_KKK_P_KK);
-  rel_K_PP_max := K_PP_norm/K_PP_norm_max;
-
-  // Reactions:
-  r1a: KKK + E1 -> E1_KKK; compartment_*(r1a_a1*E1*KKK - r1a_d1*E1_KKK);
-  r1b: E1_KKK => E1 + P_KKK; compartment_*r1b_k2*E1_KKK;
-  r2a: P_KKK + E2 -> E2_P_KKK; compartment_*(r2a_a2*E2*P_KKK - r2a_d2*E2_P_KKK);
-  r2b: E2_P_KKK => E2 + KKK; compartment_*r2b_k2*E2_P_KKK;
-  r3a: KK + P_KKK -> P_KKK_KK; compartment_*(r3a_a3*KK*P_KKK - r3a_d3*P_KKK_KK);
-  r3b: P_KKK_KK => P_KK + P_KKK; compartment_*r3b_k3*P_KKK_KK;
-  r4a: P_KK + KKPase -> KKPase_P_KK; compartment_*(r4a_a4*P_KK*KKPase - r4a_d4*KKPase_P_KK);
-  r4b: KKPase_P_KK => KK + KKPase; compartment_*r4b_k4*KKPase_P_KK;
-  r5a: P_KK + P_KKK -> P_KKK_P_KK; compartment_*(r5a_a5*P_KK*P_KKK - r5a_d5*P_KKK_P_KK);
-  r5b: P_KKK_P_KK => PP_KK + P_KKK; compartment_*r5b_k5*P_KKK_P_KK;
-  r6a: PP_KK + KKPase -> KKPase_PP_KK; compartment_*(r6a_a6*PP_KK*KKPase - r6a_d6*KKPase_PP_KK);
-  r6b: KKPase_PP_KK => P_KK + KKPase; compartment_*r6b_k6*KKPase_PP_KK;
-  r7a: K + PP_KK -> PP_KK_K; compartment_*(r7a_a7*K*PP_KK - r7a_d7*PP_KK_K);
-  r7b: PP_KK_K => P_K + PP_KK; compartment_*r7b_k7*PP_KK_K;
-  r8a: P_K + KPase -> KPase_P_K; compartment_*(r8a_a8*P_K*KPase - r8a_d8*KPase_P_K);
-  r8b: KPase_P_K => K + KPase; compartment_*r8b_k8*KPase_P_K;
-  r9a: P_K + PP_KK -> PP_KK_P_K; compartment_*(r9a_a9*P_K*PP_KK - r9a_d9*PP_KK_P_K);
-  r9b: PP_KK_P_K => PP_KK + PP_K; compartment_*r9b_k9*PP_KK_P_K;
-  r10a: PP_K + KPase -> KPase_PP_K; compartment_*(r10a_a10*PP_K*KPase - r10a_d10*KPase_PP_K);
-  r10b: KPase_PP_K => P_K + KPase; compartment_*r10b_k10*KPase_PP_K;
-
-  // Species initializations:
-  E1 = 3e-05;
-  E2 = 0.0003;
-  KKK = 0.003;
-  P_KKK = 0;
-  KK = 1.2;
-  P_KK = 0;
-  PP_KK = 0;
-  K = 1.2;
-  P_K = 0;
-  PP_K = 0;
-  KPase = 0.12;
-  KKPase = 0.0003;
-  E1_KKK = 0;
-  E2_P_KKK = 0;
-  P_KKK_KK = 0;
-  P_KKK_P_KK = 0;
-  PP_KK_K = 0;
-  PP_KK_P_K = 0;
-  KKPase_PP_KK = 0;
-  KKPase_P_KK = 0;
-  KPase_PP_K = 0;
-  KPase_P_K = 0;
-
-  // Compartment initializations:
-  compartment_ = 4e-12;
-
-  // Variable initializations:
-  K_PP_norm_max = 0.900049;
-  r1a_a1 = 1000;
-  r1a_d1 = 150;
-  r1b_k2 = 150;
-  r2a_a2 = 1000;
-  r2a_d2 = 150;
-  r2b_k2 = 150;
-  r3a_a3 = 1000;
-  r3a_d3 = 150;
-  r3b_k3 = 150;
-  r4a_a4 = 1000;
-  r4a_d4 = 150;
-  r4b_k4 = 150;
-  r5a_a5 = 1000;
-  r5a_d5 = 150;
-  r5b_k5 = 150;
-  r6a_a6 = 1000;
-  r6a_d6 = 150;
-  r6b_k6 = 150;
-  r7a_a7 = 1000;
-  r7a_d7 = 150;
-  r7b_k7 = 150;
-  r8a_a8 = 1000;
-  r8a_d8 = 150;
-  r8b_k8 = 150;
-  r9a_a9 = 1000;
-  r9a_d9 = 150;
-  r9b_k9 = 150;
-  r10a_a10 = 1000;
-  r10a_d10 = 150;
-  r10b_k10 = 150;
-
-  // Other declarations:
-  const compartment_, K_PP_norm_max;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  E1 is "MAPKKK activator (Ras)";
-  E2 is "MAPKKK inactivator";
-  KKK is "Mos";
-  P_KKK is "Mos-P";
-  KK is "Mek1";
-  P_KK is "Mek1-P";
-  PP_KK is "Mek1-PP";
-  K is "Erk2";
-  P_K is "Erk2-P";
-  PP_K is "Erk2-PP";
-  KPase is "MAPK-Pase";
-  KKPase is "MAPKK-Pase";
-  E1_KKK is "E1_Mos";
-  E2_P_KKK is "E2_Mos-P";
-  P_KKK_KK is "P-Mos_Mek1";
-  P_KKK_P_KK is "P-Mos_P-Mek1";
-  PP_KK_K is "PP-Mek1_Erk2";
-  PP_KK_P_K is "PP-Mek1_P-Erk2";
-  KKPase_PP_KK is "MAPKK-Pase_PP-Mek1";
-  KKPase_P_KK is "MAPKK-Pase_P-Mek1";
-  KPase_PP_K is "MAPK-Pase_PP-Erk2";
-  KPase_P_K is "MAPK-Pase_P-Erk2";
-  rel_K_PP_max is "relative maximal K_PP";
-  r1a is "binding of MAPKKK activator";
-  r1b is "MAPKKK activation";
-  r2a is "binding of MAPKKK inactivator";
-  r2b is "MAPKKK inactivation";
-  r3a is "binding P-MAPKKK and MAPKK";
-  r3b is "phosphorylation of MAPKK";
-  r4a is "binding MAPKK-Pase and P-MAPKK";
-  r4b is "dephosphorylation of P-MAPKK";
-  r5a is "binding P-MAPKKK and P-MAPKK";
-  r5b is "phosphorylation of P-MAPKK";
-  r6a is "binding MAPKK-Pase and PP-MAPKK";
-  r6b is "dephosphorylation of PP-MAPKK";
-  r7a is "binding MAPK and PP-MAPKK";
-  r7b is "phosphorylation of MAPK";
-  r8a is "binding MAPK-Pase and P-MAPK";
-  r8b is "dephosphorylation of P-MAPK";
-  r9a is "binding PP-MAPKK and P-MAPK";
-  r9b is "phosphorylation of P-MAPK";
-  r10a is "binding MAPK-Pase and PP-MAPK";
-  r10b is "dephosphorylation of PP-MAPK";
-
-  // CV terms:
-  E1 hypernym "http://identifiers.org/interpro/IPR003577"
-  KKK hypernym "http://identifiers.org/uniprot/P12965"
-  P_KKK hypernym "http://identifiers.org/uniprot/P12965"
-  KK hypernym "http://identifiers.org/uniprot/Q05116"
-  P_KK hypernym "http://identifiers.org/uniprot/Q05116"
-  PP_KK hypernym "http://identifiers.org/uniprot/Q05116"
-  K hypernym "http://identifiers.org/uniprot/P26696"
-  P_K hypernym "http://identifiers.org/uniprot/P26696"
-  PP_K hypernym "http://identifiers.org/uniprot/P26696"
-  KPase identity "http://identifiers.org/uniprot/Q90W58"
-  E1_KKK part "http://identifiers.org/uniprot/P12965",
-              "http://identifiers.org/interpro/IPR003577"
-  E2_P_KKK part "http://identifiers.org/uniprot/P12965"
-  P_KKK_KK part "http://identifiers.org/uniprot/P12965",
-                "http://identifiers.org/uniprot/Q05116"
-  P_KKK_P_KK part "http://identifiers.org/uniprot/P12965",
-                  "http://identifiers.org/uniprot/Q05116"
-  PP_KK_K part "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  PP_KK_P_K part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  KKPase_PP_KK part "http://identifiers.org/uniprot/Q05116"
-  KKPase_P_KK part "http://identifiers.org/uniprot/Q05116"
-  KPase_PP_K part "http://identifiers.org/uniprot/Q90W58",
-                  "http://identifiers.org/uniprot/P26696"
-  KPase_P_K part "http://identifiers.org/uniprot/P26696",
-                 "http://identifiers.org/uniprot/Q90W58"
-  r1a homolog "http://identifiers.org/reactome/REACT_996"
-  r1a hypernym "http://identifiers.org/go/GO:0031435"
-  r1b homolog "http://identifiers.org/reactome/REACT_525"
-  r1b hypernym "http://identifiers.org/ec-code/2.7.11.1",
-               "http://identifiers.org/go/GO:0008349",
-               "http://identifiers.org/go/GO:0000185"
-  r2a hypernym "http://identifiers.org/go/GO:0031435"
-  r2b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0051390",
-               "http://identifiers.org/go/GO:0006470"
-  r3a homolog "http://identifiers.org/reactome/REACT_143"
-  r3a hypernym "http://identifiers.org/go/GO:0031434",
-               "http://identifiers.org/go/GO:0031435"
-  r3b homolog "http://identifiers.org/reactome/REACT_614"
-  r3b hypernym "http://identifiers.org/ec-code/2.7.11.25",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004709"
-  r4a hypernym "http://identifiers.org/go/GO:0031434"
-  r4b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  r5a homolog "http://identifiers.org/reactome/REACT_143"
-  r5a hypernym "http://identifiers.org/go/GO:0031435",
-               "http://identifiers.org/go/GO:0031434"
-  r5b homolog "http://identifiers.org/reactome/REACT_614"
-  r5b hypernym "http://identifiers.org/ec-code/2.7.11.25",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004709",
-               "http://identifiers.org/go/GO:0000186"
-  r6a hypernym "http://identifiers.org/go/GO:0031434"
-  r6b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470",
-               "http://identifiers.org/go/GO:0051389"
-  r7a version "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  r7a hypernym "http://identifiers.org/go/GO:0031434",
-               "http://identifiers.org/go/GO:0051019"
-  r7b version "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  r7b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004708"
-  r8a hypernym "http://identifiers.org/go/GO:0051019"
-  r8b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0006470"
-  r9a version "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  r9a hypernym "http://identifiers.org/go/GO:0051019",
-               "http://identifiers.org/go/GO:0031434"
-  r9b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0004708",
-               "http://identifiers.org/go/GO:0000187"
-  r9b version "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  r10a hypernym "http://identifiers.org/go/GO:0051019"
-  r10b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470",
-                "http://identifiers.org/go/GO:0000188"
-end
-
-BIOMD0000000009 is "Huang1996 - Ultrasensitivity in MAPK cascade"
-
-BIOMD0000000009 model_entity_is "http://identifiers.org/biomodels.db/MODEL6615048798"
-BIOMD0000000009 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000009"
-BIOMD0000000009 description "http://identifiers.org/pubmed/8816754"
-BIOMD0000000009 homolog "http://identifiers.org/reactome/REACT_634"
-BIOMD0000000009 hypernym "http://identifiers.org/go/GO:0000165"
-BIOMD0000000009 taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000010.txt

@@ -1,140 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000010()
-
-  // Compartments and Species:
-  compartment uVol;
-  species MKKK in uVol, MKKK_P in uVol, MKK in uVol, MKK_P in uVol, MKK_PP in uVol;
-  species MAPK in uVol, MAPK_P in uVol, MAPK_PP in uVol;
-
-  // Reactions:
-  J0: MKKK => MKKK_P; uVol*J0_V1*MKKK/((1 + (MAPK_PP/J0_Ki)^J0_n)*(J0_K1 + MKKK));
-  J1: MKKK_P => MKKK; uVol*J1_V2*MKKK_P/(J1_KK2 + MKKK_P);
-  J2: MKK => MKK_P; uVol*J2_k3*MKKK_P*MKK/(J2_KK3 + MKK);
-  J3: MKK_P => MKK_PP; uVol*J3_k4*MKKK_P*MKK_P/(J3_KK4 + MKK_P);
-  J4: MKK_PP => MKK_P; uVol*J4_V5*MKK_PP/(J4_KK5 + MKK_PP);
-  J5: MKK_P => MKK; uVol*J5_V6*MKK_P/(J5_KK6 + MKK_P);
-  J6: MAPK => MAPK_P; uVol*J6_k7*MKK_PP*MAPK/(J6_KK7 + MAPK);
-  J7: MAPK_P => MAPK_PP; uVol*J7_k8*MKK_PP*MAPK_P/(J7_KK8 + MAPK_P);
-  J8: MAPK_PP => MAPK_P; uVol*J8_V9*MAPK_PP/(J8_KK9 + MAPK_PP);
-  J9: MAPK_P => MAPK; uVol*J9_V10*MAPK_P/(J9_KK10 + MAPK_P);
-
-  // Species initializations:
-  MKKK = 90;
-  MKKK_P = 10;
-  MKK = 280;
-  MKK_P = 10;
-  MKK_PP = 10;
-  MAPK = 280;
-  MAPK_P = 10;
-  MAPK_PP = 10;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  J0_V1 = 2.5;
-  J0_Ki = 9;
-  J0_n = 1;
-  J0_K1 = 10;
-  J1_V2 = 0.25;
-  J1_KK2 = 8;
-  J2_k3 = 0.025;
-  J2_KK3 = 15;
-  J3_k4 = 0.025;
-  J3_KK4 = 15;
-  J4_V5 = 0.75;
-  J4_KK5 = 15;
-  J5_V6 = 0.75;
-  J5_KK6 = 15;
-  J6_k7 = 0.025;
-  J6_KK7 = 15;
-  J7_k8 = 0.025;
-  J7_KK8 = 15;
-  J8_V9 = 0.5;
-  J8_KK9 = 15;
-  J9_V10 = 0.5;
-  J9_KK10 = 15;
-
-  // Other declarations:
-  const uVol;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole";
-  MKKK is "Mos";
-  MKKK_P is "Mos-P";
-  MKK is "Mek1";
-  MKK_P is "Mek1-P";
-  MKK_PP is "Mek1-PP";
-  MAPK is "Erk2";
-  MAPK_P is "Erk2-P";
-  MAPK_PP is "Erk2-PP";
-  J0 is "MAPKKK activation";
-  J1 is "MAPKKK inactivation";
-  J2 is "phosphorylation of MAPKK";
-  J3 is "phosphorylation of MAPKK-P";
-  J4 is "dephosphorylation of MAPKK-PP";
-  J5 is "dephosphorylation of MAPKK-P";
-  J6 is "phosphorylation of MAPK";
-  J7 is "phosphorylation of MAPK-P";
-  J8 is "dephosphorylation of MAPK-PP";
-  J9 is "dephosphorylation of MAPK-P";
-
-  // CV terms:
-  MKKK hypernym "http://identifiers.org/uniprot/P09560"
-  MKKK_P hypernym "http://identifiers.org/uniprot/P09560"
-  MKK hypernym "http://identifiers.org/uniprot/Q05116"
-  MKK_P hypernym "http://identifiers.org/uniprot/Q05116"
-  MKK_PP hypernym "http://identifiers.org/uniprot/Q05116"
-  MAPK hypernym "http://identifiers.org/uniprot/P26696"
-  MAPK_P hypernym "http://identifiers.org/uniprot/P26696"
-  MAPK_PP hypernym "http://identifiers.org/uniprot/P26696"
-  J0 homolog "http://identifiers.org/reactome/REACT_525"
-  J0 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-              "http://identifiers.org/go/GO:0000185",
-              "http://identifiers.org/go/GO:0008349"
-  J1 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0051390",
-              "http://identifiers.org/go/GO:0006470"
-  J2 homolog "http://identifiers.org/reactome/REACT_614"
-  J2 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-              "http://identifiers.org/go/GO:0004709",
-              "http://identifiers.org/go/GO:0006468"
-  J3 homolog "http://identifiers.org/reactome/REACT_614"
-  J3 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-              "http://identifiers.org/go/GO:0000186",
-              "http://identifiers.org/go/GO:0006468",
-              "http://identifiers.org/go/GO:0004709"
-  J4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470",
-              "http://identifiers.org/go/GO:0051389"
-  J5 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-  J6 version "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  J6 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0006468"
-  J7 version "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  J7 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0006468",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0000187"
-  J8 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0000188",
-              "http://identifiers.org/go/GO:0006470"
-  J9 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-end
-
-BIOMD0000000010 is "Kholodenko2000 - Ultrasensitivity and negative feedback bring oscillations in MAPK cascade"
-
-BIOMD0000000010 model_entity_is "http://identifiers.org/biomodels.db/MODEL6615119181"
-BIOMD0000000010 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000010"
-BIOMD0000000010 description "http://identifiers.org/pubmed/10712587"
-BIOMD0000000010 hypernym "http://identifiers.org/go/GO:0000165"
-BIOMD0000000010 homolog "http://identifiers.org/reactome/REACT_634"
-BIOMD0000000010 taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000011.txt

@@ -1,272 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MAPK_in_Solution()
-
-  // Compartments and Species:
-  compartment Cytoplasm;
-  substanceOnly species MAPK in Cytoplasm, MAPKMEKpp in Cytoplasm, MAPKp in Cytoplasm;
-  substanceOnly species MAPKPH in Cytoplasm, MAPKpMAPKPH in Cytoplasm, MAPKpMEKpp in Cytoplasm;
-  substanceOnly species MAPKpp in Cytoplasm, MAPKppMAPKPH in Cytoplasm, MEK in Cytoplasm;
-  substanceOnly species MEKp in Cytoplasm, MEKPH in Cytoplasm, MEKpMEKPH in Cytoplasm;
-  substanceOnly species MEKpp in Cytoplasm, MEKppMEKPH in Cytoplasm, MEKpRAFp in Cytoplasm;
-  substanceOnly species MEKRAFp in Cytoplasm, RAF in Cytoplasm, RAFK in Cytoplasm;
-  substanceOnly species RAFp in Cytoplasm, RAFPH in Cytoplasm, RAFpRAFPH in Cytoplasm;
-  substanceOnly species RAFRAFK in Cytoplasm;
-
-  // Reactions:
-  Reaction1: RAF + RAFK => RAFRAFK; Reaction1_a1*RAF*RAFK;
-  Reaction2: RAFRAFK => RAF + RAFK; Reaction2_d1*RAFRAFK;
-  Reaction3: RAFRAFK => RAFK + RAFp; Reaction3_k1*RAFRAFK;
-  Reaction4: RAFp + RAFPH => RAFpRAFPH; Reaction4_a2*RAFp*RAFPH;
-  Reaction5: RAFpRAFPH => RAFp + RAFPH; Reaction5_d2*RAFpRAFPH;
-  Reaction6: RAFpRAFPH => RAF + RAFPH; Reaction6_k2*RAFpRAFPH;
-  Reaction7: MEK + RAFp => MEKRAFp; Reaction7_a3*MEK*RAFp;
-  Reaction8: MEKRAFp => MEK + RAFp; Reaction8_d3*MEKRAFp;
-  Reaction9: MEKRAFp => MEKp + RAFp; Reaction9_k3*MEKRAFp;
-  Reaction10: MEKp + MEKPH => MEKpMEKPH; Reaction10_a4*MEKp*MEKPH;
-  Reaction11: MEKpMEKPH => MEKp + MEKPH; Reaction11_d4*MEKpMEKPH;
-  Reaction12: MEKpMEKPH => MEK + MEKPH; Reaction12_k4*MEKpMEKPH;
-  Reaction13: MEKp + RAFp => MEKpRAFp; Reaction13_a5*MEKp*RAFp;
-  Reaction14: MEKpRAFp => MEKp + RAFp; Reaction14_d5*MEKpRAFp;
-  Reaction15: MEKpRAFp => MEKpp + RAFp; Reaction15_k5*MEKpRAFp;
-  Reaction16: MEKPH + MEKpp => MEKppMEKPH; Reaction16_a6*MEKPH*MEKpp;
-  Reaction17: MEKppMEKPH => MEKPH + MEKpp; Reaction17_d6*MEKppMEKPH;
-  Reaction18: MEKppMEKPH => MEKp + MEKPH; Reaction18_k6*MEKppMEKPH;
-  Reaction19: MAPK + MEKpp => MAPKMEKpp; Reaction19_a7*MAPK*MEKpp;
-  Reaction20: MAPKMEKpp => MAPK + MEKpp; Reaction20_d7*MAPKMEKpp;
-  Reaction21: MAPKMEKpp => MAPKp + MEKpp; Reaction21_k7*MAPKMEKpp;
-  Reaction22: MAPKp + MAPKPH => MAPKpMAPKPH; Reaction22_a8*MAPKp*MAPKPH;
-  Reaction23: MAPKpMAPKPH => MAPKp + MAPKPH; Reaction23_d8*MAPKpMAPKPH;
-  Reaction24: MAPKpMAPKPH => MAPK + MAPKPH; Reaction24_k8*MAPKpMAPKPH;
-  Reaction25: MAPKp + MEKpp => MAPKpMEKpp; Reaction25_a9*MAPKp*MEKpp;
-  Reaction26: MAPKpMEKpp => MAPKp + MEKpp; Reaction26_d9*MAPKpMEKpp;
-  Reaction27: MAPKpMEKpp => MAPKpp + MEKpp; Reaction27_k9*MAPKpMEKpp;
-  Reaction28: MAPKPH + MAPKpp => MAPKppMAPKPH; Reaction28_a10*MAPKPH*MAPKpp;
-  Reaction29: MAPKppMAPKPH => MAPKPH + MAPKpp; Reaction29_d10*MAPKppMAPKPH;
-  Reaction30: MAPKppMAPKPH => MAPKp + MAPKPH; Reaction30_k10*MAPKppMAPKPH;
-
-  // Species initializations:
-  MAPK = 0.4/Cytoplasm;
-  MAPKMEKpp = 0;
-  MAPKp = 0;
-  MAPKPH = 0.3/Cytoplasm;
-  MAPKpMAPKPH = 0;
-  MAPKpMEKpp = 0;
-  MAPKpp = 0;
-  MAPKppMAPKPH = 0;
-  MEK = 0.2/Cytoplasm;
-  MEKp = 0;
-  MEKPH = 0.2/Cytoplasm;
-  MEKpMEKPH = 0;
-  MEKpp = 0;
-  MEKppMEKPH = 0;
-  MEKpRAFp = 0;
-  MEKRAFp = 0;
-  RAF = 0.3/Cytoplasm;
-  RAFK = 0.2/Cytoplasm;
-  RAFp = 0;
-  RAFPH = 0.3/Cytoplasm;
-  RAFpRAFPH = 0;
-  RAFRAFK = 0;
-
-  // Compartment initializations:
-  Cytoplasm = 1;
-
-  // Variable initializations:
-  Reaction1_a1 = 1;
-  Reaction2_d1 = 0.4;
-  Reaction3_k1 = 0.1;
-  Reaction4_a2 = 0.5;
-  Reaction5_d2 = 0.5;
-  Reaction6_k2 = 0.1;
-  Reaction7_a3 = 3.3;
-  Reaction8_d3 = 0.42;
-  Reaction9_k3 = 0.1;
-  Reaction10_a4 = 10;
-  Reaction11_d4 = 0.8;
-  Reaction12_k4 = 0.1;
-  Reaction13_a5 = 3.3;
-  Reaction14_d5 = 0.4;
-  Reaction15_k5 = 0.1;
-  Reaction16_a6 = 10;
-  Reaction17_d6 = 0.8;
-  Reaction18_k6 = 0.1;
-  Reaction19_a7 = 20;
-  Reaction20_d7 = 0.6;
-  Reaction21_k7 = 0.1;
-  Reaction22_a8 = 5;
-  Reaction23_d8 = 0.4;
-  Reaction24_k8 = 0.1;
-  Reaction25_a9 = 20;
-  Reaction26_d9 = 0.6;
-  Reaction27_k9 = 0.1;
-  Reaction28_a10 = 5;
-  Reaction29_d10 = 0.4;
-  Reaction30_k10 = 0.1;
-
-  // Other declarations:
-  const Cytoplasm;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  MAPKMEKpp is "MAPK_MEK-PP";
-  MAPKp is "MAPK-P";
-  MAPKPH is "MAPK phosphatase";
-  MAPKpMAPKPH is "MAPK-P_MAPKPase";
-  MAPKpMEKpp is "MAPK-P_MEK-PP";
-  MAPKpp is "MAPK-PP";
-  MAPKppMAPKPH is "MAPK-PP_MAPKPase";
-  MEKp is "MEK-P";
-  MEKPH is "MEK phosphatase";
-  MEKpMEKPH is "MEK-P_MEKPase";
-  MEKpp is "MEK-PP";
-  MEKppMEKPH is "MEK-PP_MEKPase";
-  MEKpRAFp is "MEK-P_RAF-P";
-  MEKRAFp is "MEK_RAF-P";
-  RAFp is "RAF-P";
-  RAFPH is "RAF phosphatase";
-  RAFpRAFPH is "RAF-P_RAFPase";
-  RAFRAFK is "RAF_RAFK";
-  Reaction1 is "binding of RAF and RAFK";
-  Reaction2 is "dissociation of RAF_RAFK";
-  Reaction3 is "phosphorylation of RAF";
-  Reaction4 is "binding of RAF-P and RAF phosphatase";
-  Reaction5 is "dissociation of RAF-P_RAFPase";
-  Reaction6 is "dephosphorylation of RAF-P";
-  Reaction7 is "binding of MEK and RAF-P";
-  Reaction8 is "dissociation of MEK_RAF-P";
-  Reaction9 is "phosphorylation of MEK";
-  Reaction10 is "binding of MEK-P and MEK phosphatase";
-  Reaction11 is "dissociation of MEK-P_MEKPase";
-  Reaction12 is "dephosphorylation of MEK-P";
-  Reaction13 is "binding of MEK-P and RAF-P";
-  Reaction14 is "dissociation of MEK-P_RAF-P";
-  Reaction15 is "phosphorylation of MEK-P";
-  Reaction16 is "binding of MEK-PP and MEK phosphatase";
-  Reaction17 is "dissociation of MEK-PP_MEKPase";
-  Reaction18 is "dephosphorylation of MEK-PP";
-  Reaction19 is "binding of MAPK and MEK-PP";
-  Reaction20 is "dissociation of MAPK_MEK-PP";
-  Reaction21 is "phosphorylation of MAPK";
-  Reaction22 is "binding of MAPK-P and MAPK phosphatase";
-  Reaction23 is "dissociation of MAPK-P_MAPKPase";
-  Reaction24 is "dephosphorylation of MAPK-P";
-  Reaction25 is "binding of MAPK-P and MEK-PP";
-  Reaction26 is "dissociation of MAPK-P_MEK-PP";
-  Reaction27 is "phosphorylation of MAPK-P";
-  Reaction28 is "binding of MAPK-PP and MAPK phosphatase";
-  Reaction29 is "dissociation of MAPK-PP_MAPKPase";
-  Reaction30 is "dephosphorylation of MAPK-PP";
-
-  // CV terms:
-  Cytoplasm identity "http://identifiers.org/obo.go/GO:0005737"
-  MAPK hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKMEKpp part "http://identifiers.org/uniprot/P26696",
-                 "http://identifiers.org/uniprot/Q05116"
-  MAPKp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKPH identity "http://identifiers.org/uniprot/Q90W58"
-  MAPKpMAPKPH part "http://identifiers.org/uniprot/P26696",
-                   "http://identifiers.org/uniprot/Q90W58"
-  MAPKpMEKpp part "http://identifiers.org/uniprot/Q05116",
-                  "http://identifiers.org/uniprot/P26696"
-  MAPKpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKppMAPKPH part "http://identifiers.org/uniprot/P26696",
-                    "http://identifiers.org/uniprot/Q90W58"
-  MEK hypernym "http://identifiers.org/uniprot/Q05116"
-  MEKp hypernym "http://identifiers.org/uniprot/Q05116"
-  MEKpMEKPH part "http://identifiers.org/uniprot/Q05116"
-  MEKpp hypernym "http://identifiers.org/uniprot/Q05116"
-  MEKppMEKPH part "http://identifiers.org/uniprot/Q05116"
-  MEKpRAFp part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  MEKRAFp part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116"
-  RAF hypernym "http://identifiers.org/uniprot/P09560"
-  RAFK hypernym "http://identifiers.org/interpro/IPR003577"
-  RAFp hypernym "http://identifiers.org/uniprot/P09560"
-  RAFpRAFPH part "http://identifiers.org/uniprot/P09560"
-  RAFRAFK part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/interpro/IPR003577"
-  Reaction1 homolog "http://identifiers.org/reactome/REACT_996"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0031435"
-  Reaction2 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction3 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                     "http://identifiers.org/obo.go/GO:0008349",
-                     "http://identifiers.org/obo.go/GO:0000185",
-                     "http://identifiers.org/obo.go/GO:0006468"
-  Reaction4 hypernym "http://identifiers.org/obo.go/GO:0031435"
-  Reaction5 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction6 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/obo.go/GO:0051390",
-                     "http://identifiers.org/obo.go/GO:0006470"
-  Reaction7 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                     "http://identifiers.org/obo.go/GO:0031435"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction9 homolog "http://identifiers.org/reactome/REACT_614"
-  Reaction9 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-                     "http://identifiers.org/obo.go/GO:0004709",
-                     "http://identifiers.org/obo.go/GO:0006468"
-  Reaction10 hypernym "http://identifiers.org/obo.go/GO:0031434"
-  Reaction11 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction12 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0006470"
-  Reaction13 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction13 hypernym "http://identifiers.org/obo.go/GO:0031435",
-                      "http://identifiers.org/obo.go/GO:0031434"
-  Reaction14 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction15 homolog "http://identifiers.org/reactome/REACT_614"
-  Reaction15 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-                      "http://identifiers.org/obo.go/GO:0006468",
-                      "http://identifiers.org/obo.go/GO:0004709",
-                      "http://identifiers.org/obo.go/GO:0000186"
-  Reaction16 hypernym "http://identifiers.org/obo.go/GO:0031434"
-  Reaction17 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction18 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0051389",
-                      "http://identifiers.org/obo.go/GO:0006470"
-  Reaction19 homolog "http://identifiers.org/reactome/REACT_495",
-                     "http://identifiers.org/reactome/REACT_1780"
-  Reaction19 identity "http://identifiers.org/obo.go/GO:0051019",
-                      "http://identifiers.org/obo.go/GO:0031434"
-  Reaction20 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction21 homolog "http://identifiers.org/reactome/REACT_2247",
-                     "http://identifiers.org/reactome/REACT_136"
-  Reaction21 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                      "http://identifiers.org/obo.go/GO:0006468",
-                      "http://identifiers.org/obo.go/GO:0004708"
-  Reaction22 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  Reaction23 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction24 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0006470"
-  Reaction25 homolog "http://identifiers.org/reactome/REACT_495",
-                     "http://identifiers.org/reactome/REACT_1780"
-  Reaction25 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                      "http://identifiers.org/obo.go/GO:0031434"
-  Reaction26 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction27 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                      "http://identifiers.org/obo.go/GO:0000187",
-                      "http://identifiers.org/obo.go/GO:0006468",
-                      "http://identifiers.org/obo.go/GO:0004708"
-  Reaction27 homolog "http://identifiers.org/reactome/REACT_136",
-                     "http://identifiers.org/reactome/REACT_2247"
-  Reaction28 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  Reaction29 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  Reaction30 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/obo.go/GO:0006470",
-                      "http://identifiers.org/obo.go/GO:0000188"
-end
-
-MAPK_in_Solution is "Levchenko2000_MAPK_noScaffold"
-
-MAPK_in_Solution model_entity_is "http://identifiers.org/biomodels.db/MODEL6615234250"
-MAPK_in_Solution model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000011"
-MAPK_in_Solution description "http://identifiers.org/pubmed/10823939"
-MAPK_in_Solution origin "http://identifiers.org/biomodels.db/BIOMD0000000009",
-                        "http://identifiers.org/pubmed/6501300",
-                        "http://identifiers.org/pubmed/6947258"
-MAPK_in_Solution homolog "http://identifiers.org/reactome/REACT_634"
-MAPK_in_Solution hypernym "http://identifiers.org/obo.go/GO:0000165"
-MAPK_in_Solution taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000012.txt

@@ -1,161 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000012()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species PX in cell, PY in cell, PZ in cell, X in cell, Y in cell;
-  substanceOnly species Z in cell;
-
-  // Assignment Rules:
-  beta := tau_mRNA/tau_prot;
-  alpha0 := a0_tr*eff*tau_prot/(ln(2)*KM);
-  a0_tr := ps_0*60;
-  alpha := a_tr*eff*tau_prot/(ln(2)*KM);
-  a_tr := (ps_a - ps_0)*60;
-  t_ave := tau_mRNA/ln(2);
-  kd_mRNA := ln(2)/tau_mRNA;
-  kd_prot := ln(2)/tau_prot;
-  k_tl := eff/t_ave;
-
-  // Reactions:
-  Reaction1: X => ; kd_mRNA*X;
-  Reaction2: Y => ; kd_mRNA*Y;
-  Reaction3: Z => ; kd_mRNA*Z;
-  Reaction4:  => PX; k_tl*X;
-  Reaction5:  => PY; k_tl*Y;
-  Reaction6:  => PZ; k_tl*Z;
-  Reaction7: PX => ; kd_prot*PX;
-  Reaction8: PY => ; kd_prot*PY;
-  Reaction9: PZ => ; kd_prot*PZ;
-  Reaction10:  => X; a0_tr + a_tr*KM^n/(KM^n + PZ^n);
-  Reaction11:  => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n);
-  Reaction12:  => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n);
-
-  // Species initializations:
-  PX = 0;
-  PY = 0;
-  PZ = 0;
-  X = 0;
-  Y = 20/cell;
-  Z = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  tau_mRNA = 2;
-  tau_prot = 10;
-  eff = 20;
-  KM = 40;
-  n = 2;
-  ps_a = 0.5;
-  ps_0 = 0.0005;
-
-  // Other declarations:
-  var beta, alpha0, a0_tr, alpha, a_tr, t_ave, kd_mRNA, kd_prot, k_tl;
-  const cell, tau_mRNA, tau_prot, eff, KM, n, ps_a, ps_0;
-
-  // Unit definitions:
-  unit volume = 1e-15 litre;
-  unit substance = item;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  volume is "cubic microns";
-  substance is "item";
-  time_unit is "minute";
-  PX is "LacI protein";
-  PY is "TetR protein";
-  PZ is "cI protein";
-  X is "LacI mRNA";
-  Y is "TetR mRNA";
-  Z is "cI mRNA";
-  tau_mRNA is "mRNA half life";
-  tau_prot is "protein half life";
-  eff is "translation efficiency";
-  t_ave is "average mRNA life time";
-  ps_a is "tps_active";
-  ps_0 is "tps_repr";
-  Reaction1 is "degradation of LacI transcripts";
-  Reaction2 is "degradation of TetR transcripts";
-  Reaction3 is "degradation of CI transcripts";
-  Reaction4 is "translation of LacI";
-  Reaction5 is "translation of TetR";
-  Reaction6 is "translation of CI";
-  Reaction7 is "degradation of LacI";
-  Reaction8 is "degradation of TetR";
-  Reaction9 is "degradation of CI";
-  Reaction10 is "transcription of LacI";
-  Reaction11 is "transcription of TetR";
-  Reaction12 is "transcription of CI";
-
-  // SBO terms:
-  cell.sboTerm = 290
-  PX.sboTerm = 252
-  PY.sboTerm = 252
-  PZ.sboTerm = 252
-  X.sboTerm = 250
-  Y.sboTerm = 250
-  Z.sboTerm = 250
-  tau_mRNA.sboTerm = 332
-  tau_prot.sboTerm = 332
-  alpha0.sboTerm = 485
-  a0_tr.sboTerm = 485
-  KM.sboTerm = 288
-  alpha.sboTerm = 186
-  a_tr.sboTerm = 186
-  n.sboTerm = 190
-  t_ave.sboTerm = 348
-  kd_mRNA.sboTerm = 356
-  kd_prot.sboTerm = 356
-  k_tl.sboTerm = 16
-  ps_a.sboTerm = 186
-  ps_0.sboTerm = 485
-  Reaction1.sboTerm = 179
-  Reaction2.sboTerm = 179
-  Reaction3.sboTerm = 179
-  Reaction4.sboTerm = 184
-  Reaction5.sboTerm = 184
-  Reaction6.sboTerm = 184
-  Reaction7.sboTerm = 179
-  Reaction8.sboTerm = 179
-  Reaction9.sboTerm = 179
-  Reaction10.sboTerm = 183
-  Reaction11.sboTerm = 183
-  Reaction12.sboTerm = 183
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  PX identity "http://identifiers.org/uniprot/P03023"
-  PY identity "http://identifiers.org/uniprot/P04483"
-  PZ identity "http://identifiers.org/uniprot/P03034"
-  X hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  X encodement "http://identifiers.org/uniprot/P03023"
-  Y hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  Y encodement "http://identifiers.org/uniprot/P04483"
-  Z hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  Z encodement "http://identifiers.org/uniprot/P03034"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction2 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction3 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction4 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction5 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction6 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction9 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction10 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction11 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction12 hypernym "http://identifiers.org/obo.go/GO:0006351"
-end
-
-BIOMD0000000012 is "Elowitz2000 - Repressilator"
-
-BIOMD0000000012 model_entity_is "http://identifiers.org/biomodels.db/MODEL6615351360"
-BIOMD0000000012 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000012"
-BIOMD0000000012 description "http://identifiers.org/pubmed/10659856"
-BIOMD0000000012 taxon "http://identifiers.org/taxonomy/562"
-BIOMD0000000012 hypernym "http://identifiers.org/obo.go/GO:0040029"

BioModelsRAG/data/BIOMD0000000013.txt

@@ -1,264 +0,0 @@
-// Created by libAntimony v2.13.0
-model *untitled()
-
-  // Compartments and Species:
-  compartment chloroplast, cytosol;
-  species $x_CO2 in chloroplast, RuBP_ch in chloroplast, PGA_ch in chloroplast;
-  species ATP_ch in chloroplast, BPGA_ch in chloroplast, $x_NADPH_ch in chloroplast;
-  species GAP_ch in chloroplast, Pi_ch in chloroplast, DHAP_ch in chloroplast;
-  species FBP_ch in chloroplast, F6P_ch in chloroplast, E4P_ch in chloroplast;
-  species X5P_ch in chloroplast, SBP_ch in chloroplast, S7P_ch in chloroplast;
-  species R5P_ch in chloroplast, Ru5P_ch in chloroplast, $x_Pi_cyt in cytosol;
-  species $x_GAP_cyt in cytosol, G6P_ch in chloroplast, $x_NADP_ch in chloroplast;
-  species $x_PGA_cyt in cytosol, ADP_ch in chloroplast, $x_DHAP_cyt in cytosol;
-  species $x_Proton_ch in chloroplast, G1P_ch in chloroplast, $x_Starch_ch in chloroplast;
-
-  // Reactions:
-  E1: RuBP_ch + $x_CO2 => 2 PGA_ch; Light_on*E1_Rbco_vm*RuBP_ch*chloroplast/(RuBP_ch + E1_Rbco_km*(1 + PGA_ch/E1_Rbco_KiPGA + FBP_ch/E1_Rbco_KiFBP + SBP_ch/E1_Rbco_KiSBP + Pi_ch/E1_Rbco_KiPi + x_NADPH_ch/E1_Rbco_KiNADPH));
-  E2: PGA_ch + ATP_ch => BPGA_ch + ADP_ch; Light_on*E2_PGK_v*chloroplast*(PGA_ch*ATP_ch - BPGA_ch*ADP_ch/E2_q2);
-  E3: $x_NADPH_ch + BPGA_ch + $x_Proton_ch => $x_NADP_ch + GAP_ch + Pi_ch; Light_on*E3_G3Pdh_v*chloroplast*(BPGA_ch*x_NADPH_ch*x_Proton_ch - x_NADP_ch*GAP_ch*Pi_ch/E3_q3);
-  E4: GAP_ch -> DHAP_ch; chloroplast*E4_TPI_v*(GAP_ch - DHAP_ch/E4_q4);
-  E5: GAP_ch + DHAP_ch -> FBP_ch; E5_F_Aldo_v*chloroplast*(DHAP_ch*GAP_ch - FBP_ch/E5_q5);
-  E6: FBP_ch => F6P_ch + Pi_ch; Light_on*E6_FBPase_ch_vm*FBP_ch*chloroplast/(FBP_ch + E6_FBPase_ch_km*(1 + F6P_ch/E6_FBPase_ch_KiF6P + Pi_ch/E6_FBPase_ch_KiPi));
-  E7: GAP_ch + F6P_ch -> X5P_ch + E4P_ch; chloroplast*E7_F_TKL_v*(F6P_ch*GAP_ch - E4P_ch*X5P_ch/E7_q7);
-  E8: DHAP_ch + E4P_ch -> SBP_ch; chloroplast*E8_E_Aldo_v*(E4P_ch*DHAP_ch - SBP_ch/E8_q8);
-  E9: SBP_ch => Pi_ch + S7P_ch; Light_on*E9_SBPase_ch_vm*SBP_ch*chloroplast/(SBP_ch + E9_SBPase_ch_km*(1 + Pi_ch/E9_SBPase_ch_KiPi));
-  E10: S7P_ch + GAP_ch -> R5P_ch + X5P_ch; chloroplast*E10_G_TKL_v*(GAP_ch*S7P_ch - X5P_ch*R5P_ch/E10_q10);
-  E11: R5P_ch -> Ru5P_ch; E11_R5Piso_v*chloroplast*(R5P_ch - Ru5P_ch/E11_q11);
-  E12: X5P_ch -> Ru5P_ch; chloroplast*E12_X5Pepi_v*(X5P_ch - Ru5P_ch/E12_q12);
-  E13: Ru5P_ch + ATP_ch => RuBP_ch + ADP_ch; Light_on*E13_Ru5Pk_ch_vm*Ru5P_ch*chloroplast*ATP_ch/((Ru5P_ch + E13_Ru5Pk_ch_km1*(1 + PGA_ch/E13_Ru5Pk_ch_KiPGA + RuBP_ch/E13_Ru5Pk_ch_KiRuBP + Pi_ch/E13_Ru5Pk_ch_KiPi))*(ATP_ch*(1 + ADP_ch/E13_Ru5Pk_ch_KiADP1) + E13_Ru5Pk_ch_km2*(1 + ADP_ch/E13_Ru5Pk_ch_KiADP2)));
-  E14: F6P_ch -> G6P_ch; E14_PGI_v*chloroplast*(F6P_ch - G6P_ch/E14_q14);
-  E15: G6P_ch -> G1P_ch; E15_PGM_v*chloroplast*(G6P_ch - G1P_ch/E15_q15);
-  light_reaction: Pi_ch + ADP_ch => ATP_ch; Light_on*light_reaction_LR_vm*ADP_ch*Pi_ch*chloroplast/((ADP_ch + light_reaction_LR_kmADP)*(Pi_ch + light_reaction_LR_kmPi));
-  E16: ATP_ch + G1P_ch => $x_Starch_ch + ADP_ch + 2 Pi_ch; E16_StSyn_vm*G1P_ch*ATP_ch*chloroplast/((G1P_ch + E16_stsyn_ch_km1)*(1 + ADP_ch/E16_stsyn_ch_Ki)*(ATP_ch + E16_stsyn_ch_km2) + E16_stsyn_ch_km2*Pi_ch/(E16_stsyn_ch_ka1*PGA_ch) + E16_stsyn_ch_ka2*F6P_ch + E16_stsyn_ch_ka3*FBP_ch);
-  E17: $x_Starch_ch + Pi_ch => G1P_ch; E17_StPase_Vm*Pi_ch*chloroplast/(Pi_ch + E17_StPase_km*(1 + G1P_ch/E17_StPase_kiG1P));
-  E18_DHAP: $x_Pi_cyt + DHAP_ch => $x_DHAP_cyt + Pi_ch; E18_DHAP_TP_Piap_vm*DHAP_ch*chloroplast/(E18_DHAP_TP_Piap_kDHAP_ch*(1 + (1 + E18_DHAP_TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/E18_DHAP_TP_Piap_kPi_ch + PGA_ch/E18_DHAP_TP_Piap_kPGA_ch + DHAP_ch/E18_DHAP_TP_Piap_kDHAP_ch + GAP_ch/E18_DHAP_TP_Piap_kGAP_ch)));
-  E18_PGA: $x_Pi_cyt + PGA_ch => $x_PGA_cyt + Pi_ch; E18_PGA_PGA_xpMult*E18_PGA_TP_Piap_vm*PGA_ch*chloroplast/(E18_PGA_TP_Piap_kPGA_ch*(1 + (1 + E18_PGA_TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/E18_PGA_TP_Piap_kPi_ch + PGA_ch/E18_PGA_TP_Piap_kPGA_ch + DHAP_ch/E18_PGA_TP_Piap_kDHAP_ch + GAP_ch/E18_PGA_TP_Piap_kGAP_ch)));
-  E18_GAP: $x_Pi_cyt + GAP_ch => $x_GAP_cyt + Pi_ch; E18_GAP_TP_Piap_vm*GAP_ch*chloroplast/(E18_GAP_TP_Piap_kGAP_ch*(1 + (1 + E18_GAP_TP_Piap_kPi_cyt/x_Pi_cyt)*(Pi_ch/E18_GAP_TP_Piap_kPi_ch + PGA_ch/E18_GAP_TP_Piap_kPGA_ch + DHAP_ch/E18_GAP_TP_Piap_kDHAP_ch + GAP_ch/E18_GAP_TP_Piap_kGAP_ch)));
-
-  // Species initializations:
-  x_CO2 = 1;
-  RuBP_ch = 0.33644;
-  PGA_ch = 3.35479;
-  ATP_ch = 0.49806;
-  BPGA_ch = 0.14825;
-  x_NADPH_ch = 0.21;
-  GAP_ch = 0.01334;
-  Pi_ch = 1.5662;
-  DHAP_ch = 0.29345;
-  FBP_ch = 0.02776;
-  F6P_ch = 1.36481;
-  E4P_ch = 0.41021;
-  X5P_ch = 0.00363;
-  SBP_ch = 1.56486;
-  S7P_ch = 0.00541;
-  R5P_ch = 0.00599;
-  Ru5P_ch = 0.00235;
-  x_Pi_cyt = 0.5;
-  x_GAP_cyt = 1;
-  G6P_ch = 3.1396;
-  x_NADP_ch = 0.29;
-  x_PGA_cyt = 1;
-  ADP_ch = 0.00149;
-  x_DHAP_cyt = 1;
-  x_Proton_ch = 2.512e-05;
-  G1P_ch = 0.18206;
-  x_Starch_ch = 1;
-
-  // Compartment initializations:
-  chloroplast = 1;
-  cytosol = 1;
-
-  // Variable initializations:
-  Light_on = 1;
-  E1_Rbco_vm = 340;
-  E1_Rbco_km = 0.02;
-  E1_Rbco_KiPGA = 0.84;
-  E1_Rbco_KiFBP = 0.04;
-  E1_Rbco_KiSBP = 0.075;
-  E1_Rbco_KiPi = 0.9;
-  E1_Rbco_KiNADPH = 0.07;
-  E2_PGK_v = 500000000;
-  E2_q2 = 0.00031;
-  E3_G3Pdh_v = 500000000;
-  E3_q3 = 16000000;
-  E4_TPI_v = 500000000;
-  E4_q4 = 22;
-  E5_F_Aldo_v = 500000000;
-  E5_q5 = 7.1;
-  E6_FBPase_ch_vm = 200;
-  E6_FBPase_ch_km = 0.03;
-  E6_FBPase_ch_KiF6P = 0.7;
-  E6_FBPase_ch_KiPi = 12;
-  E7_F_TKL_v = 500000000;
-  E7_q7 = 0.084;
-  E8_E_Aldo_v = 500000000;
-  E8_q8 = 13;
-  E9_SBPase_ch_vm = 40;
-  E9_SBPase_ch_km = 0.013;
-  E9_SBPase_ch_KiPi = 12;
-  E10_G_TKL_v = 500000000;
-  E10_q10 = 0.85;
-  E11_R5Piso_v = 500000000;
-  E11_q11 = 0.4;
-  E12_X5Pepi_v = 500000000;
-  E12_q12 = 0.67;
-  E13_Ru5Pk_ch_vm = 10000;
-  E13_Ru5Pk_ch_km1 = 0.05;
-  E13_Ru5Pk_ch_KiPGA = 2;
-  E13_Ru5Pk_ch_KiRuBP = 0.7;
-  E13_Ru5Pk_ch_KiPi = 4;
-  E13_Ru5Pk_ch_KiADP1 = 2.5;
-  E13_Ru5Pk_ch_km2 = 0.05;
-  E13_Ru5Pk_ch_KiADP2 = 0.4;
-  E14_PGI_v = 500000000;
-  E14_q14 = 2.3;
-  E15_PGM_v = 500000000;
-  E15_q15 = 0.058;
-  light_reaction_LR_vm = 3500;
-  light_reaction_LR_kmADP = 0.014;
-  light_reaction_LR_kmPi = 0.3;
-  E16_StSyn_vm = 40;
-  E16_stsyn_ch_km1 = 0.08;
-  E16_stsyn_ch_Ki = 10;
-  E16_stsyn_ch_km2 = 0.08;
-  E16_stsyn_ch_ka1 = 0.1;
-  E16_stsyn_ch_ka2 = 0.02;
-  E16_stsyn_ch_ka3 = 0.02;
-  E17_StPase_Vm = 40;
-  E17_StPase_km = 0.1;
-  E17_StPase_kiG1P = 0.05;
-  E18_DHAP_TP_Piap_vm = 250;
-  E18_DHAP_TP_Piap_kDHAP_ch = 0.077;
-  E18_DHAP_TP_Piap_kPi_cyt = 0.74;
-  E18_DHAP_TP_Piap_kPi_ch = 0.63;
-  E18_DHAP_TP_Piap_kPGA_ch = 0.25;
-  E18_DHAP_TP_Piap_kGAP_ch = 0.075;
-  E18_PGA_PGA_xpMult = 0.75;
-  E18_PGA_TP_Piap_vm = 250;
-  E18_PGA_TP_Piap_kPGA_ch = 0.25;
-  E18_PGA_TP_Piap_kPi_cyt = 0.74;
-  E18_PGA_TP_Piap_kPi_ch = 0.63;
-  E18_PGA_TP_Piap_kDHAP_ch = 0.077;
-  E18_PGA_TP_Piap_kGAP_ch = 0.075;
-  E18_GAP_TP_Piap_vm = 250;
-  E18_GAP_TP_Piap_kGAP_ch = 0.075;
-  E18_GAP_TP_Piap_kPi_cyt = 0.74;
-  E18_GAP_TP_Piap_kPi_ch = 0.63;
-  E18_GAP_TP_Piap_kPGA_ch = 0.25;
-  E18_GAP_TP_Piap_kDHAP_ch = 0.077;
-
-  // Other declarations:
-  const chloroplast, cytosol, Light_on;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-
-  // Display Names:
-  substance is "mM";
-
-  // CV terms:
-  chloroplast identity "http://identifiers.org/go/GO:0009570"
-  cytosol identity "http://identifiers.org/go/GO:0005829"
-  x_CO2 identity "http://identifiers.org/chebi/CHEBI:16526",
-                 "http://identifiers.org/kegg.compound/C00011"
-  RuBP_ch identity "http://identifiers.org/kegg.compound/C01182"
-  PGA_ch identity "http://identifiers.org/kegg.compound/C00197"
-  ATP_ch identity "http://identifiers.org/chebi/CHEBI:15422",
-                  "http://identifiers.org/kegg.compound/C00002"
-  BPGA_ch identity "http://identifiers.org/kegg.compound/C00236"
-  x_NADPH_ch identity "http://identifiers.org/chebi/CHEBI:16474",
-                      "http://identifiers.org/kegg.compound/C00005"
-  GAP_ch identity "http://identifiers.org/chebi/CHEBI:17138",
-                  "http://identifiers.org/kegg.compound/C00118"
-  Pi_ch identity "http://identifiers.org/chebi/CHEBI:18367",
-                 "http://identifiers.org/kegg.compound/C00009"
-  DHAP_ch identity "http://identifiers.org/chebi/CHEBI:16108",
-                   "http://identifiers.org/kegg.compound/C00111"
-  FBP_ch identity "http://identifiers.org/chebi/CHEBI:28013",
-                  "http://identifiers.org/kegg.compound/C05378"
-  F6P_ch hypernym "http://identifiers.org/chebi/CHEBI:57634"
-  E4P_ch identity "http://identifiers.org/chebi/CHEBI:48153",
-                  "http://identifiers.org/kegg.compound/C00279"
-  X5P_ch identity "http://identifiers.org/chebi/CHEBI:16332",
-                  "http://identifiers.org/kegg.compound/C00231"
-  SBP_ch identity "http://identifiers.org/chebi/CHEBI:17969",
-                  "http://identifiers.org/kegg.compound/C00447"
-  S7P_ch identity "http://identifiers.org/chebi/CHEBI:15721",
-                  "http://identifiers.org/kegg.compound/C05382"
-  R5P_ch identity "http://identifiers.org/chebi/CHEBI:17797",
-                  "http://identifiers.org/kegg.compound/C00117"
-  Ru5P_ch identity "http://identifiers.org/chebi/CHEBI:17363",
-                   "http://identifiers.org/kegg.compound/C00199"
-  x_Pi_cyt identity "http://identifiers.org/chebi/CHEBI:18367",
-                    "http://identifiers.org/kegg.compound/C00009"
-  x_GAP_cyt identity "http://identifiers.org/chebi/CHEBI:17138",
-                     "http://identifiers.org/kegg.compound/C00661"
-  G6P_ch identity "http://identifiers.org/chebi/CHEBI:14314",
-                  "http://identifiers.org/kegg.compound/C00668"
-  x_NADP_ch identity "http://identifiers.org/chebi/CHEBI:18009",
-                     "http://identifiers.org/kegg.compound/C00006"
-  x_PGA_cyt identity "http://identifiers.org/kegg.compound/C00197"
-  ADP_ch identity "http://identifiers.org/chebi/CHEBI:16761",
-                  "http://identifiers.org/kegg.compound/C00008"
-  x_DHAP_cyt identity "http://identifiers.org/chebi/CHEBI:16108",
-                      "http://identifiers.org/kegg.compound/C00111"
-  x_Proton_ch identity "http://identifiers.org/chebi/CHEBI:24636"
-  G1P_ch identity "http://identifiers.org/chebi/CHEBI:58601",
-                  "http://identifiers.org/kegg.compound/C00103"
-  x_Starch_ch identity "http://identifiers.org/kegg.compound/C00369"
-  E1 hypernym "http://identifiers.org/ec-code/4.1.1.39"
-  E1 identity "http://identifiers.org/kegg.reaction/R00024"
-  E2 hypernym "http://identifiers.org/ec-code/2.7.2.3"
-  E2 identity "http://identifiers.org/kegg.reaction/R01512",
-              "http://identifiers.org/reactome/REACT_1186"
-  E3 hypernym "http://identifiers.org/ec-code/1.2.1.13"
-  E3 identity "http://identifiers.org/kegg.reaction/R01063"
-  E4 hypernym "http://identifiers.org/ec-code/5.3.1.1"
-  E4 identity "http://identifiers.org/kegg.reaction/R01015",
-              "http://identifiers.org/reactome/REACT_775"
-  E5 hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  E5 identity "http://identifiers.org/kegg.reaction/R01070",
-              "http://identifiers.org/reactome/REACT_1602"
-  E6 hypernym "http://identifiers.org/ec-code/3.1.3.11"
-  E6 identity "http://identifiers.org/kegg.reaction/R04780"
-  E7 hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  E7 identity "http://identifiers.org/kegg.reaction/R01830",
-              "http://identifiers.org/reactome/REACT_1811"
-  E8 hypernym "http://identifiers.org/ec-code/4.1.2.13"
-  E8 identity "http://identifiers.org/kegg.reaction/R01829"
-  E9 hypernym "http://identifiers.org/ec-code/3.1.3.37"
-  E9 identity "http://identifiers.org/kegg.reaction/R01845"
-  E10 hypernym "http://identifiers.org/ec-code/2.2.1.1"
-  E10 identity "http://identifiers.org/kegg.reaction/R01641",
-               "http://identifiers.org/reactome/REACT_1629"
-  E11 hypernym "http://identifiers.org/ec-code/5.3.1.6"
-  E11 identity "http://identifiers.org/kegg.reaction/R01056",
-               "http://identifiers.org/reactome/REACT_2033"
-  E12 hypernym "http://identifiers.org/ec-code/5.1.3.1"
-  E12 identity "http://identifiers.org/kegg.reaction/R01429",
-               "http://identifiers.org/reactome/REACT_1522"
-  E13 hypernym "http://identifiers.org/ec-code/2.7.1.19"
-  E13 identity "http://identifiers.org/kegg.reaction/R01423"
-  E14 hypernym "http://identifiers.org/ec-code/5.3.1.9"
-  E14 identity "http://identifiers.org/kegg.reaction/R00771",
-               "http://identifiers.org/reactome/REACT_1164"
-  E15 identity "http://identifiers.org/kegg.reaction/R00959"
-  E15 hypernym "http://identifiers.org/ec-code/5.4.2.2"
-  light_reaction hypernym "http://identifiers.org/go/GO:0006176"
-  E16 identity "http://identifiers.org/kegg.reaction/R02111"
-  E16 hypernym "http://identifiers.org/ec-code/2.4.1.1"
-  E17 identity "http://identifiers.org/kegg.reaction/R02111"
-  E17 hypernym "http://identifiers.org/ec-code/2.4.1.1"
-  E18_DHAP hypernym "http://identifiers.org/go/GO:0051407"
-  E18_PGA hypernym "http://identifiers.org/go/GO:0051408"
-  E18_GAP hypernym "http://identifiers.org/go/GO:0051408"
-end
-
-untitled is "Poolman2004_CalvinCycle"
-
-untitled model_entity_is "http://identifiers.org/biomodels.db/MODEL6615594069"
-untitled model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000013"
-untitled description "http://identifiers.org/pubmed/15073223"
-untitled taxon "http://identifiers.org/taxonomy/4097"
-untitled hypernym "http://identifiers.org/go/GO:0019253"

BioModelsRAG/data/BIOMD0000000014.txt

@@ -1,1635 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MAPK_in_Scaffold()
-
-  // Compartments and Species:
-  compartment Cytoplasm;
-  substanceOnly species MAPKP in Cytoplasm, MEKP in Cytoplasm, RAFK in Cytoplasm;
-  substanceOnly species RAFP in Cytoplasm, K_1_0 in Cytoplasm, K_1_1 in Cytoplasm;
-  substanceOnly species K_1_2 in Cytoplasm, K_2_0 in Cytoplasm, K_2_1 in Cytoplasm;
-  substanceOnly species K_2_2 in Cytoplasm, K_3_0 in Cytoplasm, K_3_1 in Cytoplasm;
-  substanceOnly species K_K_1_0_2_2 in Cytoplasm, K_K_1_1_2_2 in Cytoplasm;
-  substanceOnly species K_K_2_0_3_1 in Cytoplasm, K_K_2_1_3_1 in Cytoplasm;
-  substanceOnly species K_MAPKP_1_1 in Cytoplasm, K_MAPKP_1_2 in Cytoplasm;
-  substanceOnly species K_MEKP_2_1 in Cytoplasm, K_MEKP_2_2 in Cytoplasm;
-  substanceOnly species K_RAFK_3_0 in Cytoplasm, K_RAFP_3_1 in Cytoplasm;
-  substanceOnly species S_m1_m1_m1 in Cytoplasm, S_m1_m1_0 in Cytoplasm, S_m1_m1_1 in Cytoplasm;
-  substanceOnly species S_m1_0_m1 in Cytoplasm, S_m1_0_0 in Cytoplasm, S_m1_0_1 in Cytoplasm;
-  substanceOnly species S_m1_1_m1 in Cytoplasm, S_m1_1_0 in Cytoplasm, S_m1_1_1 in Cytoplasm;
-  substanceOnly species S_m1_2_m1 in Cytoplasm, S_m1_2_0 in Cytoplasm, S_m1_2_1 in Cytoplasm;
-  substanceOnly species S_0_m1_m1 in Cytoplasm, S_0_m1_0 in Cytoplasm, S_0_m1_1 in Cytoplasm;
-  substanceOnly species S_0_0_m1 in Cytoplasm, S_0_0_0 in Cytoplasm, S_0_0_1 in Cytoplasm;
-  substanceOnly species S_0_1_m1 in Cytoplasm, S_0_1_0 in Cytoplasm, S_0_1_1 in Cytoplasm;
-  substanceOnly species S_0_2_m1 in Cytoplasm, S_0_2_0 in Cytoplasm, S_0_2_1 in Cytoplasm;
-  substanceOnly species S_1_m1_m1 in Cytoplasm, S_1_m1_0 in Cytoplasm, S_1_m1_1 in Cytoplasm;
-  substanceOnly species S_1_0_m1 in Cytoplasm, S_1_0_0 in Cytoplasm, S_1_0_1 in Cytoplasm;
-  substanceOnly species S_1_1_m1 in Cytoplasm, S_1_1_0 in Cytoplasm, S_1_1_1 in Cytoplasm;
-  substanceOnly species S_1_2_m1 in Cytoplasm, S_1_2_0 in Cytoplasm, S_1_2_1 in Cytoplasm;
-  substanceOnly species S_2_m1_m1 in Cytoplasm, S_2_m1_0 in Cytoplasm, S_2_m1_1 in Cytoplasm;
-  substanceOnly species S_2_0_m1 in Cytoplasm, S_2_0_0 in Cytoplasm, S_2_0_1 in Cytoplasm;
-  substanceOnly species S_2_1_m1 in Cytoplasm, S_2_1_0 in Cytoplasm, S_2_1_1 in Cytoplasm;
-  substanceOnly species S_2_2_m1 in Cytoplasm, S_2_2_0 in Cytoplasm, S_2_2_1 in Cytoplasm;
-  substanceOnly species S_RAFK_m1_m1_0 in Cytoplasm, S_RAFK_m1_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_m1_1_0 in Cytoplasm, S_RAFK_m1_2_0 in Cytoplasm;
-  substanceOnly species S_RAFK_0_m1_0 in Cytoplasm, S_RAFK_0_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_0_1_0 in Cytoplasm, S_RAFK_0_2_0 in Cytoplasm;
-  substanceOnly species S_RAFK_1_m1_0 in Cytoplasm, S_RAFK_1_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_1_1_0 in Cytoplasm, S_RAFK_1_2_0 in Cytoplasm;
-  substanceOnly species S_RAFK_2_m1_0 in Cytoplasm, S_RAFK_2_0_0 in Cytoplasm;
-  substanceOnly species S_RAFK_2_1_0 in Cytoplasm, S_RAFK_2_2_0 in Cytoplasm;
-
-  // Reactions:
-  Reaction1: RAFK + K_3_0 => K_RAFK_3_0; Reaction1_a1*RAFK*K_3_0;
-  Reaction2: K_RAFK_3_0 => RAFK + K_3_0; Reaction2_d1*K_RAFK_3_0;
-  Reaction3: K_RAFK_3_0 => RAFK + K_3_1; Reaction3_k1*K_RAFK_3_0;
-  Reaction4: RAFP + K_3_1 => K_RAFP_3_1; Reaction4_a2*RAFP*K_3_1;
-  Reaction5: K_RAFP_3_1 => RAFP + K_3_1; Reaction5_d2*K_RAFP_3_1;
-  Reaction6: K_RAFP_3_1 => RAFP + K_3_0; Reaction6_k2*K_RAFP_3_1;
-  Reaction7: K_2_0 + K_3_1 => K_K_2_0_3_1; Reaction7_a3*K_2_0*K_3_1;
-  Reaction8: K_K_2_0_3_1 => K_2_0 + K_3_1; Reaction8_d3*K_K_2_0_3_1;
-  Reaction9: K_K_2_0_3_1 => K_2_1 + K_3_1; Reaction9_k3*K_K_2_0_3_1;
-  Reaction10: MEKP + K_2_1 => K_MEKP_2_1; Reaction10_a4*MEKP*K_2_1;
-  Reaction11: K_MEKP_2_1 => MEKP + K_2_1; Reaction11_d4*K_MEKP_2_1;
-  Reaction12: K_MEKP_2_1 => MEKP + K_2_0; Reaction12_k4*K_MEKP_2_1;
-  Reaction13: K_2_1 + K_3_1 => K_K_2_1_3_1; Reaction13_a5*K_2_1*K_3_1;
-  Reaction14: K_K_2_1_3_1 => K_2_1 + K_3_1; Reaction14_d5*K_K_2_1_3_1;
-  Reaction15: K_K_2_1_3_1 => K_2_2 + K_3_1; Reaction15_k5*K_K_2_1_3_1;
-  Reaction16: MEKP + K_2_2 => K_MEKP_2_2; Reaction16_a6*MEKP*K_2_2;
-  Reaction17: K_MEKP_2_2 => MEKP + K_2_2; Reaction17_d6*K_MEKP_2_2;
-  Reaction18: K_MEKP_2_2 => MEKP + K_2_1; Reaction18_k6*K_MEKP_2_2;
-  Reaction19: K_1_0 + K_2_2 => K_K_1_0_2_2; Reaction19_a7*K_1_0*K_2_2;
-  Reaction20: K_K_1_0_2_2 => K_1_0 + K_2_2; Reaction20_d7*K_K_1_0_2_2;
-  Reaction21: K_K_1_0_2_2 => K_1_1 + K_2_2; Reaction21_k7*K_K_1_0_2_2;
-  Reaction22: MAPKP + K_1_1 => K_MAPKP_1_1; Reaction22_a8*MAPKP*K_1_1;
-  Reaction23: K_MAPKP_1_1 => MAPKP + K_1_1; Reaction23_d8*K_MAPKP_1_1;
-  Reaction24: K_MAPKP_1_1 => MAPKP + K_1_0; Reaction24_k8*K_MAPKP_1_1;
-  Reaction25: K_1_1 + K_2_2 => K_K_1_1_2_2; Reaction25_a9*K_1_1*K_2_2;
-  Reaction26: K_K_1_1_2_2 => K_1_1 + K_2_2; Reaction26_d9*K_K_1_1_2_2;
-  Reaction27: K_K_1_1_2_2 => K_1_2 + K_2_2; Reaction27_k9*K_K_1_1_2_2;
-  Reaction28: MAPKP + K_1_2 => K_MAPKP_1_2; Reaction28_a10*MAPKP*K_1_2;
-  Reaction29: K_MAPKP_1_2 => MAPKP + K_1_2; Reaction29_d10*K_MAPKP_1_2;
-  Reaction30: K_MAPKP_1_2 => MAPKP + K_1_1; Reaction30_k10*K_MAPKP_1_2;
-  Reaction31: K_1_0 + S_m1_m1_m1 => S_0_m1_m1; Reaction31_kon*K_1_0*S_m1_m1_m1;
-  Reaction32: S_0_m1_m1 => K_1_0 + S_m1_m1_m1; Reaction32_koff*S_0_m1_m1;
-  Reaction33: K_1_0 + S_m1_m1_0 => S_0_m1_0; Reaction33_kon*K_1_0*S_m1_m1_0;
-  Reaction34: S_0_m1_0 => K_1_0 + S_m1_m1_0; Reaction34_koff*S_0_m1_0;
-  Reaction35: K_1_0 + S_m1_m1_1 => S_0_m1_1; Reaction35_kon*K_1_0*S_m1_m1_1;
-  Reaction36: S_0_m1_1 => K_1_0 + S_m1_m1_1; Reaction36_koff*S_0_m1_1;
-  Reaction37: K_1_0 + S_m1_0_m1 => S_0_0_m1; Reaction37_kon*K_1_0*S_m1_0_m1;
-  Reaction38: S_0_0_m1 => K_1_0 + S_m1_0_m1; Reaction38_koff*S_0_0_m1;
-  Reaction39: K_1_0 + S_m1_0_0 => S_0_0_0; Reaction39_kon*K_1_0*S_m1_0_0;
-  Reaction40: S_0_0_0 => K_1_0 + S_m1_0_0; Reaction40_koff*S_0_0_0;
-  Reaction41: K_1_0 + S_m1_0_1 => S_0_0_1; Reaction41_kon*K_1_0*S_m1_0_1;
-  Reaction42: S_0_0_1 => K_1_0 + S_m1_0_1; Reaction42_koff*S_0_0_1;
-  Reaction43: K_1_0 + S_m1_1_m1 => S_0_1_m1; Reaction43_kon*K_1_0*S_m1_1_m1;
-  Reaction44: S_0_1_m1 => K_1_0 + S_m1_1_m1; Reaction44_koff*S_0_1_m1;
-  Reaction45: K_1_0 + S_m1_1_0 => S_0_1_0; Reaction45_kon*K_1_0*S_m1_1_0;
-  Reaction46: S_0_1_0 => K_1_0 + S_m1_1_0; Reaction46_koff*S_0_1_0;
-  Reaction47: K_1_0 + S_m1_1_1 => S_0_1_1; Reaction47_kon*K_1_0*S_m1_1_1;
-  Reaction48: S_0_1_1 => K_1_0 + S_m1_1_1; Reaction48_koff*S_0_1_1;
-  Reaction49: K_1_0 + S_m1_2_m1 => S_0_2_m1; Reaction49_kon*K_1_0*S_m1_2_m1;
-  Reaction50: S_0_2_m1 => K_1_0 + S_m1_2_m1; Reaction50_koff*S_0_2_m1;
-  Reaction51: K_1_0 + S_m1_2_0 => S_0_2_0; Reaction51_kon*K_1_0*S_m1_2_0;
-  Reaction52: S_0_2_0 => K_1_0 + S_m1_2_0; Reaction52_koff*S_0_2_0;
-  Reaction53: K_1_0 + S_m1_2_1 => S_0_2_1; Reaction53_kon*K_1_0*S_m1_2_1;
-  Reaction54: S_0_2_1 => K_1_0 + S_m1_2_1; Reaction54_koff*S_0_2_1;
-  Reaction55: K_1_1 + S_m1_m1_m1 => S_1_m1_m1; Reaction55_kpon*K_1_1*S_m1_m1_m1;
-  Reaction56: S_1_m1_m1 => K_1_1 + S_m1_m1_m1; Reaction56_kpoff*S_1_m1_m1;
-  Reaction57: K_1_1 + S_m1_m1_0 => S_1_m1_0; Reaction57_kpon*K_1_1*S_m1_m1_0;
-  Reaction58: S_1_m1_0 => K_1_1 + S_m1_m1_0; Reaction58_kpoff*S_1_m1_0;
-  Reaction59: K_1_1 + S_m1_m1_1 => S_1_m1_1; Reaction59_kpon*K_1_1*S_m1_m1_1;
-  Reaction60: S_1_m1_1 => K_1_1 + S_m1_m1_1; Reaction60_kpoff*S_1_m1_1;
-  Reaction61: K_1_1 + S_m1_0_m1 => S_1_0_m1; Reaction61_kpon*K_1_1*S_m1_0_m1;
-  Reaction62: S_1_0_m1 => K_1_1 + S_m1_0_m1; Reaction62_kpoff*S_1_0_m1;
-  Reaction63: K_1_1 + S_m1_0_0 => S_1_0_0; Reaction63_kpon*K_1_1*S_m1_0_0;
-  Reaction64: S_1_0_0 => K_1_1 + S_m1_0_0; Reaction64_kpoff*S_1_0_0;
-  Reaction65: K_1_1 + S_m1_0_1 => S_1_0_1; Reaction65_kpon*K_1_1*S_m1_0_1;
-  Reaction66: S_1_0_1 => K_1_1 + S_m1_0_1; Reaction66_kpoff*S_1_0_1;
-  Reaction67: K_1_1 + S_m1_1_m1 => S_1_1_m1; Reaction67_kpon*K_1_1*S_m1_1_m1;
-  Reaction68: S_1_1_m1 => K_1_1 + S_m1_1_m1; Reaction68_kpoff*S_1_1_m1;
-  Reaction69: K_1_1 + S_m1_1_0 => S_1_1_0; Reaction69_kpon*K_1_1*S_m1_1_0;
-  Reaction70: S_1_1_0 => K_1_1 + S_m1_1_0; Reaction70_kpoff*S_1_1_0;
-  Reaction71: K_1_1 + S_m1_1_1 => S_1_1_1; Reaction71_kpon*K_1_1*S_m1_1_1;
-  Reaction72: S_1_1_1 => K_1_1 + S_m1_1_1; Reaction72_kpoff*S_1_1_1;
-  Reaction73: K_1_1 + S_m1_2_m1 => S_1_2_m1; Reaction73_kpon*K_1_1*S_m1_2_m1;
-  Reaction74: S_1_2_m1 => K_1_1 + S_m1_2_m1; Reaction74_kpoff*S_1_2_m1;
-  Reaction75: K_1_1 + S_m1_2_0 => S_1_2_0; Reaction75_kpon*K_1_1*S_m1_2_0;
-  Reaction76: S_1_2_0 => K_1_1 + S_m1_2_0; Reaction76_kpoff*S_1_2_0;
-  Reaction77: K_1_1 + S_m1_2_1 => S_1_2_1; Reaction77_kpon*K_1_1*S_m1_2_1;
-  Reaction78: S_1_2_1 => K_1_1 + S_m1_2_1; Reaction78_kpoff*S_1_2_1;
-  Reaction79: K_1_2 + S_m1_m1_m1 => S_2_m1_m1; Reaction79_kpon*K_1_2*S_m1_m1_m1;
-  Reaction80: S_2_m1_m1 => K_1_2 + S_m1_m1_m1; Reaction80_kpoff*S_2_m1_m1;
-  Reaction81: K_1_2 + S_m1_m1_0 => S_2_m1_0; Reaction81_kpon*K_1_2*S_m1_m1_0;
-  Reaction82: S_2_m1_0 => K_1_2 + S_m1_m1_0; Reaction82_kpoff*S_2_m1_0;
-  Reaction83: K_1_2 + S_m1_m1_1 => S_2_m1_1; Reaction83_kpon*K_1_2*S_m1_m1_1;
-  Reaction84: S_2_m1_1 => K_1_2 + S_m1_m1_1; Reaction84_kpoff*S_2_m1_1;
-  Reaction85: K_1_2 + S_m1_0_m1 => S_2_0_m1; Reaction85_kpon*K_1_2*S_m1_0_m1;
-  Reaction86: S_2_0_m1 => K_1_2 + S_m1_0_m1; Reaction86_kpoff*S_2_0_m1;
-  Reaction87: K_1_2 + S_m1_0_0 => S_2_0_0; Reaction87_kpon*K_1_2*S_m1_0_0;
-  Reaction88: S_2_0_0 => K_1_2 + S_m1_0_0; Reaction88_kpoff*S_2_0_0;
-  Reaction89: K_1_2 + S_m1_0_1 => S_2_0_1; Reaction89_kpon*K_1_2*S_m1_0_1;
-  Reaction90: S_2_0_1 => K_1_2 + S_m1_0_1; Reaction90_kpoff*S_2_0_1;
-  Reaction91: K_1_2 + S_m1_1_m1 => S_2_1_m1; Reaction91_kpon*K_1_2*S_m1_1_m1;
-  Reaction92: S_2_1_m1 => K_1_2 + S_m1_1_m1; Reaction92_kpoff*S_2_1_m1;
-  Reaction93: K_1_2 + S_m1_1_0 => S_2_1_0; Reaction93_kpon*K_1_2*S_m1_1_0;
-  Reaction94: S_2_1_0 => K_1_2 + S_m1_1_0; Reaction94_kpoff*S_2_1_0;
-  Reaction95: K_1_2 + S_m1_1_1 => S_2_1_1; Reaction95_kpon*K_1_2*S_m1_1_1;
-  Reaction96: S_2_1_1 => K_1_2 + S_m1_1_1; Reaction96_kpoff*S_2_1_1;
-  Reaction97: K_1_2 + S_m1_2_m1 => S_2_2_m1; Reaction97_kpon*K_1_2*S_m1_2_m1;
-  Reaction98: S_2_2_m1 => K_1_2 + S_m1_2_m1; Reaction98_kpoff*S_2_2_m1;
-  Reaction99: K_1_2 + S_m1_2_0 => S_2_2_0; Reaction99_kpon*K_1_2*S_m1_2_0;
-  Reaction100: S_2_2_0 => K_1_2 + S_m1_2_0; Reaction100_kpoff*S_2_2_0;
-  Reaction101: K_1_2 + S_m1_2_1 => S_2_2_1; Reaction101_kpon*K_1_2*S_m1_2_1;
-  Reaction102: S_2_2_1 => K_1_2 + S_m1_2_1; Reaction102_kpoff*S_2_2_1;
-  Reaction103: K_2_0 + S_m1_m1_m1 => S_m1_0_m1; Reaction103_kon*K_2_0*S_m1_m1_m1;
-  Reaction104: S_m1_0_m1 => K_2_0 + S_m1_m1_m1; Reaction104_koff*S_m1_0_m1;
-  Reaction105: K_2_0 + S_m1_m1_0 => S_m1_0_0; Reaction105_kon*K_2_0*S_m1_m1_0;
-  Reaction106: S_m1_0_0 => K_2_0 + S_m1_m1_0; Reaction106_koff*S_m1_0_0;
-  Reaction107: K_2_0 + S_m1_m1_1 => S_m1_0_1; Reaction107_kon*K_2_0*S_m1_m1_1;
-  Reaction108: S_m1_0_1 => K_2_0 + S_m1_m1_1; Reaction108_koff*S_m1_0_1;
-  Reaction109: K_2_1 + S_m1_m1_m1 => S_m1_1_m1; Reaction109_kpon*K_2_1*S_m1_m1_m1;
-  Reaction110: S_m1_1_m1 => K_2_1 + S_m1_m1_m1; Reaction110_kpoff*S_m1_1_m1;
-  Reaction111: K_2_1 + S_m1_m1_0 => S_m1_1_0; Reaction111_kpon*K_2_1*S_m1_m1_0;
-  Reaction112: S_m1_1_0 => K_2_1 + S_m1_m1_0; Reaction112_kpoff*S_m1_1_0;
-  Reaction113: K_2_1 + S_m1_m1_1 => S_m1_1_1; Reaction113_kpon*K_2_1*S_m1_m1_1;
-  Reaction114: S_m1_1_1 => K_2_1 + S_m1_m1_1; Reaction114_kpoff*S_m1_1_1;
-  Reaction115: K_2_2 + S_m1_m1_m1 => S_m1_2_m1; Reaction115_kpon*K_2_2*S_m1_m1_m1;
-  Reaction116: S_m1_2_m1 => K_2_2 + S_m1_m1_m1; Reaction116_kpoff*S_m1_2_m1;
-  Reaction117: K_2_2 + S_m1_m1_0 => S_m1_2_0; Reaction117_kpon*K_2_2*S_m1_m1_0;
-  Reaction118: S_m1_2_0 => K_2_2 + S_m1_m1_0; Reaction118_kpoff*S_m1_2_0;
-  Reaction119: K_2_2 + S_m1_m1_1 => S_m1_2_1; Reaction119_kpon*K_2_2*S_m1_m1_1;
-  Reaction120: S_m1_2_1 => K_2_2 + S_m1_m1_1; Reaction120_kpoff*S_m1_2_1;
-  Reaction121: K_2_0 + S_0_m1_m1 => S_0_0_m1; Reaction121_kon*K_2_0*S_0_m1_m1;
-  Reaction122: S_0_0_m1 => K_2_0 + S_0_m1_m1; Reaction122_koff*S_0_0_m1;
-  Reaction123: K_2_0 + S_0_m1_0 => S_0_0_0; Reaction123_kon*K_2_0*S_0_m1_0;
-  Reaction124: S_0_0_0 => K_2_0 + S_0_m1_0; Reaction124_koff*S_0_0_0;
-  Reaction125: K_2_0 + S_0_m1_1 => S_0_0_1; Reaction125_kon*K_2_0*S_0_m1_1;
-  Reaction126: S_0_0_1 => K_2_0 + S_0_m1_1; Reaction126_koff*S_0_0_1;
-  Reaction127: K_2_1 + S_0_m1_m1 => S_0_1_m1; Reaction127_kpon*K_2_1*S_0_m1_m1;
-  Reaction128: S_0_1_m1 => K_2_1 + S_0_m1_m1; Reaction128_kpoff*S_0_1_m1;
-  Reaction129: K_2_1 + S_0_m1_0 => S_0_1_0; Reaction129_kpon*K_2_1*S_0_m1_0;
-  Reaction130: S_0_1_0 => K_2_1 + S_0_m1_0; Reaction130_kpoff*S_0_1_0;
-  Reaction131: K_2_1 + S_0_m1_1 => S_0_1_1; Reaction131_kpon*K_2_1*S_0_m1_1;
-  Reaction132: S_0_1_1 => K_2_1 + S_0_m1_1; Reaction132_kpoff*S_0_1_1;
-  Reaction133: K_2_2 + S_0_m1_m1 => S_0_2_m1; Reaction133_kpon*K_2_2*S_0_m1_m1;
-  Reaction134: S_0_2_m1 => K_2_2 + S_0_m1_m1; Reaction134_kpoff*S_0_2_m1;
-  Reaction135: K_2_2 + S_0_m1_0 => S_0_2_0; Reaction135_kpon*K_2_2*S_0_m1_0;
-  Reaction136: S_0_2_0 => K_2_2 + S_0_m1_0; Reaction136_kpoff*S_0_2_0;
-  Reaction137: K_2_2 + S_0_m1_1 => S_0_2_1; Reaction137_kpon*K_2_2*S_0_m1_1;
-  Reaction138: S_0_2_1 => K_2_2 + S_0_m1_1; Reaction138_kpoff*S_0_2_1;
-  Reaction139: K_2_0 + S_1_m1_m1 => S_1_0_m1; Reaction139_kon*K_2_0*S_1_m1_m1;
-  Reaction140: S_1_0_m1 => K_2_0 + S_1_m1_m1; Reaction140_koff*S_1_0_m1;
-  Reaction141: K_2_0 + S_1_m1_0 => S_1_0_0; Reaction141_kon*K_2_0*S_1_m1_0;
-  Reaction142: S_1_0_0 => K_2_0 + S_1_m1_0; Reaction142_koff*S_1_0_0;
-  Reaction143: K_2_0 + S_1_m1_1 => S_1_0_1; Reaction143_kon*K_2_0*S_1_m1_1;
-  Reaction144: S_1_0_1 => K_2_0 + S_1_m1_1; Reaction144_koff*S_1_0_1;
-  Reaction145: K_2_1 + S_1_m1_m1 => S_1_1_m1; Reaction145_kpon*K_2_1*S_1_m1_m1;
-  Reaction146: S_1_1_m1 => K_2_1 + S_1_m1_m1; Reaction146_kpoff*S_1_1_m1;
-  Reaction147: K_2_1 + S_1_m1_0 => S_1_1_0; Reaction147_kpon*K_2_1*S_1_m1_0;
-  Reaction148: S_1_1_0 => K_2_1 + S_1_m1_0; Reaction148_kpoff*S_1_1_0;
-  Reaction149: K_2_1 + S_1_m1_1 => S_1_1_1; Reaction149_kpon*K_2_1*S_1_m1_1;
-  Reaction150: S_1_1_1 => K_2_1 + S_1_m1_1; Reaction150_kpoff*S_1_1_1;
-  Reaction151: K_2_2 + S_1_m1_m1 => S_1_2_m1; Reaction151_kpon*K_2_2*S_1_m1_m1;
-  Reaction152: S_1_2_m1 => K_2_2 + S_1_m1_m1; Reaction152_kpoff*S_1_2_m1;
-  Reaction153: K_2_2 + S_1_m1_0 => S_1_2_0; Reaction153_kpon*K_2_2*S_1_m1_0;
-  Reaction154: S_1_2_0 => K_2_2 + S_1_m1_0; Reaction154_kpoff*S_1_2_0;
-  Reaction155: K_2_2 + S_1_m1_1 => S_1_2_1; Reaction155_kpon*K_2_2*S_1_m1_1;
-  Reaction156: S_1_2_1 => K_2_2 + S_1_m1_1; Reaction156_kpoff*S_1_2_1;
-  Reaction157: K_2_0 + S_2_m1_m1 => S_2_0_m1; Reaction157_kon*K_2_0*S_2_m1_m1;
-  Reaction158: S_2_0_m1 => K_2_0 + S_2_m1_m1; Reaction158_koff*S_2_0_m1;
-  Reaction159: K_2_0 + S_2_m1_0 => S_2_0_0; Reaction159_kon*K_2_0*S_2_m1_0;
-  Reaction160: S_2_0_0 => K_2_0 + S_2_m1_0; Reaction160_koff*S_2_0_0;
-  Reaction161: K_2_0 + S_2_m1_1 => S_2_0_1; Reaction161_kon*K_2_0*S_2_m1_1;
-  Reaction162: S_2_0_1 => K_2_0 + S_2_m1_1; Reaction162_koff*S_2_0_1;
-  Reaction163: K_2_1 + S_2_m1_m1 => S_2_1_m1; Reaction163_kpon*K_2_1*S_2_m1_m1;
-  Reaction164: S_2_1_m1 => K_2_1 + S_2_m1_m1; Reaction164_kpoff*S_2_1_m1;
-  Reaction165: K_2_1 + S_2_m1_0 => S_2_1_0; Reaction165_kpon*K_2_1*S_2_m1_0;
-  Reaction166: S_2_1_0 => K_2_1 + S_2_m1_0; Reaction166_kpoff*S_2_1_0;
-  Reaction167: K_2_1 + S_2_m1_1 => S_2_1_1; Reaction167_kpon*K_2_1*S_2_m1_1;
-  Reaction168: S_2_1_1 => K_2_1 + S_2_m1_1; Reaction168_kpoff*S_2_1_1;
-  Reaction169: K_2_2 + S_2_m1_m1 => S_2_2_m1; Reaction169_kpon*K_2_2*S_2_m1_m1;
-  Reaction170: S_2_2_m1 => K_2_2 + S_2_m1_m1; Reaction170_kpoff*S_2_2_m1;
-  Reaction171: K_2_2 + S_2_m1_0 => S_2_2_0; Reaction171_kpon*K_2_2*S_2_m1_0;
-  Reaction172: S_2_2_0 => K_2_2 + S_2_m1_0; Reaction172_kpoff*S_2_2_0;
-  Reaction173: K_2_2 + S_2_m1_1 => S_2_2_1; Reaction173_kpon*K_2_2*S_2_m1_1;
-  Reaction174: S_2_2_1 => K_2_2 + S_2_m1_1; Reaction174_kpoff*S_2_2_1;
-  Reaction175: K_3_0 + S_m1_m1_m1 => S_m1_m1_0; Reaction175_kon*K_3_0*S_m1_m1_m1;
-  Reaction176: S_m1_m1_0 => K_3_0 + S_m1_m1_m1; Reaction176_koff*S_m1_m1_0;
-  Reaction177: K_3_1 + S_m1_m1_m1 => S_m1_m1_1; Reaction177_kpon*K_3_1*S_m1_m1_m1;
-  Reaction178: S_m1_m1_1 => K_3_1 + S_m1_m1_m1; Reaction178_kpoff*S_m1_m1_1;
-  Reaction179: K_3_0 + S_m1_0_m1 => S_m1_0_0; Reaction179_kon*K_3_0*S_m1_0_m1;
-  Reaction180: S_m1_0_0 => K_3_0 + S_m1_0_m1; Reaction180_koff*S_m1_0_0;
-  Reaction181: K_3_1 + S_m1_0_m1 => S_m1_0_1; Reaction181_kpon*K_3_1*S_m1_0_m1;
-  Reaction182: S_m1_0_1 => K_3_1 + S_m1_0_m1; Reaction182_kpoff*S_m1_0_1;
-  Reaction183: K_3_0 + S_m1_1_m1 => S_m1_1_0; Reaction183_kon*K_3_0*S_m1_1_m1;
-  Reaction184: S_m1_1_0 => K_3_0 + S_m1_1_m1; Reaction184_koff*S_m1_1_0;
-  Reaction185: K_3_1 + S_m1_1_m1 => S_m1_1_1; Reaction185_kpon*K_3_1*S_m1_1_m1;
-  Reaction186: S_m1_1_1 => K_3_1 + S_m1_1_m1; Reaction186_kpoff*S_m1_1_1;
-  Reaction187: K_3_0 + S_m1_2_m1 => S_m1_2_0; Reaction187_kon*K_3_0*S_m1_2_m1;
-  Reaction188: S_m1_2_0 => K_3_0 + S_m1_2_m1; Reaction188_koff*S_m1_2_0;
-  Reaction189: K_3_1 + S_m1_2_m1 => S_m1_2_1; Reaction189_kpon*K_3_1*S_m1_2_m1;
-  Reaction190: S_m1_2_1 => K_3_1 + S_m1_2_m1; Reaction190_kpoff*S_m1_2_1;
-  Reaction191: K_3_0 + S_0_m1_m1 => S_0_m1_0; Reaction191_kon*K_3_0*S_0_m1_m1;
-  Reaction192: S_0_m1_0 => K_3_0 + S_0_m1_m1; Reaction192_koff*S_0_m1_0;
-  Reaction193: K_3_1 + S_0_m1_m1 => S_0_m1_1; Reaction193_kpon*K_3_1*S_0_m1_m1;
-  Reaction194: S_0_m1_1 => K_3_1 + S_0_m1_m1; Reaction194_kpoff*S_0_m1_1;
-  Reaction195: K_3_0 + S_0_0_m1 => S_0_0_0; Reaction195_kon*K_3_0*S_0_0_m1;
-  Reaction196: S_0_0_0 => K_3_0 + S_0_0_m1; Reaction196_koff*S_0_0_0;
-  Reaction197: K_3_1 + S_0_0_m1 => S_0_0_1; Reaction197_kpon*K_3_1*S_0_0_m1;
-  Reaction198: S_0_0_1 => K_3_1 + S_0_0_m1; Reaction198_kpoff*S_0_0_1;
-  Reaction199: K_3_0 + S_0_1_m1 => S_0_1_0; Reaction199_kon*K_3_0*S_0_1_m1;
-  Reaction200: S_0_1_0 => K_3_0 + S_0_1_m1; Reaction200_koff*S_0_1_0;
-  Reaction201: K_3_1 + S_0_1_m1 => S_0_1_1; Reaction201_kpon*K_3_1*S_0_1_m1;
-  Reaction202: S_0_1_1 => K_3_1 + S_0_1_m1; Reaction202_kpoff*S_0_1_1;
-  Reaction203: K_3_0 + S_0_2_m1 => S_0_2_0; Reaction203_kon*K_3_0*S_0_2_m1;
-  Reaction204: S_0_2_0 => K_3_0 + S_0_2_m1; Reaction204_koff*S_0_2_0;
-  Reaction205: K_3_1 + S_0_2_m1 => S_0_2_1; Reaction205_kpon*K_3_1*S_0_2_m1;
-  Reaction206: S_0_2_1 => K_3_1 + S_0_2_m1; Reaction206_kpoff*S_0_2_1;
-  Reaction207: K_3_0 + S_1_m1_m1 => S_1_m1_0; Reaction207_kon*K_3_0*S_1_m1_m1;
-  Reaction208: S_1_m1_0 => K_3_0 + S_1_m1_m1; Reaction208_koff*S_1_m1_0;
-  Reaction209: K_3_1 + S_1_m1_m1 => S_1_m1_1; Reaction209_kpon*K_3_1*S_1_m1_m1;
-  Reaction210: S_1_m1_1 => K_3_1 + S_1_m1_m1; Reaction210_kpoff*S_1_m1_1;
-  Reaction211: K_3_0 + S_1_0_m1 => S_1_0_0; Reaction211_kon*K_3_0*S_1_0_m1;
-  Reaction212: S_1_0_0 => K_3_0 + S_1_0_m1; Reaction212_koff*S_1_0_0;
-  Reaction213: K_3_1 + S_1_0_m1 => S_1_0_1; Reaction213_kpon*K_3_1*S_1_0_m1;
-  Reaction214: S_1_0_1 => K_3_1 + S_1_0_m1; Reaction214_kpoff*S_1_0_1;
-  Reaction215: K_3_0 + S_1_1_m1 => S_1_1_0; Reaction215_kon*K_3_0*S_1_1_m1;
-  Reaction216: S_1_1_0 => K_3_0 + S_1_1_m1; Reaction216_koff*S_1_1_0;
-  Reaction217: K_3_1 + S_1_1_m1 => S_1_1_1; Reaction217_kpon*K_3_1*S_1_1_m1;
-  Reaction218: S_1_1_1 => K_3_1 + S_1_1_m1; Reaction218_kpoff*S_1_1_1;
-  Reaction219: K_3_0 + S_1_2_m1 => S_1_2_0; Reaction219_kon*K_3_0*S_1_2_m1;
-  Reaction220: S_1_2_0 => K_3_0 + S_1_2_m1; Reaction220_koff*S_1_2_0;
-  Reaction221: K_3_1 + S_1_2_m1 => S_1_2_1; Reaction221_kpon*K_3_1*S_1_2_m1;
-  Reaction222: S_1_2_1 => K_3_1 + S_1_2_m1; Reaction222_kpoff*S_1_2_1;
-  Reaction223: K_3_0 + S_2_m1_m1 => S_2_m1_0; Reaction223_kon*K_3_0*S_2_m1_m1;
-  Reaction224: S_2_m1_0 => K_3_0 + S_2_m1_m1; Reaction224_koff*S_2_m1_0;
-  Reaction225: K_3_1 + S_2_m1_m1 => S_2_m1_1; Reaction225_kpon*K_3_1*S_2_m1_m1;
-  Reaction226: S_2_m1_1 => K_3_1 + S_2_m1_m1; Reaction226_kpoff*S_2_m1_1;
-  Reaction227: K_3_0 + S_2_0_m1 => S_2_0_0; Reaction227_kon*K_3_0*S_2_0_m1;
-  Reaction228: S_2_0_0 => K_3_0 + S_2_0_m1; Reaction228_koff*S_2_0_0;
-  Reaction229: K_3_1 + S_2_0_m1 => S_2_0_1; Reaction229_kpon*K_3_1*S_2_0_m1;
-  Reaction230: S_2_0_1 => K_3_1 + S_2_0_m1; Reaction230_kpoff*S_2_0_1;
-  Reaction231: K_3_0 + S_2_1_m1 => S_2_1_0; Reaction231_kon*K_3_0*S_2_1_m1;
-  Reaction232: S_2_1_0 => K_3_0 + S_2_1_m1; Reaction232_koff*S_2_1_0;
-  Reaction233: K_3_1 + S_2_1_m1 => S_2_1_1; Reaction233_kpon*K_3_1*S_2_1_m1;
-  Reaction234: S_2_1_1 => K_3_1 + S_2_1_m1; Reaction234_kpoff*S_2_1_1;
-  Reaction235: K_3_0 + S_2_2_m1 => S_2_2_0; Reaction235_kon*K_3_0*S_2_2_m1;
-  Reaction236: S_2_2_0 => K_3_0 + S_2_2_m1; Reaction236_koff*S_2_2_0;
-  Reaction237: K_3_1 + S_2_2_m1 => S_2_2_1; Reaction237_kpon*K_3_1*S_2_2_m1;
-  Reaction238: S_2_2_1 => K_3_1 + S_2_2_m1; Reaction238_kpoff*S_2_2_1;
-  Reaction239: S_0_2_m1 => S_1_2_m1; Reaction239_k7*S_0_2_m1;
-  Reaction240: S_0_2_0 => S_1_2_0; Reaction240_k7*S_0_2_0;
-  Reaction241: S_0_2_1 => S_1_2_1; Reaction241_k7*S_0_2_1;
-  Reaction242: S_1_2_m1 => S_2_2_m1; Reaction242_k9a*S_1_2_m1;
-  Reaction243: S_1_2_0 => S_2_2_0; Reaction243_k9a*S_1_2_0;
-  Reaction244: S_1_2_1 => S_2_2_1; Reaction244_k9a*S_1_2_1;
-  Reaction245: S_m1_0_1 => S_m1_1_1; Reaction245_k3*S_m1_0_1;
-  Reaction246: S_m1_1_1 => S_m1_2_1; Reaction246_k5a*S_m1_1_1;
-  Reaction247: S_0_0_1 => S_0_1_1; Reaction247_k3*S_0_0_1;
-  Reaction248: S_0_1_1 => S_0_2_1; Reaction248_k5a*S_0_1_1;
-  Reaction249: S_1_0_1 => S_1_1_1; Reaction249_k3*S_1_0_1;
-  Reaction250: S_1_1_1 => S_1_2_1; Reaction250_k5a*S_1_1_1;
-  Reaction251: S_2_0_1 => S_2_1_1; Reaction251_k3*S_2_0_1;
-  Reaction252: S_2_1_1 => S_2_2_1; Reaction252_k5a*S_2_1_1;
-  Reaction253: RAFK + S_m1_m1_0 => S_RAFK_m1_m1_0; Reaction253_k1a*RAFK*S_m1_m1_0;
-  Reaction254: S_RAFK_m1_m1_0 => RAFK + S_m1_m1_0; Reaction254_d1a*S_RAFK_m1_m1_0;
-  Reaction255: S_RAFK_m1_m1_0 => RAFK + S_m1_m1_1; Reaction255_k1*S_RAFK_m1_m1_0;
-  Reaction256: RAFK + S_m1_0_0 => S_RAFK_m1_0_0; Reaction256_k1a*RAFK*S_m1_0_0;
-  Reaction257: S_RAFK_m1_0_0 => RAFK + S_m1_0_0; Reaction257_d1a*S_RAFK_m1_0_0;
-  Reaction258: S_RAFK_m1_0_0 => RAFK + S_m1_0_1; Reaction258_k1*S_RAFK_m1_0_0;
-  Reaction259: RAFK + S_m1_1_0 => S_RAFK_m1_1_0; Reaction259_k1a*RAFK*S_m1_1_0;
-  Reaction260: S_RAFK_m1_1_0 => RAFK + S_m1_1_0; Reaction260_d1a*S_RAFK_m1_1_0;
-  Reaction261: S_RAFK_m1_1_0 => RAFK + S_m1_1_1; Reaction261_k1*S_RAFK_m1_1_0;
-  Reaction262: RAFK + S_m1_2_0 => S_RAFK_m1_2_0; Reaction262_k1a*RAFK*S_m1_2_0;
-  Reaction263: S_RAFK_m1_2_0 => RAFK + S_m1_2_0; Reaction263_d1a*S_RAFK_m1_2_0;
-  Reaction264: S_RAFK_m1_2_0 => RAFK + S_m1_2_1; Reaction264_k1*S_RAFK_m1_2_0;
-  Reaction265: RAFK + S_0_m1_0 => S_RAFK_0_m1_0; Reaction265_k1a*RAFK*S_0_m1_0;
-  Reaction266: S_RAFK_0_m1_0 => RAFK + S_0_m1_0; Reaction266_d1a*S_RAFK_0_m1_0;
-  Reaction267: S_RAFK_0_m1_0 => RAFK + S_0_m1_1; Reaction267_k1*S_RAFK_0_m1_0;
-  Reaction268: RAFK + S_0_0_0 => S_RAFK_0_0_0; Reaction268_k1a*RAFK*S_0_0_0;
-  Reaction269: S_RAFK_0_0_0 => RAFK + S_0_0_0; Reaction269_d1a*S_RAFK_0_0_0;
-  Reaction270: S_RAFK_0_0_0 => RAFK + S_0_0_1; Reaction270_k1*S_RAFK_0_0_0;
-  Reaction271: RAFK + S_0_1_0 => S_RAFK_0_1_0; Reaction271_k1a*RAFK*S_0_1_0;
-  Reaction272: S_RAFK_0_1_0 => RAFK + S_0_1_0; Reaction272_d1a*S_RAFK_0_1_0;
-  Reaction273: S_RAFK_0_1_0 => RAFK + S_0_1_1; Reaction273_k1*S_RAFK_0_1_0;
-  Reaction274: RAFK + S_0_2_0 => S_RAFK_0_2_0; Reaction274_k1a*RAFK*S_0_2_0;
-  Reaction275: S_RAFK_0_2_0 => RAFK + S_0_2_0; Reaction275_d1a*S_RAFK_0_2_0;
-  Reaction276: S_RAFK_0_2_0 => RAFK + S_0_2_1; Reaction276_k1*S_RAFK_0_2_0;
-  Reaction277: RAFK + S_1_m1_0 => S_RAFK_1_m1_0; Reaction277_k1a*RAFK*S_1_m1_0;
-  Reaction278: S_RAFK_1_m1_0 => RAFK + S_1_m1_0; Reaction278_d1a*S_RAFK_1_m1_0;
-  Reaction279: S_RAFK_1_m1_0 => RAFK + S_1_m1_1; Reaction279_k1*S_RAFK_1_m1_0;
-  Reaction280: RAFK + S_1_0_0 => S_RAFK_1_0_0; Reaction280_k1a*RAFK*S_1_0_0;
-  Reaction281: S_RAFK_1_0_0 => RAFK + S_1_0_0; Reaction281_d1a*S_RAFK_1_0_0;
-  Reaction282: S_RAFK_1_0_0 => RAFK + S_1_0_1; Reaction282_k1*S_RAFK_1_0_0;
-  Reaction283: RAFK + S_1_1_0 => S_RAFK_1_1_0; Reaction283_k1a*RAFK*S_1_1_0;
-  Reaction284: S_RAFK_1_1_0 => RAFK + S_1_1_0; Reaction284_d1a*S_RAFK_1_1_0;
-  Reaction285: S_RAFK_1_1_0 => RAFK + S_1_1_1; Reaction285_k1*S_RAFK_1_1_0;
-  Reaction286: RAFK + S_1_2_0 => S_RAFK_1_2_0; Reaction286_k1a*RAFK*S_1_2_0;
-  Reaction287: S_RAFK_1_2_0 => RAFK + S_1_2_0; Reaction287_d1a*S_RAFK_1_2_0;
-  Reaction288: S_RAFK_1_2_0 => RAFK + S_1_2_1; Reaction288_k1*S_RAFK_1_2_0;
-  Reaction289: RAFK + S_2_m1_0 => S_RAFK_2_m1_0; Reaction289_k1a*RAFK*S_2_m1_0;
-  Reaction290: S_RAFK_2_m1_0 => RAFK + S_2_m1_0; Reaction290_d1a*S_RAFK_2_m1_0;
-  Reaction291: S_RAFK_2_m1_0 => RAFK + S_2_m1_1; Reaction291_k1*S_RAFK_2_m1_0;
-  Reaction292: RAFK + S_2_0_0 => S_RAFK_2_0_0; Reaction292_k1a*RAFK*S_2_0_0;
-  Reaction293: S_RAFK_2_0_0 => RAFK + S_2_0_0; Reaction293_d1a*S_RAFK_2_0_0;
-  Reaction294: S_RAFK_2_0_0 => RAFK + S_2_0_1; Reaction294_k1*S_RAFK_2_0_0;
-  Reaction295: RAFK + S_2_1_0 => S_RAFK_2_1_0; Reaction295_k1a*RAFK*S_2_1_0;
-  Reaction296: S_RAFK_2_1_0 => RAFK + S_2_1_0; Reaction296_d1a*S_RAFK_2_1_0;
-  Reaction297: S_RAFK_2_1_0 => RAFK + S_2_1_1; Reaction297_k1*S_RAFK_2_1_0;
-  Reaction298: RAFK + S_2_2_0 => S_RAFK_2_2_0; Reaction298_k1a*RAFK*S_2_2_0;
-  Reaction299: S_RAFK_2_2_0 => RAFK + S_2_2_0; Reaction299_d1a*S_RAFK_2_2_0;
-  Reaction300: S_RAFK_2_2_0 => RAFK + S_2_2_1; Reaction300_k1*S_RAFK_2_2_0;
-
-  // Species initializations:
-  MAPKP = 0.3/Cytoplasm;
-  MEKP = 0.2/Cytoplasm;
-  RAFK = 0.1/Cytoplasm;
-  RAFP = 0.3/Cytoplasm;
-  K_1_0 = 0.4/Cytoplasm;
-  K_1_1 = 0;
-  K_1_2 = 0;
-  K_2_0 = 0.2/Cytoplasm;
-  K_2_1 = 0;
-  K_2_2 = 0;
-  K_3_0 = 0.3/Cytoplasm;
-  K_3_1 = 0;
-  K_K_1_0_2_2 = 0;
-  K_K_1_1_2_2 = 0;
-  K_K_2_0_3_1 = 0;
-  K_K_2_1_3_1 = 0;
-  K_MAPKP_1_1 = 0;
-  K_MAPKP_1_2 = 0;
-  K_MEKP_2_1 = 0;
-  K_MEKP_2_2 = 0;
-  K_RAFK_3_0 = 0;
-  K_RAFP_3_1 = 0;
-  S_m1_m1_m1 = 0.1/Cytoplasm;
-  S_m1_m1_0 = 0;
-  S_m1_m1_1 = 0;
-  S_m1_0_m1 = 0;
-  S_m1_0_0 = 0;
-  S_m1_0_1 = 0;
-  S_m1_1_m1 = 0;
-  S_m1_1_0 = 0;
-  S_m1_1_1 = 0;
-  S_m1_2_m1 = 0;
-  S_m1_2_0 = 0;
-  S_m1_2_1 = 0;
-  S_0_m1_m1 = 0;
-  S_0_m1_0 = 0;
-  S_0_m1_1 = 0;
-  S_0_0_m1 = 0;
-  S_0_0_0 = 0;
-  S_0_0_1 = 0;
-  S_0_1_m1 = 0;
-  S_0_1_0 = 0;
-  S_0_1_1 = 0;
-  S_0_2_m1 = 0;
-  S_0_2_0 = 0;
-  S_0_2_1 = 0;
-  S_1_m1_m1 = 0;
-  S_1_m1_0 = 0;
-  S_1_m1_1 = 0;
-  S_1_0_m1 = 0;
-  S_1_0_0 = 0;
-  S_1_0_1 = 0;
-  S_1_1_m1 = 0;
-  S_1_1_0 = 0;
-  S_1_1_1 = 0;
-  S_1_2_m1 = 0;
-  S_1_2_0 = 0;
-  S_1_2_1 = 0;
-  S_2_m1_m1 = 0;
-  S_2_m1_0 = 0;
-  S_2_m1_1 = 0;
-  S_2_0_m1 = 0;
-  S_2_0_0 = 0;
-  S_2_0_1 = 0;
-  S_2_1_m1 = 0;
-  S_2_1_0 = 0;
-  S_2_1_1 = 0;
-  S_2_2_m1 = 0;
-  S_2_2_0 = 0;
-  S_2_2_1 = 0;
-  S_RAFK_m1_m1_0 = 0;
-  S_RAFK_m1_0_0 = 0;
-  S_RAFK_m1_1_0 = 0;
-  S_RAFK_m1_2_0 = 0;
-  S_RAFK_0_m1_0 = 0;
-  S_RAFK_0_0_0 = 0;
-  S_RAFK_0_1_0 = 0;
-  S_RAFK_0_2_0 = 0;
-  S_RAFK_1_m1_0 = 0;
-  S_RAFK_1_0_0 = 0;
-  S_RAFK_1_1_0 = 0;
-  S_RAFK_1_2_0 = 0;
-  S_RAFK_2_m1_0 = 0;
-  S_RAFK_2_0_0 = 0;
-  S_RAFK_2_1_0 = 0;
-  S_RAFK_2_2_0 = 0;
-
-  // Compartment initializations:
-  Cytoplasm = 1;
-
-  // Variable initializations:
-  Reaction1_a1 = 1;
-  Reaction2_d1 = 0.4;
-  Reaction3_k1 = 0.1;
-  Reaction4_a2 = 0.5;
-  Reaction5_d2 = 0.5;
-  Reaction6_k2 = 0.1;
-  Reaction7_a3 = 3.3;
-  Reaction8_d3 = 0.42;
-  Reaction9_k3 = 0.1;
-  Reaction10_a4 = 10;
-  Reaction11_d4 = 0.8;
-  Reaction12_k4 = 0.1;
-  Reaction13_a5 = 3.3;
-  Reaction14_d5 = 0.4;
-  Reaction15_k5 = 0.1;
-  Reaction16_a6 = 10;
-  Reaction17_d6 = 0.8;
-  Reaction18_k6 = 0.1;
-  Reaction19_a7 = 20;
-  Reaction20_d7 = 0.6;
-  Reaction21_k7 = 0.1;
-  Reaction22_a8 = 5;
-  Reaction23_d8 = 0.4;
-  Reaction24_k8 = 0.1;
-  Reaction25_a9 = 20;
-  Reaction26_d9 = 0.6;
-  Reaction27_k9 = 0.1;
-  Reaction28_a10 = 5;
-  Reaction29_d10 = 0.4;
-  Reaction30_k10 = 0.1;
-  Reaction31_kon = 10;
-  Reaction32_koff = 0.5;
-  Reaction33_kon = 10;
-  Reaction34_koff = 0.5;
-  Reaction35_kon = 10;
-  Reaction36_koff = 0.5;
-  Reaction37_kon = 10;
-  Reaction38_koff = 0.5;
-  Reaction39_kon = 10;
-  Reaction40_koff = 0.5;
-  Reaction41_kon = 10;
-  Reaction42_koff = 0.5;
-  Reaction43_kon = 10;
-  Reaction44_koff = 0.5;
-  Reaction45_kon = 10;
-  Reaction46_koff = 0.5;
-  Reaction47_kon = 10;
-  Reaction48_koff = 0.5;
-  Reaction49_kon = 10;
-  Reaction50_koff = 0.5;
-  Reaction51_kon = 10;
-  Reaction52_koff = 0.5;
-  Reaction53_kon = 10;
-  Reaction54_koff = 0.5;
-  Reaction55_kpon = 0;
-  Reaction56_kpoff = 0.05;
-  Reaction57_kpon = 0;
-  Reaction58_kpoff = 0.05;
-  Reaction59_kpon = 0;
-  Reaction60_kpoff = 0.05;
-  Reaction61_kpon = 0;
-  Reaction62_kpoff = 0.05;
-  Reaction63_kpon = 0;
-  Reaction64_kpoff = 0.05;
-  Reaction65_kpon = 0;
-  Reaction66_kpoff = 0.05;
-  Reaction67_kpon = 0;
-  Reaction68_kpoff = 0.05;
-  Reaction69_kpon = 0;
-  Reaction70_kpoff = 0.05;
-  Reaction71_kpon = 0;
-  Reaction72_kpoff = 0.05;
-  Reaction73_kpon = 0;
-  Reaction74_kpoff = 0.05;
-  Reaction75_kpon = 0;
-  Reaction76_kpoff = 0.05;
-  Reaction77_kpon = 0;
-  Reaction78_kpoff = 0.05;
-  Reaction79_kpon = 0;
-  Reaction80_kpoff = 0.05;
-  Reaction81_kpon = 0;
-  Reaction82_kpoff = 0.05;
-  Reaction83_kpon = 0;
-  Reaction84_kpoff = 0.05;
-  Reaction85_kpon = 0;
-  Reaction86_kpoff = 0.05;
-  Reaction87_kpon = 0;
-  Reaction88_kpoff = 0.05;
-  Reaction89_kpon = 0;
-  Reaction90_kpoff = 0.05;
-  Reaction91_kpon = 0;
-  Reaction92_kpoff = 0.05;
-  Reaction93_kpon = 0;
-  Reaction94_kpoff = 0.05;
-  Reaction95_kpon = 0;
-  Reaction96_kpoff = 0.05;
-  Reaction97_kpon = 0;
-  Reaction98_kpoff = 0.05;
-  Reaction99_kpon = 0;
-  Reaction100_kpoff = 0.05;
-  Reaction101_kpon = 0;
-  Reaction102_kpoff = 0.05;
-  Reaction103_kon = 10;
-  Reaction104_koff = 0.5;
-  Reaction105_kon = 10;
-  Reaction106_koff = 0.5;
-  Reaction107_kon = 10;
-  Reaction108_koff = 0.5;
-  Reaction109_kpon = 0;
-  Reaction110_kpoff = 0.05;
-  Reaction111_kpon = 0;
-  Reaction112_kpoff = 0.05;
-  Reaction113_kpon = 0;
-  Reaction114_kpoff = 0.05;
-  Reaction115_kpon = 0;
-  Reaction116_kpoff = 0.05;
-  Reaction117_kpon = 0;
-  Reaction118_kpoff = 0.05;
-  Reaction119_kpon = 0;
-  Reaction120_kpoff = 0.05;
-  Reaction121_kon = 10;
-  Reaction122_koff = 0.5;
-  Reaction123_kon = 10;
-  Reaction124_koff = 0.5;
-  Reaction125_kon = 10;
-  Reaction126_koff = 0.5;
-  Reaction127_kpon = 0;
-  Reaction128_kpoff = 0.05;
-  Reaction129_kpon = 0;
-  Reaction130_kpoff = 0.05;
-  Reaction131_kpon = 0;
-  Reaction132_kpoff = 0.05;
-  Reaction133_kpon = 0;
-  Reaction134_kpoff = 0.05;
-  Reaction135_kpon = 0;
-  Reaction136_kpoff = 0.05;
-  Reaction137_kpon = 0;
-  Reaction138_kpoff = 0.05;
-  Reaction139_kon = 10;
-  Reaction140_koff = 0.5;
-  Reaction141_kon = 10;
-  Reaction142_koff = 0.5;
-  Reaction143_kon = 10;
-  Reaction144_koff = 0.5;
-  Reaction145_kpon = 0;
-  Reaction146_kpoff = 0.05;
-  Reaction147_kpon = 0;
-  Reaction148_kpoff = 0.05;
-  Reaction149_kpon = 0;
-  Reaction150_kpoff = 0.05;
-  Reaction151_kpon = 0;
-  Reaction152_kpoff = 0.05;
-  Reaction153_kpon = 0;
-  Reaction154_kpoff = 0.05;
-  Reaction155_kpon = 0;
-  Reaction156_kpoff = 0.05;
-  Reaction157_kon = 10;
-  Reaction158_koff = 0.5;
-  Reaction159_kon = 10;
-  Reaction160_koff = 0.5;
-  Reaction161_kon = 10;
-  Reaction162_koff = 0.5;
-  Reaction163_kpon = 0;
-  Reaction164_kpoff = 0.05;
-  Reaction165_kpon = 0;
-  Reaction166_kpoff = 0.05;
-  Reaction167_kpon = 0;
-  Reaction168_kpoff = 0.05;
-  Reaction169_kpon = 0;
-  Reaction170_kpoff = 0.05;
-  Reaction171_kpon = 0;
-  Reaction172_kpoff = 0.05;
-  Reaction173_kpon = 0;
-  Reaction174_kpoff = 0.05;
-  Reaction175_kon = 10;
-  Reaction176_koff = 0.5;
-  Reaction177_kpon = 0;
-  Reaction178_kpoff = 0.05;
-  Reaction179_kon = 10;
-  Reaction180_koff = 0.5;
-  Reaction181_kpon = 0;
-  Reaction182_kpoff = 0.05;
-  Reaction183_kon = 10;
-  Reaction184_koff = 0.5;
-  Reaction185_kpon = 0;
-  Reaction186_kpoff = 0.05;
-  Reaction187_kon = 10;
-  Reaction188_koff = 0.5;
-  Reaction189_kpon = 0;
-  Reaction190_kpoff = 0.05;
-  Reaction191_kon = 10;
-  Reaction192_koff = 0.5;
-  Reaction193_kpon = 0;
-  Reaction194_kpoff = 0.05;
-  Reaction195_kon = 10;
-  Reaction196_koff = 0.5;
-  Reaction197_kpon = 0;
-  Reaction198_kpoff = 0.05;
-  Reaction199_kon = 10;
-  Reaction200_koff = 0.5;
-  Reaction201_kpon = 0;
-  Reaction202_kpoff = 0.05;
-  Reaction203_kon = 10;
-  Reaction204_koff = 0.5;
-  Reaction205_kpon = 0;
-  Reaction206_kpoff = 0.05;
-  Reaction207_kon = 10;
-  Reaction208_koff = 0.5;
-  Reaction209_kpon = 0;
-  Reaction210_kpoff = 0.05;
-  Reaction211_kon = 10;
-  Reaction212_koff = 0.5;
-  Reaction213_kpon = 0;
-  Reaction214_kpoff = 0.05;
-  Reaction215_kon = 10;
-  Reaction216_koff = 0.5;
-  Reaction217_kpon = 0;
-  Reaction218_kpoff = 0.05;
-  Reaction219_kon = 10;
-  Reaction220_koff = 0.5;
-  Reaction221_kpon = 0;
-  Reaction222_kpoff = 0.05;
-  Reaction223_kon = 10;
-  Reaction224_koff = 0.5;
-  Reaction225_kpon = 0;
-  Reaction226_kpoff = 0.05;
-  Reaction227_kon = 10;
-  Reaction228_koff = 0.5;
-  Reaction229_kpon = 0;
-  Reaction230_kpoff = 0.05;
-  Reaction231_kon = 10;
-  Reaction232_koff = 0.5;
-  Reaction233_kpon = 0;
-  Reaction234_kpoff = 0.05;
-  Reaction235_kon = 10;
-  Reaction236_koff = 0.5;
-  Reaction237_kpon = 0;
-  Reaction238_kpoff = 0.05;
-  Reaction239_k7 = 0.1;
-  Reaction240_k7 = 0.1;
-  Reaction241_k7 = 0.1;
-  Reaction242_k9a = 0.1;
-  Reaction243_k9a = 0.1;
-  Reaction244_k9a = 0.1;
-  Reaction245_k3 = 0.1;
-  Reaction246_k5a = 0.1;
-  Reaction247_k3 = 0.1;
-  Reaction248_k5a = 0.1;
-  Reaction249_k3 = 0.1;
-  Reaction250_k5a = 0.1;
-  Reaction251_k3 = 0.1;
-  Reaction252_k5a = 0.1;
-  Reaction253_k1a = 100;
-  Reaction254_d1a = 0;
-  Reaction255_k1 = 0.1;
-  Reaction256_k1a = 100;
-  Reaction257_d1a = 0;
-  Reaction258_k1 = 0.1;
-  Reaction259_k1a = 100;
-  Reaction260_d1a = 0;
-  Reaction261_k1 = 0.1;
-  Reaction262_k1a = 100;
-  Reaction263_d1a = 0;
-  Reaction264_k1 = 0.1;
-  Reaction265_k1a = 100;
-  Reaction266_d1a = 0;
-  Reaction267_k1 = 0.1;
-  Reaction268_k1a = 100;
-  Reaction269_d1a = 0;
-  Reaction270_k1 = 0.1;
-  Reaction271_k1a = 100;
-  Reaction272_d1a = 0;
-  Reaction273_k1 = 0.1;
-  Reaction274_k1a = 100;
-  Reaction275_d1a = 0;
-  Reaction276_k1 = 0.1;
-  Reaction277_k1a = 100;
-  Reaction278_d1a = 0;
-  Reaction279_k1 = 0.1;
-  Reaction280_k1a = 100;
-  Reaction281_d1a = 0;
-  Reaction282_k1 = 0.1;
-  Reaction283_k1a = 100;
-  Reaction284_d1a = 0;
-  Reaction285_k1 = 0.1;
-  Reaction286_k1a = 100;
-  Reaction287_d1a = 0;
-  Reaction288_k1 = 0.1;
-  Reaction289_k1a = 100;
-  Reaction290_d1a = 0;
-  Reaction291_k1 = 0.1;
-  Reaction292_k1a = 100;
-  Reaction293_d1a = 0;
-  Reaction294_k1 = 0.1;
-  Reaction295_k1a = 100;
-  Reaction296_d1a = 0;
-  Reaction297_k1 = 0.1;
-  Reaction298_k1a = 100;
-  Reaction299_d1a = 0;
-  Reaction300_k1 = 0.1;
-
-  // Other declarations:
-  const Cytoplasm;
-
-  // Display Names:
-  MAPKP is "MAPK phosphatase";
-  MEKP is "MEK phosphatase";
-  RAFK is "RAF kinase";
-  RAFP is "RAF phosphatase";
-  K_1_0 is "MAPK";
-  K_1_1 is "MAPK-P";
-  K_1_2 is "MAPK-PP";
-  K_2_0 is "MEK";
-  K_2_1 is "MEK-P";
-  K_2_2 is "MEK-PP";
-  K_3_0 is "RAF";
-  K_3_1 is "RAF-P";
-  K_K_1_0_2_2 is "MAPK_MEK-PP";
-  K_K_1_1_2_2 is "MAPK-P_MEK-PP";
-  K_K_2_0_3_1 is "MEK_RAF-P";
-  K_K_2_1_3_1 is "MEK-P_RAF-P";
-  K_MAPKP_1_1 is "MAPK-P_MAPKPase";
-  K_MAPKP_1_2 is "MAPK-PP_MAPKPase";
-  K_MEKP_2_1 is "MEK-P_MEKPase";
-  K_MEKP_2_2 is "MEK-PP_MEKPase";
-  K_RAFK_3_0 is "RAF_RAFK";
-  K_RAFP_3_1 is "RAF-P_RAFPase";
-  S_m1_m1_m1 is "Scaffold";
-  S_m1_m1_0 is "Scaffold_RAF";
-  S_m1_m1_1 is "Scaffold_RAF-P";
-  S_m1_0_m1 is "Scaffold_MEK";
-  S_m1_0_0 is "Scaffold_MEK_RAF";
-  S_m1_0_1 is "Scaffold_MEK_RAF-P";
-  S_m1_1_m1 is "Scaffold_MEK-P";
-  S_m1_1_0 is "Scaffold_MEK-P_RAF";
-  S_m1_1_1 is "Scaffold_MEK-P_RAF-P";
-  S_m1_2_m1 is "Scaffold_MEK-PP";
-  S_m1_2_0 is "Scaffold_MEK-PP_RAF";
-  S_m1_2_1 is "Scaffold_MEK-PP_RAF-P";
-  S_0_m1_m1 is "Scaffold_MAPK";
-  S_0_m1_0 is "Scaffold_MAPK_RAF";
-  S_0_m1_1 is "Scaffold_MAPK_RAF-P";
-  S_0_0_m1 is "Scaffold_MAPK_MEK";
-  S_0_0_0 is "Scaffold_MAPK_MEK_RAF";
-  S_0_0_1 is "Scaffold_MAPK_MEK_RAF-P";
-  S_0_1_m1 is "Scaffold_MAPK_MEK-P";
-  S_0_1_0 is "Scaffold_MAPK_MEK-P_RAF";
-  S_0_1_1 is "Scaffold_MAPK_MEK-P_RAF-P";
-  S_0_2_m1 is "Scaffold_MAPK_MEK-PP";
-  S_0_2_0 is "Scaffold_MAPK_MEK-PP_RAF";
-  S_0_2_1 is "Scaffold_MAPK_MEK-PP_RAF-P";
-  S_1_m1_m1 is "Scaffold_MAPK-P";
-  S_1_m1_0 is "Scaffold_MAPK-P_RAF";
-  S_1_m1_1 is "Scaffold_MAPK-P_RAF-P";
-  S_1_0_m1 is "Scaffold_MAPK-P_MEK";
-  S_1_0_0 is "Scaffold_MAPK-P_MEK_RAF";
-  S_1_0_1 is "Scaffold_MAPK-P_MEK_RAF-P";
-  S_1_1_m1 is "Scaffold_MAPK-P_MEK-P";
-  S_1_1_0 is "Scaffold_MAPK-P_MEK-P_RAF";
-  S_1_1_1 is "Scaffold_MAPK-P_MEK-P_RAF-P";
-  S_1_2_m1 is "Scaffold_MAPK-P_MEK-PP";
-  S_1_2_0 is "Scaffold_MAPK-P_MEK-PP_RAF";
-  S_1_2_1 is "Scaffold_MAPK-P_MEK-PP_RAF-P";
-  S_2_m1_m1 is "Scaffold_MAPK-PP";
-  S_2_m1_0 is "Scaffold_MAPK-PP_RAF";
-  S_2_m1_1 is "Scaffold_MAPK-PP_RAF-P";
-  S_2_0_m1 is "Scaffold_MAPK-PP_MEK";
-  S_2_0_0 is "Scaffold_MAPK-PP_MEK_RAF";
-  S_2_0_1 is "Scaffold_MAPK-PP_MEK_RAF-P";
-  S_2_1_m1 is "Scaffold_MAPK-PP_MEK-P";
-  S_2_1_0 is "Scaffold_MAPK-PP_MEK-P_RAF";
-  S_2_1_1 is "Scaffold_MAPK-PP_MEK-P_RAF-P";
-  S_2_2_m1 is "Scaffold_MAPK-PP_MEK-PP";
-  S_2_2_0 is "Scaffold_MAPK-PP_MEK-PP_RAF";
-  S_2_2_1 is "Scaffold_MAPK-PP_MEK-PP_RAF-P";
-  S_RAFK_m1_m1_0 is "Scaffold_RAF";
-  S_RAFK_m1_0_0 is "Scaffold_MEK_RAF";
-  S_RAFK_m1_1_0 is "Scaffold_MEK-P_RAF";
-  S_RAFK_m1_2_0 is "Scaffold_MEK-PP_RAF";
-  S_RAFK_0_m1_0 is "Scaffold_MAPK_RAF";
-  S_RAFK_0_0_0 is "Scaffold_MAPK_MEK_RAF";
-  S_RAFK_0_1_0 is "Scaffold_MAPK_MEK-P_RAF";
-  S_RAFK_0_2_0 is "Scaffold_MAPK_MEK-PP_RAF";
-  S_RAFK_1_m1_0 is "Scaffold_MAPK-P_RAF";
-  S_RAFK_1_0_0 is "Scaffold_MAPK-P_MEK_RAF";
-  S_RAFK_1_1_0 is "Scaffold_MAPK-P_MEK-P_RAF";
-  S_RAFK_1_2_0 is "Scaffold_MAPK-P_MEK-PP_RAF";
-  S_RAFK_2_m1_0 is "Scaffold_MAPK-PP_RAF";
-  S_RAFK_2_0_0 is "Scaffold_MAPK-PP_MEK_RAF";
-  S_RAFK_2_1_0 is "Scaffold_MAPK-PP_MEK-P_RAF";
-  S_RAFK_2_2_0 is "Scaffold_MAPK-PP_MEK-PP_RAF";
-  Reaction1 is "binding of RAF and RAFK";
-  Reaction2 is "dissociation of RAF_RAFK";
-  Reaction3 is "phosphorylation of RAF";
-  Reaction4 is "binding of RAF-P and RAF phosphatase";
-  Reaction5 is "dissociation of RAF-P_RAFPase";
-  Reaction6 is "dephosphorylation of RAF-P";
-  Reaction7 is "binding of MEK and RAF-P";
-  Reaction8 is "dissociation of MEK_RAF-P";
-  Reaction9 is "phosphorylation of MEK";
-  Reaction10 is "binding of MEK-P and MEK phosphatase";
-  Reaction11 is "dissociation of MEK-P_MEKPase";
-  Reaction12 is "dephosphorylation of MEK-P";
-  Reaction13 is "binding of MEK-P and RAF-P";
-  Reaction14 is "dissociation of MEK-P_RAF-P";
-  Reaction15 is "phosphorylation of MEK-P";
-  Reaction16 is "binding of MEK-PP and MEK phosphatase";
-  Reaction17 is "dissociation of MEK-PP_MEKPase";
-  Reaction18 is "dephosphorylation of MEK-PP";
-  Reaction19 is "binding of MAPK and MEK-PP";
-  Reaction20 is "dissociation of MAPK_MEK-PP";
-  Reaction21 is "phosphorylation of MAPK";
-  Reaction22 is "binding of MAPK-P and MAPK phosphatase";
-  Reaction23 is "dissociation of MAPK-P_MAPKPase";
-  Reaction24 is "dephosphorylation of MAPK-P";
-  Reaction25 is "binding of MAPK-P and MEK-PP";
-  Reaction26 is "dissociation of MAPK-P_MEK-PP";
-  Reaction27 is "phosphorylation of MAPK-P";
-  Reaction28 is "binding of MAPK-PP and MAPK phosphatase";
-  Reaction29 is "dissociation of MAPK-PP_MAPKPase";
-  Reaction30 is "dephosphorylation of MAPK-PP";
-  Reaction31 is "binding of MAPK on scaffold";
-  Reaction32 is "dissociation of MAPK from scaffold";
-  Reaction33 is "binding of MAPK on scaffold";
-  Reaction34 is "dissociation of MAPK from scaffold";
-  Reaction35 is "binding of MAPK on scaffold";
-  Reaction36 is "dissociation of MAPK from scaffold";
-  Reaction37 is "binding of MAPK on scaffold";
-  Reaction38 is "dissociation of MAPK from scaffold";
-  Reaction39 is "binding of MAPK on scaffold";
-  Reaction40 is "dissociation of MAPK from scaffold";
-  Reaction41 is "binding of MAPK on scaffold";
-  Reaction42 is "dissociation of MAPK from scaffold";
-  Reaction43 is "binding of MAPK on scaffold";
-  Reaction44 is "dissociation of MAPK from scaffold";
-  Reaction45 is "binding of MAPK on scaffold";
-  Reaction46 is "dissociation of MAPK from scaffold";
-  Reaction47 is "binding of MAPK on scaffold";
-  Reaction48 is "dissociation of MAPK from scaffold";
-  Reaction49 is "binding of MAPK on scaffold";
-  Reaction50 is "dissociation of MAPK from scaffold";
-  Reaction51 is "binding of MAPK on scaffold";
-  Reaction52 is "dissociation of MAPK from scaffold";
-  Reaction53 is "binding of MAPK on scaffold";
-  Reaction54 is "dissociation of MAPK from scaffold";
-  Reaction55 is "binding of MAPK-P on scaffold";
-  Reaction56 is "dissociation of MAPK-P from scaffold";
-  Reaction57 is "binding of MAPK-P on scaffold";
-  Reaction58 is "dissociation of MAPK-P from scaffold";
-  Reaction59 is "binding of MAPK-P on scaffold";
-  Reaction60 is "dissociation of MAPK-P from scaffold";
-  Reaction61 is "binding of MAPK-P on scaffold";
-  Reaction62 is "dissociation of MAPK-P from scaffold";
-  Reaction63 is "binding of MAPK-P on scaffold";
-  Reaction64 is "dissociation of MAPK-P from scaffold";
-  Reaction65 is "binding of MAPK-P on scaffold";
-  Reaction66 is "dissociation of MAPK-P from scaffold";
-  Reaction67 is "binding of MAPK-P on scaffold";
-  Reaction68 is "dissociation of MAPK-P from scaffold";
-  Reaction69 is "binding of MAPK-P on scaffold";
-  Reaction70 is "dissociation of MAPK-P from scaffold";
-  Reaction71 is "binding of MAPK-P on scaffold";
-  Reaction72 is "dissociation of MAPK-P from scaffold";
-  Reaction73 is "binding of MAPK-P on scaffold";
-  Reaction74 is "dissociation of MAPK-P from scaffold";
-  Reaction75 is "binding of MAPK-P on scaffold";
-  Reaction76 is "dissociation of MAPK-P from scaffold";
-  Reaction77 is "binding of MAPK-P on scaffold";
-  Reaction78 is "dissociation of MAPK-P from scaffold";
-  Reaction79 is "binding of MAPK-PP on scaffold";
-  Reaction80 is "dissociation of MAPK-PP from scaffold";
-  Reaction81 is "binding of MAPK-PP on scaffold";
-  Reaction82 is "dissociation of MAPK-PP from scaffold";
-  Reaction83 is "binding of MAPK-PP on scaffold";
-  Reaction84 is "dissociation of MAPK-PP from scaffold";
-  Reaction85 is "binding of MAPK-PP on scaffold";
-  Reaction86 is "dissociation of MAPK-PP from scaffold";
-  Reaction87 is "binding of MAPK-PP on scaffold";
-  Reaction88 is "dissociation of MAPK-PP from scaffold";
-  Reaction89 is "binding of MAPK-PP on scaffold";
-  Reaction90 is "dissociation of MAPK-PP from scaffold";
-  Reaction91 is "binding of MAPK-PP on scaffold";
-  Reaction92 is "dissociation of MAPK-PP from scaffold";
-  Reaction93 is "binding of MAPK-PP on scaffold";
-  Reaction94 is "dissociation of MAPK-PP from scaffold";
-  Reaction95 is "binding of MAPK-PP on scaffold";
-  Reaction96 is "dissociation of MAPK-PP from scaffold";
-  Reaction97 is "binding of MAPK-PP on scaffold";
-  Reaction98 is "dissociation of MAPK-PP from scaffold";
-  Reaction99 is "binding of MAPK-PP on scaffold";
-  Reaction100 is "dissociation of MAPK-PP from scaffold";
-  Reaction101 is "binding of MAPK-PP on scaffold";
-  Reaction102 is "dissociation of MAPK-PP from scaffold";
-  Reaction103 is "binding of MEK on scaffold";
-  Reaction104 is "dissociation of MEK from scaffold";
-  Reaction105 is "binding of MEK on scaffold";
-  Reaction106 is "dissociation of MEK from scaffold";
-  Reaction107 is "binding of MEK on scaffold";
-  Reaction108 is "dissociation of MEK from scaffold";
-  Reaction109 is "binding of MEK-P on scaffold";
-  Reaction110 is "dissociation of MEK-P from scaffold";
-  Reaction111 is "binding of MEK-P on scaffold";
-  Reaction112 is "dissociation of MEK-P from scaffold";
-  Reaction113 is "binding of MEK-P on scaffold";
-  Reaction114 is "dissociation of MEK-P from scaffold";
-  Reaction115 is "binding of MEK-PP on scaffold";
-  Reaction116 is "dissociation of MEK-PP from scaffold";
-  Reaction117 is "binding of MEK-PP on scaffold";
-  Reaction118 is "dissociation of MEK-PP from scaffold";
-  Reaction119 is "binding of MEK-PP on scaffold";
-  Reaction120 is "dissociation of MEK-PP from scaffold";
-  Reaction121 is "binding of MEK on scaffold";
-  Reaction122 is "dissociation of MEK from scaffold";
-  Reaction123 is "binding of MEK on scaffold";
-  Reaction124 is "dissociation of MEK from scaffold";
-  Reaction125 is "binding of MEK on scaffold";
-  Reaction126 is "dissociation of MEK from scaffold";
-  Reaction127 is "binding of MEK-P on scaffold";
-  Reaction128 is "dissociation of MEK-P from scaffold";
-  Reaction129 is "binding of MEK-P on scaffold";
-  Reaction130 is "dissociation of MEK-P from scaffold";
-  Reaction131 is "binding of MEK-P on scaffold";
-  Reaction132 is "dissociation of MEK-P from scaffold";
-  Reaction133 is "binding of MEK-PP on scaffold";
-  Reaction134 is "dissociation of MEK-PP from scaffold";
-  Reaction135 is "binding of MEK-PP on scaffold";
-  Reaction136 is "dissociation of MEK-PP from scaffold";
-  Reaction137 is "binding of MEK-PP on scaffold";
-  Reaction138 is "dissociation of MEK-PP from scaffold";
-  Reaction139 is "binding of MEK on scaffold";
-  Reaction140 is "dissociation of MEK from scaffold";
-  Reaction141 is "binding of MEK on scaffold";
-  Reaction142 is "dissociation of MEK from scaffold";
-  Reaction143 is "binding of MEK on scaffold";
-  Reaction144 is "dissociation of MEK from scaffold";
-  Reaction145 is "binding of MEK-P on scaffold";
-  Reaction146 is "dissociation of MEK-P from scaffold";
-  Reaction147 is "binding of MEK-P on scaffold";
-  Reaction148 is "dissociation of MEK-P from scaffold";
-  Reaction149 is "binding of MEK-P on scaffold";
-  Reaction150 is "dissociation of MEK-P from scaffold";
-  Reaction151 is "binding of MEK-PP on scaffold";
-  Reaction152 is "dissociation of MEK-PP from scaffold";
-  Reaction153 is "binding of MEK-PP on scaffold";
-  Reaction154 is "dissociation of MEK-PP from scaffold";
-  Reaction155 is "binding of MEK-PP on scaffold";
-  Reaction156 is "dissociation of MEK-PP from scaffold";
-  Reaction157 is "binding of MEK on scaffold";
-  Reaction158 is "dissociation of MEK from scaffold";
-  Reaction159 is "binding of MEK on scaffold";
-  Reaction160 is "dissociation of MEK from scaffold";
-  Reaction161 is "binding of MEK on scaffold";
-  Reaction162 is "dissociation of MEK from scaffold";
-  Reaction163 is "binding of MEK-P on scaffold";
-  Reaction164 is "dissociation of MEK-P from scaffold";
-  Reaction165 is "binding of MEK-P on scaffold";
-  Reaction166 is "dissociation of MEK-P from scaffold";
-  Reaction167 is "binding of MEK-P on scaffold";
-  Reaction168 is "dissociation of MEK-P from scaffold";
-  Reaction169 is "binding of MEK-PP on scaffold";
-  Reaction170 is "dissociation of MEK-PP from scaffold";
-  Reaction171 is "binding of MEK-PP on scaffold";
-  Reaction172 is "dissociation of MEK-PP from scaffold";
-  Reaction173 is "binding of MEK-PP on scaffold";
-  Reaction174 is "dissociation of MEK-PP from scaffold";
-  Reaction175 is "binding of RAF on scaffold";
-  Reaction176 is "dissociation of RAF from scaffold";
-  Reaction177 is "binding of RAF-P on scaffold";
-  Reaction178 is "dissociation of RAF-P from scaffold";
-  Reaction179 is "binding of RAF on scaffold";
-  Reaction180 is "dissociation of RAF from scaffold";
-  Reaction181 is "binding of RAF-P on scaffold";
-  Reaction182 is "dissociation of RAF-P from scaffold";
-  Reaction183 is "binding of RAF on scaffold";
-  Reaction184 is "dissociation of RAF from scaffold";
-  Reaction185 is "binding of RAF-P on scaffold";
-  Reaction186 is "dissociation of RAF-P from scaffold";
-  Reaction187 is "binding of RAF on scaffold";
-  Reaction188 is "dissociation of RAF from scaffold";
-  Reaction189 is "binding of RAF-P on scaffold";
-  Reaction190 is "dissociation of RAF-P from scaffold";
-  Reaction191 is "binding of RAF on scaffold";
-  Reaction192 is "dissociation of RAF from scaffold";
-  Reaction193 is "binding of RAF-P on scaffold";
-  Reaction194 is "dissociation of RAF-P from scaffold";
-  Reaction195 is "binding of RAF on scaffold";
-  Reaction196 is "dissociation of RAF from scaffold";
-  Reaction197 is "binding of RAF-P on scaffold";
-  Reaction198 is "dissociation of RAF from scaffold";
-  Reaction199 is "binding of RAF on scaffold";
-  Reaction200 is "dissociation of RAF from scaffold";
-  Reaction201 is "binding of RAF-P on scaffold";
-  Reaction202 is "dissociation of RAF-P from scaffold";
-  Reaction203 is "binding of RAF on scaffold";
-  Reaction204 is "dissociation of RAF from scaffold";
-  Reaction205 is "binding of RAF-P on scaffold";
-  Reaction206 is "dissociation of RAF-P from scaffold";
-  Reaction207 is "binding of RAF on scaffold";
-  Reaction208 is "dissociation of RAF from scaffold";
-  Reaction209 is "binding of RAF-P on scaffold";
-  Reaction210 is "dissociation of RAF-P from scaffold";
-  Reaction211 is "binding of RAF on scaffold";
-  Reaction212 is "dissociation of RAF from scaffold";
-  Reaction213 is "binding of RAF-P on scaffold";
-  Reaction214 is "dissociation of RAF-P from scaffold";
-  Reaction215 is "binding of RAF on scaffold";
-  Reaction216 is "dissociation of RAF from scaffold";
-  Reaction217 is "binding of RAF-P on scaffold";
-  Reaction218 is "dissociation of RAF-P from scaffold";
-  Reaction219 is "binding of RAF on scaffold";
-  Reaction220 is "dissociation of RAF from scaffold";
-  Reaction221 is "binding of RAF-P on scaffold";
-  Reaction222 is "dissociation of RAF-P from scaffold";
-  Reaction223 is "binding of RAF on scaffold";
-  Reaction224 is "dissociation of RAF from scaffold";
-  Reaction225 is "binding of RAF-P on scaffold";
-  Reaction226 is "dissociation of RAF-P from scaffold";
-  Reaction227 is "binding of RAF on scaffold";
-  Reaction228 is "dissociation of RAF from scaffold";
-  Reaction229 is "binding of RAF-P on scaffold";
-  Reaction230 is "dissociation of RAF-P from scaffold";
-  Reaction231 is "binding of RAF on scaffold";
-  Reaction232 is "dissociation of RAF from scaffold";
-  Reaction233 is "binding of RAF-P on scaffold";
-  Reaction234 is "dissociation of RAF-P from scaffold";
-  Reaction235 is "binding of RAF on scaffold";
-  Reaction236 is "dissociation of RAF from scaffold";
-  Reaction237 is "binding of RAF-P on scaffold";
-  Reaction238 is "dissociation of RAF-P from scaffold";
-  Reaction239 is "phosphorylation of MAPK on scaffold";
-  Reaction240 is "phosphorylation of MAPK on scaffold";
-  Reaction241 is "phosphorylation of MAPK on scaffold";
-  Reaction242 is "phosphorylation of MAPK-P on scaffold";
-  Reaction243 is "phosphorylation of MAPK-P on scaffold";
-  Reaction244 is "phosphorylation of MAPK-P on scaffold";
-  Reaction245 is "phosphorylation of MEK on scaffold";
-  Reaction246 is "phosphorylation of MEK-P on scaffold";
-  Reaction247 is "phosphorylation of MEK on scaffold";
-  Reaction248 is "phosphorylation of MEK-P on scaffold";
-  Reaction249 is "phosphorylation of MEK on scaffold";
-  Reaction250 is "phosphorylation of MEK-P on scaffold";
-  Reaction251 is "phosphorylation of MEK on scaffold";
-  Reaction252 is "phosphorylation of MEK-P on scaffold";
-  Reaction253 is "binding of RAF and RAFK";
-  Reaction254 is "dissociation of RAF_RAFK";
-  Reaction255 is "phosphorylation of RAF on scaffold";
-  Reaction256 is "binding of RAF and RAFK";
-  Reaction257 is "dissociation of RAF_RAFK";
-  Reaction258 is "phosphorylation of RAF on scaffold";
-  Reaction259 is "binding of RAF and RAFK";
-  Reaction260 is "dissociation of RAF_RAFK";
-  Reaction261 is "phosphorylation of RAF on scaffold";
-  Reaction262 is "binding of RAF and RAFK";
-  Reaction263 is "dissociation of RAF_RAFK";
-  Reaction264 is "phosphorylation of RAF on scaffold";
-  Reaction265 is "binding of RAF and RAFK";
-  Reaction266 is "dissociation of RAF_RAFK";
-  Reaction267 is "phosphorylation of RAF on scaffold";
-  Reaction268 is "binding of RAF and RAFK";
-  Reaction269 is "dissociation of RAF_RAFK";
-  Reaction270 is "phosphorylation of RAF on scaffold";
-  Reaction271 is "binding of RAF and RAFK";
-  Reaction272 is "dissociation of RAF_RAFK";
-  Reaction273 is "phosphorylation of RAF on scaffold";
-  Reaction274 is "binding of RAF and RAFK";
-  Reaction275 is "dissociation of RAF_RAFK";
-  Reaction276 is "phosphorylation of RAF on scaffold";
-  Reaction277 is "binding of RAF and RAFK";
-  Reaction278 is "dissociation of RAF_RAFK";
-  Reaction279 is "phosphorylation of RAF on scaffold";
-  Reaction280 is "binding of RAF and RAFK";
-  Reaction281 is "dissociation of RAF_RAFK";
-  Reaction282 is "phosphorylation of RAF on scaffold";
-  Reaction283 is "binding of RAF and RAFK";
-  Reaction284 is "dissociation of RAF_RAFK";
-  Reaction285 is "phosphorylation of RAF on scaffold";
-  Reaction286 is "binding of RAF and RAFK";
-  Reaction287 is "dissociation of RAF_RAFK";
-  Reaction288 is "phosphorylation of RAF on scaffold";
-  Reaction289 is "binding of RAF and RAFK";
-  Reaction290 is "dissociation of RAF_RAFK";
-  Reaction291 is "phosphorylation of RAF on scaffold";
-  Reaction292 is "binding of RAF and RAFK";
-  Reaction293 is "dissociation of RAF_RAFK";
-  Reaction294 is "phosphorylation of RAF on scaffold";
-  Reaction295 is "binding of RAF and RAFK";
-  Reaction296 is "dissociation of RAF_RAFK";
-  Reaction297 is "phosphorylation of RAF on scaffold";
-  Reaction298 is "binding of RAF and RAFK";
-  Reaction299 is "dissociation of RAF_RAFK";
-  Reaction300 is "phosphorylation of RAF on scaffold";
-
-  // CV terms:
-  Cytoplasm hypernym "http://identifiers.org/go/GO:0005737"
-  MAPKP identity "http://identifiers.org/uniprot/Q90W58"
-  RAFK hypernym "http://identifiers.org/interpro/IPR003577"
-  K_1_0 hypernym "http://identifiers.org/uniprot/P26696"
-  K_1_1 hypernym "http://identifiers.org/uniprot/P26696"
-  K_1_2 hypernym "http://identifiers.org/uniprot/P26696"
-  K_2_0 hypernym "http://identifiers.org/uniprot/Q05116"
-  K_2_1 hypernym "http://identifiers.org/uniprot/Q05116"
-  K_2_2 identity "http://identifiers.org/uniprot/Q05116"
-  K_3_0 hypernym "http://identifiers.org/uniprot/P09560"
-  K_3_1 hypernym "http://identifiers.org/uniprot/P09560"
-  K_K_1_0_2_2 part "http://identifiers.org/uniprot/Q05116",
-                   "http://identifiers.org/uniprot/P26696"
-  K_K_1_1_2_2 part "http://identifiers.org/uniprot/Q05116",
-                   "http://identifiers.org/uniprot/P26696"
-  K_K_2_0_3_1 part "http://identifiers.org/uniprot/P09560",
-                   "http://identifiers.org/uniprot/Q05116"
-  K_K_2_1_3_1 part "http://identifiers.org/uniprot/P09560",
-                   "http://identifiers.org/uniprot/Q05116"
-  K_MAPKP_1_1 part "http://identifiers.org/uniprot/P26696",
-                   "http://identifiers.org/uniprot/Q90W58"
-  K_MAPKP_1_2 part "http://identifiers.org/uniprot/P26696",
-                   "http://identifiers.org/uniprot/Q90W58"
-  K_MEKP_2_1 part "http://identifiers.org/uniprot/Q05116"
-  K_MEKP_2_2 part "http://identifiers.org/uniprot/Q05116"
-  K_RAFK_3_0 part "http://identifiers.org/uniprot/P09560"
-  K_RAFP_3_1 part "http://identifiers.org/uniprot/P09560"
-  S_m1_m1_0 part "http://identifiers.org/uniprot/P09560"
-  S_m1_m1_1 part "http://identifiers.org/uniprot/P09560"
-  S_m1_0_m1 part "http://identifiers.org/uniprot/Q05116"
-  S_m1_0_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_0_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_1_m1 part "http://identifiers.org/uniprot/Q05116"
-  S_m1_1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_2_m1 part "http://identifiers.org/uniprot/Q05116"
-  S_m1_2_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_m1_2_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/Q05116"
-  S_0_m1_m1 part "http://identifiers.org/uniprot/P26696"
-  S_0_m1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_m1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_0_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_0_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_0_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_1_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_1_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_1_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_2_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_0_2_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_0_2_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_m1_m1 part "http://identifiers.org/uniprot/P26696"
-  S_1_m1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_m1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_0_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_0_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_0_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_1_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_1_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_1_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_2_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_1_2_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_1_2_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_m1_m1 part "http://identifiers.org/uniprot/P26696"
-  S_2_m1_0 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_m1_1 part "http://identifiers.org/uniprot/P09560",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_0_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_0_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_0_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_1_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_1_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_1_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_2_m1 part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  S_2_2_0 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_2_2_1 part "http://identifiers.org/uniprot/P09560",
-               "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  S_RAFK_m1_m1_0 part "http://identifiers.org/uniprot/P09560"
-  S_RAFK_m1_0_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/Q05116"
-  S_RAFK_m1_1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/Q05116"
-  S_RAFK_m1_2_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/Q05116"
-  S_RAFK_0_m1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/P26696"
-  S_RAFK_0_0_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_0_1_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_0_2_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_m1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_0_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_1_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_1_2_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_m1_0 part "http://identifiers.org/uniprot/P09560",
-                     "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_0_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_1_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  S_RAFK_2_2_0 part "http://identifiers.org/uniprot/P09560",
-                    "http://identifiers.org/uniprot/Q05116",
-                    "http://identifiers.org/uniprot/P26696"
-  Reaction1 homolog "http://identifiers.org/reactome/REACT_996"
-  Reaction1 hypernym "http://identifiers.org/go/GO:0031435",
-                     "http://identifiers.org/go/GO:0006461"
-  Reaction2 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction3 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                     "http://identifiers.org/go/GO:0008349",
-                     "http://identifiers.org/go/GO:0000185"
-  Reaction4 hypernym "http://identifiers.org/go/GO:0031435"
-  Reaction5 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction6 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                     "http://identifiers.org/go/GO:0006470"
-  Reaction7 hypernym "http://identifiers.org/go/GO:0031434",
-                     "http://identifiers.org/go/GO:0031435"
-  Reaction7 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction8 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction9 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-                     "http://identifiers.org/go/GO:0004709",
-                     "http://identifiers.org/go/GO:0006468"
-  Reaction10 hypernym "http://identifiers.org/go/GO:0031435"
-  Reaction11 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction12 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/go/GO:0006470"
-  Reaction13 hypernym "http://identifiers.org/go/GO:0031434",
-                      "http://identifiers.org/go/GO:0031435"
-  Reaction13 homolog "http://identifiers.org/reactome/REACT_143"
-  Reaction14 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction15 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                      "http://identifiers.org/go/GO:0000186",
-                      "http://identifiers.org/go/GO:0004709",
-                      "http://identifiers.org/go/GO:0006468"
-  Reaction15 homolog "http://identifiers.org/reactome/REACT_614"
-  Reaction16 hypernym "http://identifiers.org/go/GO:0031434"
-  Reaction17 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction18 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/go/GO:0006470"
-  Reaction19 hypernym "http://identifiers.org/go/GO:0051019",
-                      "http://identifiers.org/go/GO:0031434"
-  Reaction19 homolog "http://identifiers.org/reactome/REACT_1780",
-                     "http://identifiers.org/reactome/REACT_495"
-  Reaction20 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction21 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                      "http://identifiers.org/go/GO:0004708",
-                      "http://identifiers.org/go/GO:0006468"
-  Reaction21 homolog "http://identifiers.org/reactome/REACT_136",
-                     "http://identifiers.org/reactome/REACT_2247"
-  Reaction22 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction23 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction24 hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  Reaction25 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction26 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction27 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                      "http://identifiers.org/go/GO:0000187",
-                      "http://identifiers.org/go/GO:0004708"
-  Reaction28 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction29 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction30 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                      "http://identifiers.org/go/GO:0000188"
-  Reaction31 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction32 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction33 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction34 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction35 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction36 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction37 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction38 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction39 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction40 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction41 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction42 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction43 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction44 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction45 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction46 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction47 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction48 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction49 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction50 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction51 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction52 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction53 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction54 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction55 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction56 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction57 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction58 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction59 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction60 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction61 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction62 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction63 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction64 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction65 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction66 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction67 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction68 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction69 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction70 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction71 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction72 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction73 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction74 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction75 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction76 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction77 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction78 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction79 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction80 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction81 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction82 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction83 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction84 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction85 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction86 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction87 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction88 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction89 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction90 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction91 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction92 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction93 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction94 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction95 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction96 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction97 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction98 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction99 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction101 hypernym "http://identifiers.org/go/GO:0051019"
-  Reaction102 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction104 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction106 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction108 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction110 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction112 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction114 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction116 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction118 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction120 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction122 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction124 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction126 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction128 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction130 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction132 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction134 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction136 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction138 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction140 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction142 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction144 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction146 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction148 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction150 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction152 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction154 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction156 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction158 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction160 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction162 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction164 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction166 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction168 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction170 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction172 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction174 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction176 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction178 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction180 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction182 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction184 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction186 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction188 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction190 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction192 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction194 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction196 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction198 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction200 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction202 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction204 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction206 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction208 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction210 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction212 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction214 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction216 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction218 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction220 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction222 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction224 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction226 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction228 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction230 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction232 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction234 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction236 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction238 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction239 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction240 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction241 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction242 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000187",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction243 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000187",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction244 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000187",
-                       "http://identifiers.org/go/GO:0004708"
-  Reaction245 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction246 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction247 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction248 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction249 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction250 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction251 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction252 identity "http://identifiers.org/ec-code/2.7.1.37",
-                       "http://identifiers.org/go/GO:0000186",
-                       "http://identifiers.org/go/GO:0004709"
-  Reaction253 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction254 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction255 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction256 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction257 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction258 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction259 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction260 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction261 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction262 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction263 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction264 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction265 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction266 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction267 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction268 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction269 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction270 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction271 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction272 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction273 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction274 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction275 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction276 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction277 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction278 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction279 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction280 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction281 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction282 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction283 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction284 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction285 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction286 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction287 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction288 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0000185",
-                       "http://identifiers.org/go/GO:0008349"
-  Reaction289 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction290 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction291 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction292 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction293 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction294 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction295 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction296 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction297 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-  Reaction298 hypernym "http://identifiers.org/reactome/REACT_996",
-                       "http://identifiers.org/go/GO:0031435"
-  Reaction299 hypernym "http://identifiers.org/go/GO:0043241"
-  Reaction300 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                       "http://identifiers.org/go/GO:0008349",
-                       "http://identifiers.org/go/GO:0000185"
-end
-
-MAPK_in_Scaffold is "Levchenko2000_MAPK_Scaffold"
-
-MAPK_in_Scaffold model_entity_is "http://identifiers.org/biomodels.db/MODEL6616691524"
-MAPK_in_Scaffold model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000014"
-MAPK_in_Scaffold description "http://identifiers.org/pubmed/10823939"
-MAPK_in_Scaffold origin "http://identifiers.org/biomodels.db/BIOMD0000000011"
-MAPK_in_Scaffold hypernym "http://identifiers.org/go/GO:0005078",
-                          "http://identifiers.org/go/GO:0000165"
-MAPK_in_Scaffold homolog "http://identifiers.org/reactome/REACT_634"
-MAPK_in_Scaffold taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000015.txt

@@ -1,411 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000015()
-
-  // Compartments and Species:
-  compartment cell;
-  substanceOnly species PRPP in cell, IMP in cell, SAMP in cell, ATP in cell;
-  substanceOnly species SAM in cell, Ade in cell, XMP in cell, GTP in cell;
-  substanceOnly species dATP in cell, dGTP in cell, RNA in cell, DNA_ in cell;
-  substanceOnly species HX in cell, Xa in cell, Gua in cell, UA in cell, $R5P in cell;
-  substanceOnly species $Pi in cell;
-
-  // Reactions:
-  ada: ATP => HX; ada_aada*ATP^ada_fada4;
-  ade: Ade => ; ade_aade*Ade^ade_fade6;
-  adna: dATP => DNA_; adna_aadna*dATP^adna_fdnap9*dGTP^adna_fdnap10;
-  adrnr: ATP => dATP; adrnr_aadrnr*ATP^adrnr_fadrnr4*dATP^adrnr_fadrnr9*dGTP^adrnr_fadrnr10;
-  ampd: ATP => IMP; ampd_aampd*ATP^ampd_fampd4*GTP^ampd_fampd8*Pi^ampd_fampd18;
-  aprt: PRPP + Ade => ATP; aprt_aaprt*PRPP^aprt_faprt1*ATP^aprt_faprt4*Ade^aprt_faprt6;
-  arna: ATP => RNA; arna_aarna*ATP^arna_frnap4*GTP^arna_frnap8;
-  asuc: IMP => SAMP; asuc_aasuc*IMP^asuc_fasuc2*ATP^asuc_fasuc4*GTP^asuc_fasuc8*Pi^asuc_fasuc18;
-  asli: SAMP => ATP; asli_aasli*SAMP^asli_fasli3*ATP^asli_fasli4;
-  dada: dATP => HX; dada_adada*dATP^dada_fdada9;
-  den: PRPP => IMP; den_aden*PRPP^den_fden1*IMP^den_fden2*ATP^den_fden4*GTP^den_fden8*Pi^den_fden18;
-  dgnuc: dGTP => Gua; dgnuc_adgnuc*dGTP^dgnuc_fdgnuc10;
-  dnaa: DNA_ => dATP; dnaa_adnaa*DNA_^dnaa_fdnan12;
-  dnag: DNA_ => dGTP; dnag_adnag*DNA_^dnag_fdnan12;
-  gdna: dGTP => DNA_; gdna_agdna*dATP^gdna_fdnap9*dGTP^gdna_fdnap10;
-  gdrnr: GTP => dGTP; gdrnr_agdrnr*GTP^gdrnr_fgdrnr8*dATP^gdrnr_fgdrnr9*dGTP^gdrnr_fgdrnr10;
-  gmpr: GTP => IMP; gmpr_agmpr*IMP^gmpr_fgmpr2*ATP^gmpr_fgmpr4*XMP^gmpr_fgmpr7*GTP^gmpr_fgmpr8;
-  gmps: XMP => GTP; gmps_agmps*ATP^gmps_fgmps4*XMP^gmps_fgmps7;
-  gnuc: GTP => Gua; gnuc_agnuc*GTP^gnuc_fgnuc8*Pi^gnuc_fgnuc18;
-  gprt: Gua + PRPP => GTP; gprt_agprt*PRPP^gprt_fgprt1*GTP^gprt_fgprt8*Gua^gprt_fgprt15;
-  grna: GTP => RNA; grna_agrna*ATP^grna_frnap4*GTP^grna_frnap8;
-  gua: Gua => Xa; gua_agua*Gua^gua_fgua15;
-  hprt: HX + PRPP => IMP; hprt_ahprt*PRPP^hprt_fhprt1*IMP^hprt_fhprt2*HX^hprt_fhprt13;
-  hx: HX => ; hx_ahx*HX^hx_fhx13;
-  hxd: HX => Xa; hxd_ahxd*HX^hxd_fhxd13;
-  impd: IMP => XMP; impd_aimpd*IMP^impd_fimpd2*XMP^impd_fimpd7*GTP^impd_fimpd8;
-  inuc: IMP => HX; inuc_ainuc*IMP^inuc_finuc2*Pi^inuc_finuc18;
-  mat: ATP => SAM; mat_amat*ATP^mat_fmat4*SAM^mat_fmat5;
-  polyam: SAM => Ade; polyam_apolyam*SAM^polyam_fpolyam5;
-  prpps: $R5P => PRPP; prpps_aprpps*PRPP^prpps_fprpps1*ATP^prpps_fprpps4*GTP^prpps_fprpps8*R5P^prpps_fprpps17*Pi^prpps_fprpps18;
-  pyr: PRPP => ; pyr_apyr*PRPP^pyr_fpyr1;
-  rnaa: RNA => ATP; rnaa_arnaa*RNA^rnaa_frnan11;
-  rnag: RNA => GTP; rnag_arnag*RNA^rnag_frnan11;
-  trans: SAM => ATP; trans_atrans*SAM^trans_ftrans5;
-  ua: UA => ; ua_aua*UA^ua_fua16;
-  x: Xa => ; x_ax*Xa^x_fx14;
-  xd: Xa => UA; xd_axd*Xa^xd_fxd14;
-
-  // Species initializations:
-  PRPP = 5.01742/cell;
-  IMP = 98.2634/cell;
-  SAMP = 0.198189/cell;
-  ATP = 2475.35/cell;
-  SAM = 3.99187/cell;
-  Ade = 0.98473/cell;
-  XMP = 24.793/cell;
-  GTP = 410.223/cell;
-  dATP = 6.01413/cell;
-  dGTP = 3.02581/cell;
-  RNA = 28680.5/cell;
-  DNA_ = 5179.34/cell;
-  HX = 9.51785/cell;
-  Xa = 5.05941/cell;
-  Gua = 5.50638/cell;
-  UA = 100.293/cell;
-  R5P = 18/cell;
-  Pi = 1400/cell;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  ada_aada = 0.001062;
-  ada_fada4 = 0.97;
-  ade_aade = 0.01;
-  ade_fade6 = 0.55;
-  adna_aadna = 3.2789;
-  adna_fdnap9 = 0.42;
-  adna_fdnap10 = 0.33;
-  adrnr_aadrnr = 0.0602;
-  adrnr_fadrnr4 = 0.1;
-  adrnr_fadrnr9 = -0.3;
-  adrnr_fadrnr10 = 0.87;
-  ampd_aampd = 0.02688;
-  ampd_fampd4 = 0.8;
-  ampd_fampd8 = -0.03;
-  ampd_fampd18 = -0.1;
-  aprt_aaprt = 233.8;
-  aprt_faprt1 = 0.5;
-  aprt_faprt4 = -0.8;
-  aprt_faprt6 = 0.75;
-  arna_aarna = 614.5;
-  arna_frnap4 = 0.05;
-  arna_frnap8 = 0.13;
-  asuc_aasuc = 3.5932;
-  asuc_fasuc2 = 0.4;
-  asuc_fasuc4 = -0.24;
-  asuc_fasuc8 = 0.2;
-  asuc_fasuc18 = -0.05;
-  asli_aasli = 66544;
-  asli_fasli3 = 0.99;
-  asli_fasli4 = -0.95;
-  dada_adada = 0.03333;
-  dada_fdada9 = 1;
-  den_aden = 5.2728;
-  den_fden1 = 2;
-  den_fden2 = -0.06;
-  den_fden4 = -0.25;
-  den_fden8 = -0.2;
-  den_fden18 = -0.08;
-  dgnuc_adgnuc = 0.03333;
-  dgnuc_fdgnuc10 = 1;
-  dnaa_adnaa = 0.001938;
-  dnaa_fdnan12 = 1;
-  dnag_adnag = 0.001318;
-  dnag_fdnan12 = 1;
-  gdna_agdna = 2.2296;
-  gdna_fdnap9 = 0.42;
-  gdna_fdnap10 = 0.33;
-  gdrnr_agdrnr = 0.1199;
-  gdrnr_fgdrnr8 = 0.4;
-  gdrnr_fgdrnr9 = -1.2;
-  gdrnr_fgdrnr10 = -0.39;
-  gmpr_agmpr = 0.3005;
-  gmpr_fgmpr2 = -0.15;
-  gmpr_fgmpr4 = -0.07;
-  gmpr_fgmpr7 = -0.76;
-  gmpr_fgmpr8 = 0.7;
-  gmps_agmps = 0.3738;
-  gmps_fgmps4 = 0.12;
-  gmps_fgmps7 = 0.16;
-  gnuc_agnuc = 0.2511;
-  gnuc_fgnuc8 = 0.9;
-  gnuc_fgnuc18 = -0.34;
-  gprt_agprt = 361.69;
-  gprt_fgprt1 = 1.2;
-  gprt_fgprt8 = -1.2;
-  gprt_fgprt15 = 0.42;
-  grna_agrna = 409.6;
-  grna_frnap4 = 0.05;
-  grna_frnap8 = 0.13;
-  gua_agua = 0.4919;
-  gua_fgua15 = 0.5;
-  hprt_ahprt = 12.569;
-  hprt_fhprt1 = 1.1;
-  hprt_fhprt2 = -0.89;
-  hprt_fhprt13 = 0.48;
-  hx_ahx = 0.003793;
-  hx_fhx13 = 1.12;
-  hxd_ahxd = 0.2754;
-  hxd_fhxd13 = 0.65;
-  impd_aimpd = 1.2823;
-  impd_fimpd2 = 0.15;
-  impd_fimpd7 = -0.09;
-  impd_fimpd8 = -0.03;
-  inuc_ainuc = 0.9135;
-  inuc_finuc2 = 0.8;
-  inuc_finuc18 = -0.36;
-  mat_amat = 7.2067;
-  mat_fmat4 = 0.2;
-  mat_fmat5 = -0.6;
-  polyam_apolyam = 0.29;
-  polyam_fpolyam5 = 0.9;
-  prpps_aprpps = 0.9;
-  prpps_fprpps1 = -0.03;
-  prpps_fprpps4 = -0.45;
-  prpps_fprpps8 = -0.04;
-  prpps_fprpps17 = 0.65;
-  prpps_fprpps18 = 0.7;
-  pyr_apyr = 1.2951;
-  pyr_fpyr1 = 1.27;
-  rnaa_arnaa = 0.06923;
-  rnaa_frnan11 = 1;
-  rnag_arnag = 0.04615;
-  rnag_frnan11 = 1;
-  trans_atrans = 8.8539;
-  trans_ftrans5 = 0.33;
-  ua_aua = 8.744e-05;
-  ua_fua16 = 2.21;
-  x_ax = 0.0012;
-  x_fx14 = 2;
-  xd_axd = 0.949;
-  xd_fxd14 = 0.55;
-
-  // Other declarations:
-  const cell;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-  PRPP is "phosphoribosylpyrophosphate";
-  IMP is "inosine monophosphate";
-  SAMP is "adenylosuccinate";
-  ATP is "ATP_ADP_AMP_Ado";
-  SAM is "s-adenosyl-L-methionine";
-  Ade is "adenine";
-  XMP is "xanthosine monophosphate";
-  GTP is "GTP_GDP_GMP";
-  dATP is "dATP_dADP_dAMP_dAdo";
-  dGTP is "dGTP_dGDP_dGMP";
-  HX is "dIno_Ino_HX";
-  Xa is "xanthine";
-  Gua is "guanine";
-  UA is "uric acid";
-  R5P is "ribose-5-phosphate";
-  Pi is "phosphate";
-
-  // CV terms:
-  cell hypernym "http://identifiers.org/go/GO:0005623"
-  PRPP identity "http://identifiers.org/chebi/CHEBI:17111",
-                "http://identifiers.org/kegg.compound/C00119"
-  IMP identity "http://identifiers.org/chebi/CHEBI:17202",
-               "http://identifiers.org/kegg.compound/C00130"
-  SAMP identity "http://identifiers.org/chebi/CHEBI:15919",
-                "http://identifiers.org/kegg.compound/C03794"
-  ATP part "http://identifiers.org/chebi/CHEBI:15422",
-           "http://identifiers.org/chebi/CHEBI:16335",
-           "http://identifiers.org/chebi/CHEBI:16027",
-           "http://identifiers.org/chebi/CHEBI:16761"
-  ATP part "http://identifiers.org/kegg.compound/C00008",
-           "http://identifiers.org/kegg.compound/C00212",
-           "http://identifiers.org/kegg.compound/C00020",
-           "http://identifiers.org/kegg.compound/C00002",
-           "http://identifiers.org/chebi/CHEBI:16761"
-  SAM identity "http://identifiers.org/chebi/CHEBI:15414",
-               "http://identifiers.org/kegg.compound/C00019"
-  Ade identity "http://identifiers.org/chebi/CHEBI:16708",
-               "http://identifiers.org/kegg.compound/C00147"
-  XMP identity "http://identifiers.org/chebi/CHEBI:15652",
-               "http://identifiers.org/kegg.compound/C00655"
-  GTP part "http://identifiers.org/kegg.compound/C00035",
-           "http://identifiers.org/kegg.compound/C00144",
-           "http://identifiers.org/kegg.compound/C00044",
-           "http://identifiers.org/chebi/CHEBI:17552"
-  GTP part "http://identifiers.org/chebi/CHEBI:17345",
-           "http://identifiers.org/chebi/CHEBI:17552",
-           "http://identifiers.org/chebi/CHEBI:15996"
-  dATP part "http://identifiers.org/kegg.compound/C00131",
-            "http://identifiers.org/kegg.compound/C00206",
-            "http://identifiers.org/kegg.compound/C00360",
-            "http://identifiers.org/kegg.compound/C00559",
-            "http://identifiers.org/chebi/CHEBI:16284"
-  dATP part "http://identifiers.org/chebi/CHEBI:16284",
-            "http://identifiers.org/chebi/CHEBI:16174",
-            "http://identifiers.org/chebi/CHEBI:17256",
-            "http://identifiers.org/chebi/CHEBI:17713"
-  dGTP part "http://identifiers.org/kegg.compound/C00286",
-            "http://identifiers.org/kegg.compound/C00362",
-            "http://identifiers.org/kegg.compound/C00361",
-            "http://identifiers.org/chebi/CHEBI:16497"
-  dGTP part "http://identifiers.org/chebi/CHEBI:28862",
-            "http://identifiers.org/chebi/CHEBI:16192",
-            "http://identifiers.org/chebi/CHEBI:16497"
-  RNA identity "http://identifiers.org/kegg.compound/C00046"
-  DNA_ identity "http://identifiers.org/kegg.compound/C00039",
-                "http://identifiers.org/chebi/CHEBI:16991"
-  HX part "http://identifiers.org/kegg.compound/C00262",
-          "http://identifiers.org/kegg.compound/C05512",
-          "http://identifiers.org/kegg.compound/C00294"
-  HX part "http://identifiers.org/chebi/CHEBI:17596",
-          "http://identifiers.org/chebi/CHEBI:17368",
-          "http://identifiers.org/chebi/CHEBI:28997"
-  Xa identity "http://identifiers.org/chebi/CHEBI:17712",
-              "http://identifiers.org/kegg.compound/C00385"
-  Gua part "http://identifiers.org/kegg.compound/C00242",
-           "http://identifiers.org/kegg.compound/C00330",
-           "http://identifiers.org/kegg.compound/C00387"
-  Gua part "http://identifiers.org/chebi/CHEBI:16450",
-           "http://identifiers.org/chebi/CHEBI:16235",
-           "http://identifiers.org/chebi/CHEBI:17172"
-  UA identity "http://identifiers.org/chebi/CHEBI:17775",
-              "http://identifiers.org/kegg.compound/C00366"
-  R5P identity "http://identifiers.org/chebi/CHEBI:17797",
-               "http://identifiers.org/kegg.compound/C00117"
-  Pi identity "http://identifiers.org/chebi/CHEBI:18367",
-              "http://identifiers.org/kegg.compound/C00009"
-  ada hypernym "http://identifiers.org/ec-code/3.5.4.4"
-  ada version "http://identifiers.org/kegg.reaction/R01560",
-              "http://identifiers.org/reactome/REACT_1687"
-  ade hypernym "http://identifiers.org/go/GO:0006146"
-  adna hypernym "http://identifiers.org/ec-code/2.7.7.7"
-  adna identity "http://identifiers.org/kegg.reaction/R00375"
-  adrnr version "http://identifiers.org/ec-code/1.17.4.2",
-                "http://identifiers.org/ec-code/1.17.4.1",
-                "http://identifiers.org/kegg.reaction/R02017",
-                "http://identifiers.org/kegg.reaction/R02014",
-                "http://identifiers.org/reactome/REACT_2136"
-  ampd identity "http://identifiers.org/kegg.reaction/R00181"
-  ampd hypernym "http://identifiers.org/ec-code/3.5.4.6"
-  aprt hypernym "http://identifiers.org/ec-code/2.4.2.7"
-  aprt identity "http://identifiers.org/kegg.reaction/R00190"
-  arna hypernym "http://identifiers.org/ec-code/2.7.7.6"
-  arna identity "http://identifiers.org/kegg.reaction/R00435"
-  asuc hypernym "http://identifiers.org/ec-code/6.3.4.4"
-  asuc identity "http://identifiers.org/kegg.reaction/R01135",
-                "http://identifiers.org/reactome/REACT_42"
-  asli hypernym "http://identifiers.org/ec-code/4.3.2.2"
-  asli identity "http://identifiers.org/kegg.reaction/R01083",
-                "http://identifiers.org/reactome/REACT_1042"
-  dada hypernym "http://identifiers.org/ec-code/3.5.4.4"
-  dada identity "http://identifiers.org/kegg.reaction/R02556",
-                "http://identifiers.org/reactome/REACT_2135"
-  den part "http://identifiers.org/reactome/REACT_108",
-           "http://identifiers.org/reactome/REACT_812",
-           "http://identifiers.org/reactome/REACT_1463",
-           "http://identifiers.org/reactome/REACT_589",
-           "http://identifiers.org/reactome/REACT_1917",
-           "http://identifiers.org/reactome/REACT_1509",
-           "http://identifiers.org/reactome/REACT_740",
-           "http://identifiers.org/reactome/REACT_285",
-           "http://identifiers.org/reactome/REACT_1427",
-           "http://identifiers.org/reactome/REACT_263"
-  den part "http://identifiers.org/ec-code/2.4.2.14",
-           "http://identifiers.org/ec-code/6.3.4.13",
-           "http://identifiers.org/ec-code/2.1.2.2",
-           "http://identifiers.org/ec-code/6.3.5.3",
-           "http://identifiers.org/ec-code/6.3.3.1",
-           "http://identifiers.org/ec-code/4.1.1.21",
-           "http://identifiers.org/ec-code/6.3.2.6",
-           "http://identifiers.org/ec-code/4.3.2.2",
-           "http://identifiers.org/ec-code/2.1.2.3",
-           "http://identifiers.org/ec-code/3.5.4.10"
-  den part "http://identifiers.org/kegg.reaction/R04144",
-           "http://identifiers.org/kegg.reaction/R04325",
-           "http://identifiers.org/kegg.reaction/R04463",
-           "http://identifiers.org/kegg.reaction/R04208",
-           "http://identifiers.org/kegg.reaction/R04209",
-           "http://identifiers.org/kegg.reaction/R04559",
-           "http://identifiers.org/kegg.reaction/R04560",
-           "http://identifiers.org/kegg.reaction/R04591",
-           "http://identifiers.org/kegg.reaction/R01127",
-           "http://identifiers.org/kegg.reaction/R01072"
-  dgnuc hypernym "http://identifiers.org/ec-code/3.1.3.5"
-  dgnuc identity "http://identifiers.org/kegg.reaction/R01968",
-                 "http://identifiers.org/reactome/REACT_1209"
-  dnaa hypernym "http://identifiers.org/go/GO:0006308"
-  dnag hypernym "http://identifiers.org/go/GO:0006308"
-  gdna identity "http://identifiers.org/kegg.reaction/R00376"
-  gdna hypernym "http://identifiers.org/ec-code/2.7.7.7"
-  gdrnr version "http://identifiers.org/ec-code/1.17.4.2",
-                "http://identifiers.org/ec-code/1.17.4.1",
-                "http://identifiers.org/kegg.reaction/R02019",
-                "http://identifiers.org/kegg.reaction/R02020",
-                "http://identifiers.org/reactome/REACT_906"
-  gmpr hypernym "http://identifiers.org/ec-code/1.7.1.7"
-  gmpr identity "http://identifiers.org/kegg.reaction/R01134"
-  gmps hypernym "http://identifiers.org/ec-code/6.3.5.2"
-  gmps identity "http://identifiers.org/kegg.reaction/R01231",
-                "http://identifiers.org/reactome/REACT_628"
-  gnuc hypernym "http://identifiers.org/ec-code/3.1.3.5"
-  gnuc identity "http://identifiers.org/kegg.reaction/R01227",
-                "http://identifiers.org/reactome/REACT_1774"
-  gprt hypernym "http://identifiers.org/ec-code/2.4.2.7"
-  gprt identity "http://identifiers.org/kegg.reaction/R01229"
-  grna hypernym "http://identifiers.org/ec-code/2.7.7.6"
-  grna identity "http://identifiers.org/kegg.reaction/R00441"
-  gua hypernym "http://identifiers.org/ec-code/3.5.4.3"
-  gua identity "http://identifiers.org/kegg.reaction/R01676",
-               "http://identifiers.org/reactome/REACT_1442"
-  hprt hypernym "http://identifiers.org/ec-code/2.4.2.8"
-  hprt identity "http://identifiers.org/kegg.reaction/R01132"
-  hx hypernym "http://identifiers.org/go/GO:0009114"
-  hxd hypernym "http://identifiers.org/ec-code/1.17.3.2"
-  hxd identity "http://identifiers.org/kegg.reaction/R01769",
-               "http://identifiers.org/reactome/REACT_401"
-  impd hypernym "http://identifiers.org/ec-code/1.1.1.205"
-  impd identity "http://identifiers.org/kegg.reaction/R01130",
-                "http://identifiers.org/reactome/REACT_1488"
-  inuc identity "http://identifiers.org/kegg.reaction/R01126",
-                "http://identifiers.org/reactome/REACT_430"
-  inuc hypernym "http://identifiers.org/ec-code/3.1.3.5"
-  mat identity "http://identifiers.org/kegg.reaction/R00177"
-  mat hypernym "http://identifiers.org/ec-code/2.5.1.6"
-  polyam part "http://identifiers.org/kegg.reaction/R02869",
-              "http://identifiers.org/kegg.reaction/R00178",
-              "http://identifiers.org/kegg.reaction/R01401"
-  polyam part "http://identifiers.org/ec-code/3.2.2.16",
-              "http://identifiers.org/ec-code/2.5.1.22",
-              "http://identifiers.org/ec-code/4.1.1.50"
-  polyam parthood "http://identifiers.org/kegg.pathway/map00330"
-  prpps identity "http://identifiers.org/kegg.reaction/R01049"
-  prpps hypernym "http://identifiers.org/ec-code/2.7.6.1"
-  pyr identity "http://identifiers.org/kegg.reaction/R01870",
-               "http://identifiers.org/reactome/REACT_33"
-  pyr parthood "http://identifiers.org/kegg.pathway/map00240"
-  pyr hypernym "http://identifiers.org/ec-code/2.4.2.10"
-  rnaa hypernym "http://identifiers.org/go/GO:0006401"
-  rnag hypernym "http://identifiers.org/go/GO:0006401"
-  trans identity "http://identifiers.org/go/GO:0008757"
-  ua hypernym "http://identifiers.org/go/GO:0007588"
-  x hypernym "http://identifiers.org/go/GO:0009115"
-  xd identity "http://identifiers.org/kegg.reaction/R02107",
-              "http://identifiers.org/reactome/REACT_624"
-  xd hypernym "http://identifiers.org/ec-code/1.17.3.2"
-end
-
-BIOMD0000000015 is "Curto1998 - purine metabolism"
-
-BIOMD0000000015 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617035399"
-BIOMD0000000015 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000015"
-BIOMD0000000015 description "http://identifiers.org/pubmed/9664759"
-BIOMD0000000015 taxon "http://identifiers.org/taxonomy/9606"
-BIOMD0000000015 identity "http://identifiers.org/kegg.pathway/hsa00230",
-                         "http://identifiers.org/reactome/REACT_522"
-BIOMD0000000015 hypernym "http://identifiers.org/go/GO:0006144"

BioModelsRAG/data/BIOMD0000000016.txt

@@ -1,119 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter1995()
-
-  // Compartments and Species:
-  compartment default, CYTOPLASM, compartment_0000004;
-  species $EmptySet in default, M in CYTOPLASM, P0 in CYTOPLASM, P1 in CYTOPLASM;
-  species P2 in CYTOPLASM, Pn in compartment_0000004, $Pt in CYTOPLASM;
-
-  // Assignment Rules:
-  Pt := P0 + P1 + P2 + Pn;
-
-  // Reactions:
-  rM: $EmptySet => M; default*rM_Vs*rM_KI^rM_n/(rM_KI^rM_n + Pn^rM_n);
-  rTL: $EmptySet => P0; rTL_ks*M*default;
-  rP01: P0 => P1; CYTOPLASM*rP01_V1*P0/(rP01_K1 + P0);
-  rP10: P1 => P0; CYTOPLASM*rP10_V2*P1/(rP10_K2 + P1);
-  rP12: P1 => P2; CYTOPLASM*rP12_V3*P1/(rP12_K3 + P1);
-  rP21: P2 => P1; CYTOPLASM*rP21_V4*P2/(rP21_K4 + P2);
-  rP2n: P2 => Pn; rP2n_k1*P2*CYTOPLASM;
-  rPn2: Pn => P2; rPn2_k2*Pn*compartment_0000004;
-  rmRNAd: M => $EmptySet; rmRNAd_Vm*M*CYTOPLASM/(rmRNAd_Km + M);
-  rVd: P2 => $EmptySet; CYTOPLASM*rVd_Vd*P2/(rVd_Kd + P2);
-
-  // Species initializations:
-  EmptySet = 0;
-  M = 0.1;
-  P0 = 0.25;
-  P1 = 0.25;
-  P2 = 0.25;
-  Pn = 0.25;
-
-  // Compartment initializations:
-  default = 1e-15;
-  CYTOPLASM = 1e-15;
-  compartment_0000004 = 1e-15;
-
-  // Variable initializations:
-  rM_Vs = 0.76;
-  rM_KI = 1;
-  rM_n = 4;
-  rTL_ks = 0.38;
-  rP01_V1 = 3.2;
-  rP01_K1 = 2;
-  rP10_V2 = 1.58;
-  rP10_K2 = 2;
-  rP12_V3 = 5;
-  rP12_K3 = 2;
-  rP21_V4 = 2.5;
-  rP21_K4 = 2;
-  rP2n_k1 = 1.9;
-  rPn2_k2 = 1.3;
-  rmRNAd_Km = 0.5;
-  rmRNAd_Vm = 0.65;
-  rVd_Vd = 0.95;
-  rVd_Kd = 0.2;
-
-  // Other declarations:
-  const default, CYTOPLASM, compartment_0000004;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "heure (default)";
-  compartment_0000004 is "NUCLEUS";
-  M is "PER mRNA";
-  P0 is "unphosphorylated PER";
-  P1 is "monophosphorylated PER";
-  P2 is "biphosphorylated PER";
-  Pn is "nuclear PER";
-  Pt is "total PER";
-  rM is "transcription of PER";
-  rTL is "translation of PER";
-  rP01 is "first phosphorylation of PER";
-  rP10 is "removal of the first PER phosphate";
-  rP12 is "second phosphorylation of PER";
-  rP21 is "removal of the second PER phosphate";
-  rP2n is "translocation of PER to the nucleus";
-  rPn2 is "translocation of PER to the cytoplasm";
-  rmRNAd is "degradation of PER mRNA";
-  rVd is "degradation of PER";
-
-  // CV terms:
-  CYTOPLASM identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000004 identity "http://identifiers.org/go/GO:0005634"
-  M hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  P0 hypernym "http://identifiers.org/uniprot/P07663"
-  P1 hypernym "http://identifiers.org/uniprot/P07663"
-  P2 hypernym "http://identifiers.org/uniprot/P07663"
-  Pn identity "http://identifiers.org/uniprot/P07663"
-  Pt identity "http://identifiers.org/uniprot/P07663"
-  rM hypernym "http://identifiers.org/go/GO:0006355",
-              "http://identifiers.org/go/GO:0009299"
-  rTL hypernym "http://identifiers.org/go/GO:0006412"
-  rP01 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                "http://identifiers.org/go/GO:0006468"
-  rP10 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470"
-  rP12 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                "http://identifiers.org/go/GO:0006468"
-  rP21 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                "http://identifiers.org/go/GO:0006470"
-  rP2n hypernym "http://identifiers.org/go/GO:0006606"
-  rPn2 hypernym "http://identifiers.org/go/GO:0006611"
-  rmRNAd hypernym "http://identifiers.org/go/GO:0006402"
-  rVd hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-Goldbeter1995 is "Goldbeter1995_CircClock"
-
-Goldbeter1995 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617161845"
-Goldbeter1995 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000016"
-Goldbeter1995 description "http://identifiers.org/pubmed/8587874"
-Goldbeter1995 identity "http://identifiers.org/kegg.pathway/dme04710"
-Goldbeter1995 taxon "http://identifiers.org/taxonomy/7227"
-Goldbeter1995 hypernym "http://identifiers.org/go/GO:0042752"

BioModelsRAG/data/BIOMD0000000017.txt

@@ -1,218 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Hoefnagel2002_PyruvateBranches()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species $PO4 in compartment_;
-  substanceOnly species ADP in compartment_, NAD in compartment_, ATP in compartment_;
-  substanceOnly species NADH in compartment_, pyruvate in compartment_, $lactate in compartment_;
-  substanceOnly species CoA in compartment_, $halfglucose in compartment_;
-  substanceOnly species AcCoA in compartment_, AcP in compartment_, $Ac in compartment_;
-  substanceOnly species AcO in compartment_, $EtOH in compartment_, AcLac in compartment_;
-  substanceOnly species AcetoinIn in compartment_, $AcetoinOut in compartment_;
-  substanceOnly species $Butanediol in compartment_, $O2 in compartment_;
-
-  // Reactions:
-  R1: ADP + NAD + $halfglucose => ATP + NADH + pyruvate; 2*R1_V_1*(halfglucose/(2*R1_Kglc_1))*(NAD/R1_Knad_1)*(ADP/R1_Kadp_1)/((1 + halfglucose/(2*R1_Kglc_1) + pyruvate/R1_Kpyr_1)*(1 + NAD/R1_Knad_1 + NADH/R1_Knadh_1)*(1 + ADP/R1_Kadp_1 + ATP/R1_Katp_1));
-  R2: NADH + pyruvate => NAD + $lactate; R2_V_2*((pyruvate*NADH - lactate*NAD/R2_Keq_2)/(R2_Kpyr_2*R2_Knadh_2))/((1 + pyruvate/R2_Kpyr_2 + lactate/R2_Klac_2)*(1 + NADH/R2_Knadh_2 + NAD/R2_Knad_2));
-  R3: NAD + pyruvate + CoA => NADH + AcCoA; R3_V_3*(pyruvate/R3_Kpyr_3)*(NAD/R3_Knad_3)*(CoA/R3_Kcoa_3)*(NAD/(NAD + R3_Ki_3*NADH))/((1 + pyruvate/R3_Kpyr_3)*(1 + NAD/R3_Knad_3 + NADH/R3_Knadh_3)*(1 + CoA/R3_Kcoa_3 + AcCoA/R3_Kaccoa_3));
-  R4: AcCoA + $PO4 => CoA + AcP; R4_V_4*((AcCoA*PO4 - AcP*CoA/R4_Keq_4)/(R4_Kiaccoa_4*R4_Kpi_4))/(1 + AcCoA/R4_Kiaccoa_4 + PO4/R4_Kipi_4 + AcP/R4_Kiacp_4 + CoA/R4_Kicoa_4 + AcCoA*PO4/(R4_Kiaccoa_4*R4_Kpi_4) + AcP*CoA/(R4_Kacp_4*R4_Kicoa_4));
-  R5: ADP + AcP => ATP + $Ac; R5_V_5*((AcP*ADP - Ac*ATP/R5_Keq_5)/(R5_Kadp_5*R5_Kacp_5))/((1 + AcP/R5_Kacp_5 + Ac/R5_Kac_5)*(1 + ADP/R5_Kadp_5 + ATP/R5_Katp_5));
-  R6: NADH + AcCoA => NAD + CoA + AcO; R6_V_6*((AcCoA*NADH - CoA*NAD*AcO/R6_Keq_6)/(R6_Kaccoa_6*R6_Knadh_6))/((1 + NAD/R6_Knad_6 + NADH/R6_Knadh_6)*(1 + AcCoA/R6_Kaccoa_6 + CoA/R6_Kcoa_6)*(1 + AcO/R6_Kaco_6));
-  R7: NADH + AcO => NAD + $EtOH; R7_V_7*((AcO*NADH - EtOH*NAD/R7_Keq_7)/(R7_Kaco_7*R7_Knadh_7))/((1 + NAD/R7_Knad_7 + NADH/R7_Knadh_7)*(1 + AcO/R7_Kaco_7 + EtOH/R7_Ketoh_7));
-  R8: 2 pyruvate => AcLac; R8_V_8*(pyruvate/R8_Kpyr_8)*(1 - AcLac/(pyruvate*R8_Keq_8))*(pyruvate/R8_Kpyr_8 + AcLac/R8_Kaclac_8)^(R8_n_8 - 1)/(1 + (pyruvate/R8_Kpyr_8 + AcLac/R8_Kaclac_8)^R8_n_8);
-  R9: AcLac => AcetoinIn; R9_V_9*(AcLac/R9_Kaclac_9)/(1 + AcLac/R9_Kaclac_9 + AcetoinIn/R9_Kacet_9);
-  R10: AcetoinIn => $AcetoinOut; R10_V_10*(AcetoinIn/R10_Kacet_10)/(1 + AcetoinIn/R10_Kacet_10);
-  R11: NADH + AcetoinIn => NAD + $Butanediol; R11_V_11*((AcetoinIn*NADH - Butanediol*NAD/R11_Keq_11)/(R11_Kacet_11*R11_Knadh_11))/((1 + AcetoinIn/R11_Kacet_11 + Butanediol/R11_Kbut_11)*(1 + NADH/R11_Knadh_11 + NAD/R11_Knad_11));
-  R12: ATP => ADP; R12_V_12*(ATP/(ADP*R12_Katp_12))^R12_n_12/(1 + (ATP/(ADP*R12_Katp_12))^R12_n_12);
-  R13: NADH + $O2 => NAD; R13_V_13*(NADH*O2/(R13_Knadh_13*R13_Ko_13))/((1 + NADH/R13_Knadh_13 + NAD/R13_Knad_13)*(1 + O2/R13_Ko_13));
-  R14: AcLac => AcetoinIn; R14_k_14*AcLac;
-
-  // Species initializations:
-  ADP = 4.9/compartment_;
-  NAD = 6.33/compartment_;
-  ATP = 0.1/compartment_;
-  NADH = 3.67/compartment_;
-  pyruvate = 1/compartment_;
-  lactate = 0.1/compartment_;
-  CoA = 1/compartment_;
-  halfglucose = 30/compartment_;
-  AcCoA = 0;
-  AcP = 0;
-  Ac = 1/compartment_;
-  AcO = 0;
-  EtOH = 1/compartment_;
-  AcLac = 0;
-  AcetoinIn = 0;
-  AcetoinOut = 0;
-  Butanediol = 0.01/compartment_;
-  O2 = 0.2/compartment_;
-  PO4 = 10/compartment_;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  R1_V_1 = 2397;
-  R1_Kglc_1 = 0.1;
-  R1_Knad_1 = 0.1412;
-  R1_Kadp_1 = 0.04699;
-  R1_Kpyr_1 = 2.5;
-  R1_Knadh_1 = 0.08999;
-  R1_Katp_1 = 0.01867;
-  R2_V_2 = 5118;
-  R2_Keq_2 = 21120.69;
-  R2_Kpyr_2 = 1.5;
-  R2_Knadh_2 = 0.08;
-  R2_Klac_2 = 100;
-  R2_Knad_2 = 2.4;
-  R3_V_3 = 259;
-  R3_Kpyr_3 = 1;
-  R3_Knad_3 = 0.4;
-  R3_Kcoa_3 = 0.014;
-  R3_Ki_3 = 46.4159;
-  R3_Knadh_3 = 0.1;
-  R3_Kaccoa_3 = 0.008;
-  R4_V_4 = 42;
-  R4_Keq_4 = 0.0065;
-  R4_Kiaccoa_4 = 0.2;
-  R4_Kpi_4 = 2.6;
-  R4_Kipi_4 = 2.6;
-  R4_Kiacp_4 = 0.2;
-  R4_Kicoa_4 = 0.029;
-  R4_Kacp_4 = 0.7;
-  R5_V_5 = 2700;
-  R5_Keq_5 = 174.217;
-  R5_Kadp_5 = 0.5;
-  R5_Kacp_5 = 0.16;
-  R5_Kac_5 = 7;
-  R5_Katp_5 = 0.07;
-  R6_V_6 = 97;
-  R6_Keq_6 = 1;
-  R6_Kaccoa_6 = 0.007;
-  R6_Knadh_6 = 0.025;
-  R6_Knad_6 = 0.08;
-  R6_Kcoa_6 = 0.008;
-  R6_Kaco_6 = 10;
-  R7_V_7 = 162;
-  R7_Keq_7 = 12354.9;
-  R7_Kaco_7 = 0.03;
-  R7_Knadh_7 = 0.05;
-  R7_Knad_7 = 0.08;
-  R7_Ketoh_7 = 1;
-  R8_V_8 = 600;
-  R8_Kpyr_8 = 50;
-  R8_Keq_8 = 9000000000000;
-  R8_Kaclac_8 = 100;
-  R8_n_8 = 2.4;
-  R9_V_9 = 106;
-  R9_Kaclac_9 = 10;
-  R9_Kacet_9 = 100;
-  R10_V_10 = 200;
-  R10_Kacet_10 = 5;
-  R11_V_11 = 105;
-  R11_Keq_11 = 1400;
-  R11_Kacet_11 = 0.06;
-  R11_Knadh_11 = 0.02;
-  R11_Kbut_11 = 2.6;
-  R11_Knad_11 = 0.16;
-  R12_V_12 = 900;
-  R12_Katp_12 = 6.196;
-  R12_n_12 = 2.58;
-  R13_V_13 = 118;
-  R13_Knadh_13 = 0.041;
-  R13_Ko_13 = 0.2;
-  R13_Knad_13 = 1;
-  R14_k_14 = 0.0003;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  pyruvate identity "http://identifiers.org/chebi/CHEBI:15361",
-                    "http://identifiers.org/kegg.compound/C00022"
-  lactate identity "http://identifiers.org/chebi/CHEBI:24996",
-                   "http://identifiers.org/kegg.compound/C00186"
-  CoA identity "http://identifiers.org/chebi/CHEBI:15346",
-               "http://identifiers.org/kegg.compound/C00010"
-  AcCoA identity "http://identifiers.org/chebi/CHEBI:15351",
-                 "http://identifiers.org/kegg.compound/C00024"
-  AcP identity "http://identifiers.org/chebi/CHEBI:15350",
-               "http://identifiers.org/kegg.compound/C00227"
-  Ac identity "http://identifiers.org/chebi/CHEBI:30089",
-              "http://identifiers.org/kegg.compound/C00033"
-  AcO identity "http://identifiers.org/chebi/CHEBI:15343",
-               "http://identifiers.org/kegg.compound/C00084"
-  EtOH identity "http://identifiers.org/chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  AcLac identity "http://identifiers.org/chebi/CHEBI:16444",
-                 "http://identifiers.org/kegg.compound/C00900"
-  AcetoinIn identity "http://identifiers.org/chebi/CHEBI:15688",
-                     "http://identifiers.org/kegg.compound/C00466"
-  AcetoinOut identity "http://identifiers.org/chebi/CHEBI:15688",
-                      "http://identifiers.org/kegg.compound/C00466"
-  Butanediol version "http://identifiers.org/chebi/CHEBI:16812",
-                     "http://identifiers.org/chebi/CHEBI:16982",
-                     "http://identifiers.org/kegg.compound/C03046",
-                     "http://identifiers.org/kegg.compound/C03044"
-  O2 identity "http://identifiers.org/chebi/CHEBI:15379",
-              "http://identifiers.org/kegg.compound/C00007"
-  PO4 identity "http://identifiers.org/chebi/CHEBI:18367",
-               "http://identifiers.org/kegg.compound/C00009"
-  R1 parthood "http://identifiers.org/kegg.pathway/map00010"
-  R2 version "http://identifiers.org/ec-code/1.1.1.27",
-             "http://identifiers.org/ec-code/1.1.1.28",
-             "http://identifiers.org/kegg.reaction/R00703",
-             "http://identifiers.org/kegg.reaction/R00704",
-             "http://identifiers.org/reactome/REACT_178"
-  R3 hypernym "http://identifiers.org/ec-code/1.2.1.51"
-  R3 identity "http://identifiers.org/kegg.reaction/R00209"
-  R4 hypernym "http://identifiers.org/ec-code/2.3.1.8"
-  R4 identity "http://identifiers.org/kegg.reaction/R00230"
-  R5 hypernym "http://identifiers.org/ec-code/2.7.2.1"
-  R5 identity "http://identifiers.org/kegg.reaction/R00315"
-  R6 hypernym "http://identifiers.org/ec-code/1.2.1.10"
-  R6 identity "http://identifiers.org/kegg.reaction/R00228"
-  R7 hypernym "http://identifiers.org/ec-code/1.1.1.1"
-  R7 identity "http://identifiers.org/kegg.reaction/R00754",
-              "http://identifiers.org/reactome/REACT_799"
-  R8 hypernym "http://identifiers.org/ec-code/2.2.1.6"
-  R8 identity "http://identifiers.org/kegg.reaction/R00006"
-  R9 identity "http://identifiers.org/kegg.reaction/R02947"
-  R9 hypernym "http://identifiers.org/ec-code/4.1.1.5"
-  R10 hypernym "http://identifiers.org/go/GO:0015562"
-  R11 version "http://identifiers.org/ec-code/1.1.1.4",
-              "http://identifiers.org/ec-code/1.1.1.76",
-              "http://identifiers.org/kegg.reaction/R02344",
-              "http://identifiers.org/kegg.reaction/R02946"
-  R12 hypernym "http://identifiers.org/go/GO:0016887"
-  R13 hypernym "http://identifiers.org/go/GO:0006116"
-end
-
-Hoefnagel2002_PyruvateBranches is "Hoefnagel2002_PyruvateBranches"
-
-Hoefnagel2002_PyruvateBranches model_entity_is "http://identifiers.org/biomodels.db/MODEL6617235316"
-Hoefnagel2002_PyruvateBranches model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000017"
-Hoefnagel2002_PyruvateBranches description "http://identifiers.org/pubmed/11932446"
-Hoefnagel2002_PyruvateBranches hypernym "http://identifiers.org/go/GO:0006090",
-                                        "http://identifiers.org/go/GO:0006089"
-Hoefnagel2002_PyruvateBranches parthood "http://identifiers.org/kegg.pathway/map00620",
-                                        "http://identifiers.org/kegg.pathway/map00650"
-Hoefnagel2002_PyruvateBranches taxon "http://identifiers.org/taxonomy/1358"
-Hoefnagel2002_PyruvateBranches property "http://identifiers.org/mamo/MAMO_0000046"

BioModelsRAG/data/BIOMD0000000018.txt

@@ -1,341 +0,0 @@
-// Created by libAntimony v2.13.0
-model *MorrisonAllegra()
-
-  // Compartments and Species:
-  compartment ext_, cell;
-  species FH2f in cell, $FH2b in cell, DHFRf in cell, $DHFRtot in cell, MTX1b in cell;
-  species MTX2b in cell, MTX3b in cell, MTX4b in cell, MTX5b in cell, FH4 in cell;
-  species CH2FH4 in cell, CH3FH4 in cell, CHOFH4 in cell, FFH2 in cell, HCHO in cell;
-  species FGAR in cell, AICAR in cell, MTX1 in cell, MTX2 in cell, MTX3 in cell;
-  species MTX4 in cell, MTX5 in cell, $EMTX in ext_, $dUMP in cell, $GAR in cell;
-  species $serine in cell, $formate in cell, $ATP in cell, $glutamine in cell;
-  species $glycine in cell, $NADP in cell, $NADPH in cell, $homocysteine in cell;
-
-  // Assignment Rules:
-  FH2b := FH2f*DHFRf/Keq;
-  DHFRtot := FH2b + DHFRf + MTX1b + MTX2b + MTX3b + MTX4b + MTX5b;
-
-  // Reactions:
-  SHMT: FH4 + $serine => CH2FH4; cell*(SHMT_Vm*(serine/SHMT_Km2/(1 + serine/SHMT_Km2))*(FH4/SHMT_Km1)/(1 + FH4/SHMT_Km1));
-  SHMTr: CH2FH4 => FH4; cell*(SHMTr_Vm*(glycine/SHMTr_Km2/(1 + glycine/SHMTr_Km2))*(CH2FH4/SHMTr_Km1)/(1 + CH2FH4/SHMTr_Km1));
-  HCHOtoCH2FH4: FH4 + HCHO => CH2FH4; cell*HCHOtoCH2FH4_hp*FH4*HCHO;
-  CH2FH4toHCHO: CH2FH4 => FH4 + HCHO; cell*CH2FH4toHCHO_hl*CH2FH4;
-  MTHFR: CH2FH4 + $NADPH => CH3FH4; cell*(MTHFR_Vm*CH2FH4*NADPH/(NADPH*CH2FH4 + CH2FH4*MTHFR_Km2 + (NADPH + MTHFR_Km2)*MTHFR_Km1*(1 + MTX1/MTHFR_Ki21 + MTX2/MTHFR_Ki22 + MTX3/MTHFR_Ki23 + MTX4/MTHFR_Ki24 + MTX5/MTHFR_Ki25 + FH2f/MTHFR_Ki1)));
-  MTR: CH3FH4 + $homocysteine => FH4; cell*(MTR_Vm*(homocysteine/MTR_Km2/(1 + homocysteine/MTR_Km2))*(CH3FH4/MTR_Km1)/(1 + CH3FH4/MTR_Km1));
-  HCOOHtoCHOFH4: FH4 + $formate + $ATP => CHOFH4; cell*(HCOOHtoCHOFH4_Vm/((1 + HCOOHtoCHOFH4_Km1/FH4)*(1 + HCOOHtoCHOFH4_Km2/ATP)*(1 + HCOOHtoCHOFH4_Km3/formate)));
-  GARFT: CHOFH4 + $GAR => FGAR + FH4; cell*(GARFT_Vm*CHOFH4*GAR/(GAR*CHOFH4 + CHOFH4*GARFT_Km2 + (GAR + GARFT_Km2)*GARFT_Km1*(1 + MTX1/GARFT_Ki21 + MTX2/GARFT_Ki22 + MTX3/GARFT_Ki23 + MTX4/GARFT_Ki24 + MTX5/GARFT_Ki25 + FH2f/GARFT_Ki1 + FFH2/GARFT_Ki1f)));
-  ATIC7: CHOFH4 + AICAR => FH4; cell*(ATIC7_Vm*CHOFH4*AICAR/(AICAR*CHOFH4 + CHOFH4*ATIC7_Km2 + (AICAR + ATIC7_Km2)*ATIC7_Km1*(1 + MTX1/ATIC7_Ki21 + MTX2/ATIC7_Ki22 + MTX3/ATIC7_Ki23 + MTX4/ATIC7_Ki24 + MTX5/ATIC7_Ki25 + FH2f/ATIC7_Ki1 + FFH2/ATIC7_Ki1f)));
-  MTHFD: CH2FH4 + $NADP => CHOFH4; cell*MTHFD_Vm*(CH2FH4/MTHFD_Km1/(1 + CH2FH4/MTHFD_Km1))*(NADP/MTHFD_Km2/(1 + NADP/MTHFD_Km2));
-  TYMS: CH2FH4 + $dUMP => FH2f; cell*(TYMS_Vm*CH2FH4*dUMP/(dUMP*CH2FH4*(1 + MTX1/TYMS_Ki21 + MTX2/TYMS_Ki22 + MTX3/TYMS_Ki23 + MTX4/TYMS_Ki24 + MTX5/TYMS_Ki25 + FH2f/TYMS_Ki1) + TYMS_Km1*dUMP*((FFH2/TYMS_Ki1f)*(MTX1/TYMS_Ki21) + (1 + FFH2/TYMS_Ki1f)*(1 + MTX2/TYMS_Ki22 + MTX3/TYMS_Ki23 + MTX4/TYMS_Ki24 + MTX5/TYMS_Ki25 + FH2f/TYMS_Ki1)) + TYMS_Km1*TYMS_Km2*(1 + MTX2/TYMS_Ki22 + MTX3/TYMS_Ki23 + MTX4/TYMS_Ki24 + MTX5/TYMS_Ki25 + FH2f/TYMS_Ki1)));
-  DHFReductase: FH2f => FH4; cell*DHFReductase_kter*FH2b;
-  FFH2syn: FH2f => FFH2; cell*FFH2syn_Vm*FH2f;
-  ATIC12: FFH2 + AICAR => FH2f; cell*(ATIC12_Vm*FFH2*AICAR/(AICAR*FFH2 + FFH2*ATIC12_Km2 + (AICAR + ATIC12_Km2)*ATIC12_Km1*(1 + MTX1/ATIC12_Ki21 + MTX2/ATIC12_Ki22 + MTX3/ATIC12_Ki23 + MTX4/ATIC12_Ki24 + MTX5/ATIC12_Ki25 + FH2f/ATIC12_Ki1 + FFH2/ATIC12_Ki1f)));
-  AICARsyn: FGAR => AICAR; cell*AICARsyn_Vm*(glutamine/AICARsyn_Km1/(1 + glutamine/AICARsyn_Km1))*(FGAR/AICARsyn_Km2/(1 + FGAR/AICARsyn_Km2));
-  FPGS12: MTX1 => MTX2; cell*FPGS12_Vm*MTX1;
-  FPGS23: MTX2 => MTX3; cell*FPGS23_Vm*MTX2;
-  FPGS34: MTX3 => MTX4; cell*FPGS34_Vm*MTX3;
-  FPGS45: MTX4 => MTX5; cell*FPGS45_Vm*MTX4;
-  GGH21: MTX2 => MTX1; cell*GGH21_Vm*MTX2;
-  GGH32: MTX3 => MTX2; cell*GGH32_Vm*MTX3;
-  GGH43: MTX4 => MTX3; cell*GGH43_Vm*MTX4;
-  GGH54: MTX5 => MTX4; cell*GGH54_Vm*MTX5;
-  RFC: $EMTX => MTX1; ext_*(RFC_Vm*EMTX/(RFC_Km + EMTX));
-  MTX1export: MTX1 => ; cell*MTX1export_Vm*MTX1;
-  MTX2export: MTX2 => ; cell*MTX2export_Vm*MTX2;
-  MTX3export: MTX3 => ; cell*MTX3export_Vm*MTX3;
-  MTX4export: MTX4 => ; cell*MTX4export_Vm*MTX4;
-  MTX5export: MTX5 => ; cell*MTX5export_Vm*MTX5;
-  MTX1on: MTX1 + DHFRf => MTX1b; cell*MTX1on_Vm*DHFRf*MTX1;
-  MTX2on: MTX2 + DHFRf => MTX2b; cell*MTX2on_Vm*DHFRf*MTX2;
-  MTX3on: MTX3 + DHFRf => MTX3b; cell*MTX3on_Vm*DHFRf*MTX3;
-  MTX4on: MTX4 + DHFRf => MTX4b; cell*MTX4on_Vm*DHFRf*MTX4;
-  MTX5on: MTX5 + DHFRf => MTX5b; cell*MTX5on_Vm*DHFRf*MTX5;
-  MTX1off: MTX1b => MTX1 + DHFRf; cell*MTX1off_Vm*MTX1b;
-  MTX2off: MTX2b => MTX2 + DHFRf; cell*MTX2off_Vm*MTX2b;
-  MTX3off: MTX3b => MTX3 + DHFRf; cell*MTX3off_Vm*MTX3b;
-  MTX4off: MTX4b => MTX4 + DHFRf; cell*MTX4off_Vm*MTX4b;
-  MTX5off: MTX5b => MTX5 + DHFRf; cell*MTX5off_Vm*MTX5b;
-  DHFRfsyn:  => DHFRf; cell*(DHFRfsyn_k0 + DHFRfsyn_k1*EMTX);
-  DHFRdeg: DHFRf => ; DHFRdeg_Vm*cell*(DHFRf + FH2b);
-  FH2bdeg:  => FH2f; cell*FH2bdeg_Vm*FH2b;
-  MTX1deg: MTX1b => MTX1; cell*MTX1deg_Vm*MTX1b;
-  MTX2deg: MTX2b => MTX2; cell*MTX2deg_Vm*MTX2b;
-  MTX3deg: MTX3b => MTX3; cell*MTX3deg_Vm*MTX3b;
-  MTX4deg: MTX4b => MTX4; cell*MTX4deg_Vm*MTX4b;
-  MTX5deg: MTX5b => MTX5; cell*MTX5deg_Vm*MTX5b;
-
-  // Species initializations:
-  FH2f = 0.0012;
-  DHFRf = 0.64;
-  MTX1b = 0;
-  MTX2b = 0;
-  MTX3b = 0;
-  MTX4b = 0;
-  MTX5b = 0;
-  FH4 = 0.46;
-  CH2FH4 = 0.26;
-  CH3FH4 = 1.63;
-  CHOFH4 = 1;
-  FFH2 = 0.000332;
-  HCHO = 0.0074;
-  FGAR = 16.49;
-  AICAR = 3.695;
-  MTX1 = 0;
-  MTX2 = 0;
-  MTX3 = 0;
-  MTX4 = 0;
-  MTX5 = 0;
-  EMTX = 0;
-  dUMP = 20.76;
-  GAR = 689.6;
-  serine = 123.3;
-  formate = 500;
-  ATP = 2980;
-  glutamine = 7170;
-  glycine = 1600;
-  NADP = 6.73;
-  NADPH = 294;
-  homocysteine = 10;
-
-  // Compartment initializations:
-  ext_ = 1;
-  cell = 1;
-
-  // Variable initializations:
-  Keq = 0.32;
-  SHMT_Vm = 18330;
-  SHMT_Km1 = 1.7;
-  SHMT_Km2 = 210;
-  SHMTr_Vm = 12200000;
-  SHMTr_Km1 = 3200;
-  SHMTr_Km2 = 10000;
-  HCHOtoCH2FH4_hp = 23.2;
-  CH2FH4toHCHO_hl = 0.3;
-  MTHFR_Vm = 224.8;
-  MTHFR_Km1 = 50;
-  MTHFR_Km2 = 50;
-  MTHFR_Ki1 = 0.4;
-  MTHFR_Ki21 = 59;
-  MTHFR_Ki22 = 21.3;
-  MTHFR_Ki23 = 7.68;
-  MTHFR_Ki24 = 2.77;
-  MTHFR_Ki25 = 1;
-  MTR_Vm = 22600;
-  MTR_Km1 = 125;
-  MTR_Km2 = 2900;
-  HCOOHtoCHOFH4_Vm = 3600;
-  HCOOHtoCHOFH4_Km1 = 230;
-  HCOOHtoCHOFH4_Km2 = 56;
-  HCOOHtoCHOFH4_Km3 = 1600;
-  GARFT_Vm = 4126;
-  GARFT_Km1 = 4.9;
-  GARFT_Km2 = 52;
-  GARFT_Ki1 = 5;
-  GARFT_Ki1f = 1;
-  GARFT_Ki21 = 84;
-  GARFT_Ki22 = 60;
-  GARFT_Ki23 = 43;
-  GARFT_Ki24 = 31;
-  GARFT_Ki25 = 22;
-  ATIC7_Vm = 31675;
-  ATIC7_Km1 = 5.5;
-  ATIC7_Km2 = 24;
-  ATIC7_Ki1 = 2.89;
-  ATIC7_Ki1f = 5.3;
-  ATIC7_Ki21 = 40;
-  ATIC7_Ki22 = 31.5;
-  ATIC7_Ki23 = 2.33;
-  ATIC7_Ki24 = 3.61;
-  ATIC7_Ki25 = 5.89;
-  MTHFD_Vm = 68500;
-  MTHFD_Km1 = 3;
-  MTHFD_Km2 = 21.8;
-  TYMS_Vm = 58;
-  TYMS_Km1 = 2.5;
-  TYMS_Km2 = 1.8;
-  TYMS_Ki1 = 3;
-  TYMS_Ki1f = 1.6;
-  TYMS_Ki21 = 13;
-  TYMS_Ki22 = 0.08;
-  TYMS_Ki23 = 0.07;
-  TYMS_Ki24 = 0.065;
-  TYMS_Ki25 = 0.047;
-  DHFReductase_kter = 2109.4;
-  FFH2syn_Vm = 65;
-  ATIC12_Vm = 9503;
-  ATIC12_Km1 = 5.3;
-  ATIC12_Km2 = 24;
-  ATIC12_Ki1 = 2.89;
-  ATIC12_Ki1f = 5.5;
-  ATIC12_Ki21 = 40;
-  ATIC12_Ki22 = 31.5;
-  ATIC12_Ki23 = 2.33;
-  ATIC12_Ki24 = 3.61;
-  ATIC12_Ki25 = 5.89;
-  AICARsyn_Vm = 4656;
-  AICARsyn_Km1 = 100;
-  AICARsyn_Km2 = 100;
-  FPGS12_Vm = 0.129;
-  FPGS23_Vm = 0.369;
-  FPGS34_Vm = 0.118;
-  FPGS45_Vm = 0.185;
-  GGH21_Vm = 0.195;
-  GGH32_Vm = 0.025;
-  GGH43_Vm = 0.031;
-  GGH54_Vm = 0.191;
-  RFC_Vm = 82.2;
-  RFC_Km = 8.2;
-  MTX1export_Vm = 4.65;
-  MTX2export_Vm = 0;
-  MTX3export_Vm = 0.063;
-  MTX4export_Vm = 0.063;
-  MTX5export_Vm = 0.063;
-  MTX1on_Vm = 23100;
-  MTX2on_Vm = 44300;
-  MTX3on_Vm = 85100;
-  MTX4on_Vm = 163000;
-  MTX5on_Vm = 314000;
-  MTX1off_Vm = 0.42;
-  MTX2off_Vm = 0.42;
-  MTX3off_Vm = 0.42;
-  MTX4off_Vm = 0.42;
-  MTX5off_Vm = 0.42;
-  DHFRfsyn_k0 = 0.0192;
-  DHFRfsyn_k1 = 0.04416;
-  DHFRdeg_Vm = 0.03;
-  FH2bdeg_Vm = 0.03;
-  MTX1deg_Vm = 0.03;
-  MTX2deg_Vm = 0.03;
-  MTX3deg_Vm = 0.03;
-  MTX4deg_Vm = 0.03;
-  MTX5deg_Vm = 0.03;
-
-  // Other declarations:
-  const ext_, cell, Keq;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "micromole (new default)";
-  time_unit is "heure (new default)";
-  FH2f is "dihydrofolate free";
-  FH2b is "dihydrofolate bound";
-  DHFRf is "dihydrofolate reductase free";
-  DHFRtot is "dihydrofolate reductase total";
-  FH4 is "tetrahydrofolate";
-  CH2FH4 is "5,10-methylene-tetrahydrofolate";
-  CH3FH4 is "5-methyl-tetrahydrofolate";
-  CHOFH4 is "10-formyl-tetrahydrofolate";
-  FFH2 is "10-formyl-dihydrofolate";
-
-  // CV terms:
-  ext_ identity "http://identifiers.org/go/GO:0005615"
-  cell identity "http://identifiers.org/go/GO:0005623"
-  FH2f hypernym "http://identifiers.org/chebi/CHEBI:15633",
-                "http://identifiers.org/kegg.compound/C00415"
-  FH2b hypernym "http://identifiers.org/chebi/CHEBI:15633",
-                "http://identifiers.org/kegg.compound/C00415"
-  DHFRf identity "http://identifiers.org/uniprot/P00374"
-  DHFRtot identity "http://identifiers.org/uniprot/P00374"
-  MTX1b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX2b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX3b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX4b identity "http://identifiers.org/kegg.compound/C01937"
-  MTX5b identity "http://identifiers.org/kegg.compound/C01937"
-  FH4 identity "http://identifiers.org/chebi/CHEBI:20506",
-               "http://identifiers.org/kegg.compound/C00101"
-  CH2FH4 identity "http://identifiers.org/chebi/CHEBI:15636",
-                  "http://identifiers.org/kegg.compound/C00143"
-  CH3FH4 identity "http://identifiers.org/chebi/CHEBI:15641",
-                  "http://identifiers.org/kegg.compound/C00440"
-  CHOFH4 identity "http://identifiers.org/chebi/CHEBI:15637",
-                  "http://identifiers.org/kegg.compound/C00234"
-  FFH2 identity "http://identifiers.org/chebi/CHEBI:15634",
-                "http://identifiers.org/kegg.compound/C03204"
-  HCHO identity "http://identifiers.org/chebi/CHEBI:16842",
-                "http://identifiers.org/kegg.compound/C00067"
-  FGAR identity "http://identifiers.org/kegg.compound/C04376"
-  AICAR identity "http://identifiers.org/chebi/CHEBI:18406",
-                 "http://identifiers.org/kegg.compound/C04677"
-  MTX1 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX2 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX3 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX4 identity "http://identifiers.org/kegg.compound/C01937"
-  MTX5 identity "http://identifiers.org/kegg.compound/C01937"
-  EMTX identity "http://identifiers.org/kegg.compound/C01937"
-  dUMP identity "http://identifiers.org/chebi/CHEBI:17622",
-                "http://identifiers.org/kegg.compound/C00365"
-  GAR identity "http://identifiers.org/kegg.compound/C03838"
-  serine identity "http://identifiers.org/chebi/CHEBI:17115",
-                  "http://identifiers.org/kegg.compound/C00065"
-  formate identity "http://identifiers.org/chebi/CHEBI:15740",
-                   "http://identifiers.org/kegg.compound/C00058"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  glutamine identity "http://identifiers.org/chebi/CHEBI:18050",
-                     "http://identifiers.org/kegg.compound/C00064"
-  glycine identity "http://identifiers.org/chebi/CHEBI:15428",
-                   "http://identifiers.org/kegg.compound/C00037"
-  NADP identity "http://identifiers.org/chebi/CHEBI:18009",
-                "http://identifiers.org/kegg.compound/C00006"
-  NADPH identity "http://identifiers.org/chebi/CHEBI:16474",
-                 "http://identifiers.org/kegg.compound/C00005"
-  homocysteine identity "http://identifiers.org/chebi/CHEBI:17230",
-                        "http://identifiers.org/kegg.compound/C05330"
-  SHMT identity "http://identifiers.org/kegg.reaction/R00945"
-  SHMT hypernym "http://identifiers.org/ec-code/2.1.2.1"
-  SHMTr identity "http://identifiers.org/kegg.reaction/R00945"
-  SHMTr hypernym "http://identifiers.org/ec-code/2.1.2.1"
-  MTHFR identity "http://identifiers.org/kegg.reaction/R01224"
-  MTHFR hypernym "http://identifiers.org/ec-code/1.5.1.20"
-  MTR identity "http://identifiers.org/kegg.reaction/R00946"
-  MTR hypernym "http://identifiers.org/ec-code/2.1.1.13"
-  HCOOHtoCHOFH4 identity "http://identifiers.org/kegg.reaction/R00943"
-  HCOOHtoCHOFH4 hypernym "http://identifiers.org/ec-code/6.3.4.3"
-  GARFT identity "http://identifiers.org/kegg.reaction/R04325",
-                 "http://identifiers.org/reactome/REACT_1509"
-  GARFT hypernym "http://identifiers.org/ec-code/2.1.2.2"
-  ATIC7 identity "http://identifiers.org/kegg.reaction/R04560",
-                 "http://identifiers.org/reactome/REACT_812"
-  ATIC7 hypernym "http://identifiers.org/ec-code/2.1.2.3"
-  MTHFD part "http://identifiers.org/ec-code/1.5.1.5",
-             "http://identifiers.org/ec-code/6.3.4.3",
-             "http://identifiers.org/kegg.reaction/R01220",
-             "http://identifiers.org/kegg.reaction/R01655"
-  TYMS identity "http://identifiers.org/kegg.reaction/R02101"
-  TYMS hypernym "http://identifiers.org/ec-code/2.1.1.45"
-  DHFReductase identity "http://identifiers.org/kegg.reaction/R00939"
-  DHFReductase hypernym "http://identifiers.org/ec-code/1.5.1.3"
-  FFH2syn identity "http://identifiers.org/kegg.reaction/R02238"
-  FFH2syn hypernym "http://identifiers.org/ec-code/6.3.4.17"
-  ATIC12 hypernym "http://identifiers.org/ec-code/2.1.2.3"
-  ATIC12 identity "http://identifiers.org/kegg.reaction/R04560"
-  AICARsyn hypernym "http://identifiers.org/ec-code/6.3.5.3"
-  FPGS12 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  FPGS23 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  FPGS34 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  FPGS45 hypernym "http://identifiers.org/ec-code/6.3.2.17"
-  GGH21 hypernym "http://identifiers.org/ec-code/3.4.19.9"
-  GGH32 hypernym "http://identifiers.org/ec-code/3.4.19.9"
-  GGH43 identity "http://identifiers.org/ec-code/3.4.19.9"
-  GGH54 identity "http://identifiers.org/ec-code/3.4.19.9"
-  RFC identity "http://identifiers.org/go/GO:0008517"
-  MTX1export identity "http://identifiers.org/go/GO:0008517"
-  MTX2export identity "http://identifiers.org/go/GO:0008517"
-  MTX3export identity "http://identifiers.org/go/GO:0008517"
-  MTX4export hypernym "http://identifiers.org/go/GO:0008517"
-  MTX5export hypernym "http://identifiers.org/go/GO:0008517"
-end
-
-MorrisonAllegra is "Morrison1989 - Folate Cycle"
-
-MorrisonAllegra model_entity_is "http://identifiers.org/biomodels.db/MODEL6617317313"
-MorrisonAllegra model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000018"
-MorrisonAllegra description "http://identifiers.org/pubmed/2732237"
-MorrisonAllegra taxon "http://identifiers.org/taxonomy/9606"
-MorrisonAllegra part "http://identifiers.org/kegg.pathway/map00670",
-                     "http://identifiers.org/kegg.pathway/map00790"
-MorrisonAllegra hypernym "http://identifiers.org/go/GO:0046655"
-MorrisonAllegra property "http://identifiers.org/doid/DOID:1612"

BioModelsRAG/data/BIOMD0000000019.txt

@@ -1,652 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000019()
-
-  // Compartments and Species:
-  compartment c1, c2, c3;
-  substanceOnly species $x1 in c1, x2 in c1, x3 in c2, x4 in c2, x5 in c2;
-  substanceOnly species x6 in c2, x7 in c2, x8 in c2, x9 in c2, x10 in c2;
-  substanceOnly species x11 in c2, x12 in c2, x13 in c3, x14 in c2, x15 in c3;
-  substanceOnly species x16 in c2, x17 in c2, x18 in c2, x19 in c2, x20 in c2;
-  substanceOnly species x21 in c2, x22 in c2, x23 in c2, x24 in c2, x25 in c2;
-  substanceOnly species x26 in c2, x27 in c2, x28 in c2, x29 in c2, x30 in c2;
-  substanceOnly species x31 in c2, x32 in c2, x33 in c2, x34 in c2, x35 in c2;
-  substanceOnly species x36 in c2, x37 in c2, x38 in c2, x39 in c2, x40 in c2;
-  substanceOnly species x41 in c2, x42 in c2, x43 in c2, x44 in c2, x45 in c2;
-  substanceOnly species x46 in c2, x47 in c2, x48 in c2, x49 in c2, x50 in c2;
-  substanceOnly species x51 in c2, x52 in c2, x53 in c2, x54 in c2, x55 in c2;
-  substanceOnly species x56 in c2, x57 in c2, x58 in c2, x59 in c2, x60 in c2;
-  substanceOnly species x61 in c2, x62 in c2, x63 in c2, x64 in c2, x65 in c2;
-  substanceOnly species x66 in c2, x67 in c2, x68 in c2, x69 in c2, x70 in c2;
-  substanceOnly species x71 in c2, x72 in c2, x73 in c2, x74 in c2, x75 in c2;
-  substanceOnly species x76 in c2, x77 in c2, x78 in c2, x79 in c2, x80 in c2;
-  substanceOnly species x81 in c2, x82 in c2, x83 in c2, x84 in c2, x85 in c2;
-  substanceOnly species x86 in c2, x87 in c2, x88 in c2, x89 in c2, x90 in c2;
-  substanceOnly species x91 in c2, x92 in c2, x93 in c2, x94 in c2, $Raf_act in c2;
-  substanceOnly species $Ras_GTP in c2, $MEK_PP in c2, $ERK_PP in c2, $SHC_P_t in c2;
-  substanceOnly species $EGF_EGFR_act in c2;
-
-  // Assignment Rules:
-  Raf_act := x45 + x46 + x48 + x50 + x72 + x73 + x74 + x76;
-  Ras_GTP := x42 + x28 + x70 + x69;
-  MEK_PP := x51 + x77;
-  ERK_PP := x59 + x83;
-  SHC_P_t := x33 + x34 + x35 + x36 + x37 + x38 + x39 + x40 + x91 + x92 + x93 + x94 + x64 + x65 + x66 + x67 + x68;
-  EGF_EGFR_act := x5 + x7 + x15 + x23 + x25 + x27 + x29 + x32 + x33 + x34 + x35 + x36 + x37 + x88 + x89 + x90 + x91 + x92 + x93 + x94 + x8 + x11 + x17 + x18 + x19 + x20 + x21 + x63 + x64 + x65 + x66 + x67 + x68;
-  k5 := piecewise(1.55, C < 3100, 0.2, C > 100000, C*-1.35e-5 + 1.55);
-  C := RT/(kr1/(k1*x1) + 1);
-
-  // Reactions:
-  v1: $x1 + x2 -> x3; k1*x1*x2 - kr1*x3;
-  v2: 2 x3 -> x4; k2*x3*x3 - kr2*x4;
-  v3: x4 -> x5; k3*x4 - kr3*x5;
-  v4: x23 + x12 -> x7; k4*x23*x12 - kr4*x7;
-  v5: x7 -> x18 + x9; k5*x7;
-  v6: x2 -> x6; k6*x2 - kr6*x6;
-  v7: x5 => x8; k7*x5;
-  v8: x5 + x14 -> x15; k8*x5*x14 - kr8*x15;
-  v9: x23 => x18; k7*x23;
-  v10: x6 + x16 -> x10; k10*x6*x16 - kr10*x10;
-  v11: 2 x10 -> x11; k2*x10*x10 - kr2*x11;
-  v12: x11 -> x8; k3*x11 - kr3*x8;
-  v13:  => x2; k13;
-  v14: x8 + x14 -> x17; k14*x8*x14 - kr14*x17;
-  v15: x9 => x12; k15*x9;
-  v16: x22 + x15 -> x23; k16*x22*x15 - kr16*x23;
-  v17: x24 + x23 -> x25; k17*x24*x23 - kr17*x25;
-  v18: x26 + x25 -> x27; k18*x26*x25 - kr18*x27;
-  v19: x27 -> x28 + x25; k19*x27 - kr19*x28*x25;
-  v20: x25 + x43 -> x29; k20*x25*x43 - kr20*x29;
-  v21: x29 -> x25 + x26; k21*x29 - kr21*x25*x26;
-  v22: x31 + x15 -> x32; k22*x31*x15 - kr22*x32;
-  v23: x32 -> x33; k23*x32 - kr23*x33;
-  v24: x22 + x33 -> x34; k24*x22*x33 - kr24*x34;
-  v25: x24 + x34 -> x35; k25*x24*x34 - kr25*x35;
-  v26: x26 + x35 -> x36; k18*x26*x35 - kr18*x36;
-  v27: x36 -> x35 + x28; k19*x36 - kr19*x35*x28;
-  v28: x28 + x41 -> x42; k28*x28*x41 - kr28*x42;
-  v29: x42 -> x43 + x45; k29*x42 - kr29*x43*x45;
-  v30: x35 + x43 -> x37; k20*x35*x43 - kr20*x37;
-  v31: x37 -> x35 + x26; k21*x37 - kr21*x35*x26;
-  v32: x35 -> x15 + x38; k32*x35 - kr32*x15*x38;
-  v33: x38 -> x40 + x30; k33*x38 - kr33*x40*x30;
-  v34: x25 -> x15 + x30; k34*x25 - kr34*x15*x30;
-  v35: x30 -> x24 + x22; k35*x30 - kr35*x24*x22;
-  v36: x40 => x31; Vm36*x40/(Km36 + x40);
-  v37: x33 -> x15 + x40; k37*x33 - kr37*x15*x40;
-  v38: x22 + x40 -> x39; k24*x22*x40 - kr24*x39;
-  v39: x34 -> x15 + x39; k37*x34 - kr37*x15*x39;
-  v40: x24 + x39 -> x38; k40*x24*x39 - kr40*x38;
-  v41: x30 + x33 -> x35; k41*x30*x33 - kr41*x35;
-  v42: x44 + x45 -> x46; k42*x44*x45 - kr42*x46;
-  v43: x46 -> x41 + x44; k43*x46;
-  v44: x47 + x45 -> x48; k44*x47*x45 - kr44*x48;
-  v45: x48 -> x49 + x45; k45*x48;
-  v46: x49 + x45 -> x50; k44*x49*x45 - kr44*x50;
-  v47: x50 -> x51 + x45; k47*x50;
-  v48: x51 + x53 -> x52; k48*x51*x53 - kr48*x52;
-  v49: x52 -> x49 + x53; k49*x52;
-  v50: x53 + x49 -> x54; k50*x53*x49 - kr50*x54;
-  v51: x54 -> x47 + x53; k49*x54;
-  v52: x55 + x51 -> x56; k52*x55*x51 - kr52*x56;
-  v53: x56 -> x51 + x57; k53*x56;
-  v54: x51 + x57 -> x58; k52*x51*x57 - kr52*x58;
-  v55: x58 -> x59 + x51; k55*x58;
-  v56: x59 + x60 -> x61; k56*x59*x60 - kr56*x61;
-  v57: x61 -> x57 + x60; k57*x61;
-  v58: x60 + x57 -> x62; k58*x60*x57 - kr58*x62;
-  v59: x62 -> x55 + x60; k59*x62;
-  v60: x6 => x86; k60*x6;
-  v61: x16 => x13; k61*x16;
-  v62: x8 => x87; k60*x8;
-  v63: x17 + x22 -> x18; k16*x17*x22 - kr16*x18;
-  v64: x24 + x18 -> x19; k17*x24*x18 - kr17*x19;
-  v65: x26 + x19 -> x20; k18*x26*x19 - kr18*x20;
-  v66: x20 -> x69 + x19; k19*x20 - kr19*x69*x19;
-  v67: x71 + x19 -> x21; k20*x71*x19 - kr20*x21;
-  v68: x21 -> x19 + x26; k21*x21 - kr21*x19*x26;
-  v69: x31 + x17 -> x63; k22*x31*x17 - kr22*x63;
-  v70: x63 -> x64; k23*x63 - kr23*x64;
-  v71: x22 + x64 -> x65; k24*x22*x64 - kr24*x65;
-  v72: x24 + x65 -> x66; k25*x24*x65 - kr25*x66;
-  v73: x26 + x66 -> x67; k18*x26*x66 - kr18*x67;
-  v74: x67 -> x66 + x69; k19*x67 - kr19*x66*x69;
-  v75: x69 + x41 -> x70; k28*x69*x41 - kr28*x70;
-  v76: x70 -> x71 + x72; k29*x70 - kr29*x71*x72;
-  v77: x71 + x66 -> x68; k20*x71*x66 - kr20*x68;
-  v78: x68 -> x66 + x26; k21*x68 - kr21*x66*x26;
-  v79: x66 -> x17 + x38; k32*x66 - kr32*x17*x38;
-  v80: x19 -> x17 + x30; k34*x19 - kr34*x17*x30;
-  v81: x64 -> x17 + x40; k37*x64 - kr37*x17*x40;
-  v82: x65 -> x17 + x39; k37*x65 - kr37*x17*x39;
-  v83: x30 + x64 -> x66; k41*x30*x64 - kr41*x66;
-  v84: x44 + x72 -> x73; k42*x44*x72 - kr42*x73;
-  v85: x73 -> x41 + x44; k43*x73;
-  v86: x47 + x72 -> x74; k44*x47*x72 - kr44*x74;
-  v87: x74 -> x75 + x72; k45*x74;
-  v88: x72 + x75 -> x76; k44*x72*x75 - kr44*x76;
-  v89: x76 -> x72 + x77; k47*x76;
-  v90: x77 + x53 -> x78; k48*x77*x53 - kr48*x78;
-  v91: x78 -> x75 + x53; k49*x78;
-  v92: x53 + x75 -> x79; k50*x53*x75 - kr50*x79;
-  v93: x79 -> x47 + x53; k49*x79;
-  v94: x55 + x77 -> x80; k52*x55*x77 - kr52*x80;
-  v95: x80 -> x81 + x77; k53*x80;
-  v96: x77 + x81 -> x82; k52*x77*x81 - kr52*x82;
-  v97: x82 -> x83 + x77; k55*x82;
-  v98: x83 + x60 -> x84; k56*x83*x60 - kr56*x84;
-  v99: x84 -> x81 + x60; k57*x84;
-  v100: x60 + x81 -> x85; k58*x60*x81 - kr58*x85;
-  v101: x85 -> x55 + x60; k59*x85;
-  v102: x15 -> x17; k6*x15 - kr6*x17;
-  v103: x32 -> x63; k6*x32 - kr6*x63;
-  v104: x33 -> x64; k6*x33 - kr6*x64;
-  v105: x25 -> x19; k6*x25 - kr6*x19;
-  v106: x25 + x12 -> x88; k4*x25*x12 - kr4*x88;
-  v107: x88 -> x9 + x19; k5*x88;
-  v108: x27 -> x20; k6*x27 - kr6*x20;
-  v109: x27 + x12 -> x89; k4*x27*x12 - kr4*x89;
-  v110: x89 -> x9 + x20; k5*x89;
-  v111: x29 -> x21; k6*x29 - kr6*x21;
-  v112: x29 + x12 -> x90; k4*x29*x12 - kr4*x90;
-  v113: x90 -> x9 + x21; k5*x90;
-  v114: x34 -> x65; k6*x34 - kr6*x65;
-  v115: x34 + x12 -> x91; k4*x34*x12 - kr4*x91;
-  v116: x91 -> x9 + x65; k5*x91;
-  v117: x35 -> x66; k6*x35 - kr6*x66;
-  v118: x35 + x12 -> x92; k4*x35*x12 - kr4*x92;
-  v119: x92 -> x9 + x66; k5*x92;
-  v120: x36 -> x67; k6*x36 - kr6*x67;
-  v121: x36 + x12 -> x93; k4*x36*x12 - kr4*x93;
-  v122: x93 -> x9 + x67; k5*x93;
-  v123: x37 -> x68; k6*x37 - kr6*x68;
-  v124: x37 + x12 -> x94; k4*x37*x12 - kr4*x94;
-  v125: x94 -> x68 + x9; k5*x94;
-
-  // Species initializations:
-  x1 = 4962/c1;
-  x2 = 50000/c1;
-  x3 = 0;
-  x4 = 0;
-  x5 = 0;
-  x6 = 0;
-  x7 = 0;
-  x8 = 0;
-  x9 = 0;
-  x10 = 0;
-  x11 = 0;
-  x12 = 81000/c2;
-  x13 = 0;
-  x14 = 12000/c2;
-  x15 = 0;
-  x16 = 0;
-  x17 = 0;
-  x18 = 0;
-  x19 = 0;
-  x20 = 0;
-  x21 = 0;
-  x22 = 11000/c2;
-  x23 = 0;
-  x24 = 26300/c2;
-  x25 = 0;
-  x26 = 72000/c2;
-  x27 = 0;
-  x28 = 0;
-  x29 = 0;
-  x30 = 40000/c2;
-  x31 = 101000/c2;
-  x32 = 0;
-  x33 = 0;
-  x34 = 0;
-  x35 = 0;
-  x36 = 0;
-  x37 = 0;
-  x38 = 0;
-  x39 = 0;
-  x40 = 0;
-  x41 = 40000/c2;
-  x42 = 0;
-  x43 = 0;
-  x44 = 40000/c2;
-  x45 = 0;
-  x46 = 0;
-  x47 = 22000000/c2;
-  x48 = 0;
-  x49 = 0;
-  x50 = 0;
-  x51 = 0;
-  x52 = 0;
-  x53 = 40000/c2;
-  x54 = 0;
-  x55 = 21000000/c2;
-  x56 = 0;
-  x57 = 0;
-  x58 = 0;
-  x59 = 0;
-  x60 = 10000000/c2;
-  x61 = 0;
-  x62 = 0;
-  x63 = 0;
-  x64 = 0;
-  x65 = 0;
-  x66 = 0;
-  x67 = 0;
-  x68 = 0;
-  x69 = 0;
-  x70 = 0;
-  x71 = 0;
-  x72 = 0;
-  x73 = 0;
-  x74 = 0;
-  x75 = 0;
-  x76 = 0;
-  x77 = 0;
-  x78 = 0;
-  x79 = 0;
-  x80 = 0;
-  x81 = 0;
-  x82 = 0;
-  x83 = 0;
-  x84 = 0;
-  x85 = 0;
-  x86 = 0;
-  x87 = 0;
-  x88 = 0;
-  x89 = 0;
-  x90 = 0;
-  x91 = 0;
-  x92 = 0;
-  x93 = 0;
-  x94 = 0;
-
-  // Compartment initializations:
-  c1 = 1;
-  c2 = 1;
-  c3 = 4.3e-06;
-
-  // Variable initializations:
-  k1 = 0.003;
-  k1 has pipmin;
-  kr1 = 0.228;
-  kr1 has pmin;
-  kr2 = 6;
-  kr2 has pmin;
-  k2 = 0.001;
-  k2 has pipmin;
-  k3 = 60;
-  k3 has pmin;
-  kr3 = 0.6;
-  kr3 has pmin;
-  k4 = 1.038e-05;
-  k4 has pipmin;
-  kr4 = 0.0996;
-  kr4 has pmin;
-  k5 has pmin;
-  k6 = 0.003;
-  k6 has pmin;
-  kr6 = 0.3;
-  kr6 has pmin;
-  k7 = 0.003;
-  k7 has pmin;
-  k8 = 0.0001;
-  k8 has pipmin;
-  kr8 = 12;
-  kr8 has pmin;
-  k10 = 3.25581;
-  k10 has pipmin;
-  kr10 = 0.66;
-  kr10 has pmin;
-  kr11 = 6;
-  kr11 has pmin;
-  k11 = 0.001;
-  k11 has pipmin;
-  kr12 = 0.6;
-  kr12 has pmin;
-  k12 = 60;
-  k12 has pmin;
-  k13 = 130.2;
-  k13 has ipmin;
-  k14 = 0.0001;
-  k14 has pipmin;
-  kr14 = 12;
-  kr14 has pmin;
-  k15 = 600000;
-  k15 has pmin;
-  kr16 = 16.5;
-  kr16 has pmin;
-  k16 = 0.001;
-  k16 has pipmin;
-  kr17 = 3.6;
-  kr17 has pmin;
-  k17 = 0.001;
-  k17 has pipmin;
-  kr18 = 78;
-  kr18 has pmin;
-  k18 = 0.0015;
-  k18 has pipmin;
-  kr19 = 1e-05;
-  kr19 has pipmin;
-  k19 = 30;
-  k19 has pmin;
-  kr20 = 24;
-  kr20 has pmin;
-  k20 = 0.00021;
-  k20 has pipmin;
-  k21 = 1.38;
-  k21 has pmin;
-  kr21 = 2.2e-05;
-  kr21 has pipmin;
-  k22 = 0.0021;
-  k22 has pipmin;
-  kr22 = 6;
-  kr22 has pmin;
-  k23 = 360;
-  k23 has pmin;
-  kr23 = 36;
-  kr23 has pmin;
-  k24 = 0.001;
-  k24 has pipmin;
-  kr24 = 33;
-  kr24 has pmin;
-  kr25 = 1.284;
-  kr25 has pmin;
-  k25 = 0.001;
-  k25 has pipmin;
-  k28 = 0.0001;
-  k28 has pipmin;
-  kr28 = 0.318;
-  kr28 has pmin;
-  k29 = 60;
-  k29 has pmin;
-  kr29 = 7e-05;
-  kr29 has pipmin;
-  kr32 = 2.4e-05;
-  kr32 has pipmin;
-  k32 = 6;
-  k32 has pmin;
-  k33 = 12;
-  k33 has pmin;
-  kr33 = 0.0021;
-  kr33 has pipmin;
-  k34 = 1.8;
-  k34 has pmin;
-  kr34 = 0.00045;
-  kr34 has pipmin;
-  k35 = 0.09;
-  k35 has pmin;
-  kr35 = 0.00045;
-  kr35 has pipmin;
-  Vm36 = 61200;
-  Vm36 has ipmin;
-  Km36 = 200000000000000;
-  Km36 has substance;
-  k37 = 18;
-  k37 has pmin;
-  kr37 = 9e-05;
-  kr37 has pipmin;
-  k40 = 0.003;
-  k40 has pipmin;
-  kr40 = 3.84;
-  kr40 has pmin;
-  kr41 = 2.574;
-  kr41 has pmin;
-  k41 = 0.003;
-  k41 has pipmin;
-  k42 = 0.0071;
-  k42 has pipmin;
-  kr42 = 12;
-  kr42 has pmin;
-  k43 = 60;
-  k43 has pmin;
-  kr44 = 1.0998;
-  kr44 has pmin;
-  k44 = 0.00111;
-  k44 has pipmin;
-  k45 = 210;
-  k45 has pmin;
-  k47 = 174;
-  k47 has pmin;
-  kr48 = 48;
-  kr48 has pmin;
-  k48 = 0.00143;
-  k48 has pipmin;
-  k49 = 3.48;
-  k49 has pmin;
-  kr50 = 30;
-  kr50 has pmin;
-  k50 = 2.5e-05;
-  k50 has pipmin;
-  k52 = 0.00534;
-  k52 has pipmin;
-  kr52 = 1.98;
-  kr52 has pmin;
-  k53 = 960;
-  k53 has pmin;
-  k55 = 342;
-  k55 has pmin;
-  kr56 = 36;
-  kr56 has pmin;
-  k56 = 0.00145;
-  k56 has pipmin;
-  k57 = 16.2;
-  k57 has pmin;
-  kr58 = 30;
-  kr58 has pmin;
-  k58 = 0.0005;
-  k58 has pipmin;
-  k59 = 18;
-  k59 has pmin;
-  k60 = 0.04002;
-  k60 has pmin;
-  k61 = 0.01002;
-  k61 has pmin;
-  RT = 50000;
-  RT has substance;
-
-  // Other declarations:
-  var k5, C;
-  const c1, c2, c3, k1, kr1, kr2, k2, k3, kr3, k4, kr4, k6, kr6, k7, k8, kr8;
-  const k10, kr10, kr11, k11, kr12, k12, k13, k14, kr14, k15, kr16, k16, kr17;
-  const k17, kr18, k18, kr19, k19, kr20, k20, k21, kr21, k22, kr22, k23, kr23;
-  const k24, kr24, kr25, k25, k28, kr28, k29, kr29, kr32, k32, k33, kr33;
-  const k34, kr34, k35, kr35, Vm36, Km36, k37, kr37, k40, kr40, kr41, k41;
-  const k42, kr42, k43, kr44, k44, k45, k47, kr48, k48, k49, kr50, k50, k52;
-  const kr52, k53, k55, kr56, k56, k57, kr58, k58, k59, k60, k61, RT;
-
-  // Unit definitions:
-  unit substance = item;
-  unit time_unit = 60 second;
-  unit volume = 1e-12 litre;
-  unit pmin = 1 / 60 second;
-  unit ipmin = item / 60 second;
-  unit pipmin = 1 / (60 second * item);
-  unit piplpmin = 1e-12 litre / (item * 60 second);
-
-  // Display Names:
-  substance is "items";
-  time_unit is "min";
-  volume is "pl";
-  pmin is "permin";
-  ipmin is "itemspermin";
-  pipmin is "peritempermin";
-  piplpmin is "plperitempermin";
-  c1 is "extracellular volume";
-  c2 is "cytoplasm";
-  c3 is "endosomal volume";
-  x1 is "EGF";
-  x2 is "EGFR";
-  x3 is "EGF-EGFR";
-  x4 is "EGF-EGFR^2";
-  x5 is "EGF-EGFR*^2";
-  x6 is "EGFRi";
-  x7 is "EGF-EGFR*^2-GAP-Grb2-Prot";
-  x8 is "EGF-EGFRi*^2";
-  x9 is "Proti";
-  x10 is "EGF-EGFRi";
-  x11 is "EGF-EGFRi^2";
-  x12 is "Prot";
-  x13 is "EGFideg";
-  x14 is "GAP";
-  x15 is "EGF-EGFR*^2-GAP";
-  x16 is "EGFi";
-  x17 is "EGF-EGFRi*^2-GAP";
-  x18 is "EGF-EGFRi*^2-GAP-Grb2";
-  x19 is "EGF-EGFRi*^2-GAP-Grb2-Sos";
-  x20 is "EGF-EGFRi*^2-GAP-Grb2-Sos-Ras-GDP";
-  x21 is "EGF-EGFRi*^2-GAP-Grb2-Sos-Ras-GTP";
-  x22 is "Grb2";
-  x23 is "EGF-EGFR*^2-GAP-Grb2";
-  x24 is "Sos";
-  x25 is "EGF-EGFR*^2-GAP-Grb2-Sos";
-  x26 is "Ras-GDP";
-  x27 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GDP";
-  x28 is "Ras-GTP";
-  x29 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GTP";
-  x30 is "Grb2-Sos";
-  x31 is "Shc";
-  x32 is "EGF-EGFR*^2-GAP-Shc";
-  x33 is "EGF-EGFR*^2-GAP-Shc*";
-  x34 is "EGF-EGFR*^2-GAP-Shc*-Grb2";
-  x35 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos";
-  x36 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GDP";
-  x37 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GTP";
-  x38 is "Shc*-Grb2-Sos";
-  x39 is "Shc*-Grb2";
-  x40 is "Shc*";
-  x41 is "Raf";
-  x42 is "Raf-Ras-GTP";
-  x43 is "Ras-GTP*";
-  x44 is "Phosphotase1";
-  x45 is "Raf*";
-  x46 is "Raf*-P'ase";
-  x47 is "MEK";
-  x48 is "MEK-Raf*";
-  x49 is "MEK-P";
-  x50 is "MEK-P-Raf*";
-  x51 is "MEK-PP";
-  x52 is "MEK-PP-P'ase2";
-  x53 is "Phosphatase2";
-  x54 is "MEK-P-P'ase2";
-  x55 is "ERK";
-  x56 is "ERK-MEK-PP";
-  x57 is "ERK-P";
-  x58 is "ERK-P-MEK-PP";
-  x59 is "ERK-PP";
-  x60 is "Phosphotase3";
-  x61 is "ERK-PP-P'ase3";
-  x62 is "ERK-P-P'ase3";
-  x63 is "EGF-EGFRi*^2-GAP-Shc";
-  x64 is "EGF-EGFRi*^2-GAP-Shc*";
-  x65 is "EGF-EGFRi*^2-GAP-Shc*-Grb2";
-  x66 is "EGF-EGFRi*^2-GAP-Shc*-Grb2-Sos";
-  x67 is "EGF-EGFRi*^2-GAP-Shc*-Grb2-Sos-Ras-GDP";
-  x68 is "EGF-EGFRi*^2-GAP-Shc*-Grb2-Sos-Ras-GTP";
-  x69 is "Rasi-GTP";
-  x70 is "Rafi-Rasi-GTP";
-  x71 is "Rasi-GTP*";
-  x72 is "Rafi*";
-  x73 is "Rafi*-P'ase";
-  x74 is "MEKi-Rafi*";
-  x75 is "MEKi-P";
-  x76 is "MEKi-P-Rafi*";
-  x77 is "MEKi-PP";
-  x78 is "MEKi-PP-P'ase2i";
-  x79 is "MEKi-P-P'ase2i";
-  x80 is "ERKi-MEKi-PP";
-  x81 is "ERKi-P";
-  x82 is "ERKi-P-MEKi-PP";
-  x83 is "ERKi-PP";
-  x84 is "ERKi-PP-P'ase3i";
-  x85 is "ERKi-P-P'ase3i";
-  x86 is "EGFRideg";
-  x87 is "EGF-EGFRi*^2deg";
-  x88 is "EGF-EGFR*^2-GAP-Grb2-Sos-Prot";
-  x89 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GDP-Prot";
-  x90 is "EGF-EGFR*^2-GAP-Grb2-Sos-Ras-GTP-Prot";
-  x91 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Prot";
-  x92 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Prot";
-  x93 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GDP-Prot";
-  x94 is "EGF-EGFR*^2-GAP-Shc*-Grb2-Sos-Ras-GTP-Prot";
-  Raf_act is "t_Raf*";
-  Ras_GTP is "t_Ras_GTP";
-  MEK_PP is "t_MEK_PP";
-  ERK_PP is "t_ERK_PP";
-  SHC_P_t is "t_SHC_P_t";
-  EGF_EGFR_act is "t_EGF_EGFR*";
-  C is "C_internalization";
-  RT is "total_Receptors";
-
-  // CV terms:
-  c1 identity "http://identifiers.org/go/GO:0005615"
-  c2 identity "http://identifiers.org/go/GO:0005737"
-  c3 identity "http://identifiers.org/go/GO:0005768"
-  x3 hypernym "http://identifiers.org/reactome/REACT_9893"
-  x3 version "http://identifiers.org/uniprot/P01133",
-             "http://identifiers.org/uniprot/P00533"
-  x4 hypernym "http://identifiers.org/reactome/REACT_9820"
-  x4 version "http://identifiers.org/uniprot/P01133",
-             "http://identifiers.org/uniprot/P00533"
-  x5 hypernym "http://identifiers.org/kegg.compound/C00562"
-  x5 version "http://identifiers.org/uniprot/P00533",
-             "http://identifiers.org/uniprot/P01133"
-  x6 hypernym "http://identifiers.org/uniprot/P00533"
-  x7 version "http://identifiers.org/uniprot/P20936",
-             "http://identifiers.org/uniprot/P62993",
-             "http://identifiers.org/uniprot/P00533",
-             "http://identifiers.org/uniprot/P01133",
-             "http://identifiers.org/go/GO:0030119"
-  x8 version "http://identifiers.org/uniprot/P00533",
-             "http://identifiers.org/uniprot/P01133"
-  x9 hypernym "http://identifiers.org/go/GO:0030119"
-  x10 version "http://identifiers.org/uniprot/P01133",
-              "http://identifiers.org/uniprot/P00533"
-  x14 hypernym "http://identifiers.org/interpro/IPR001936"
-  x14 hypernym "http://identifiers.org/uniprot/P20936"
-  x14 description "http://identifiers.org/omim/139150"
-  x22 hypernym "http://identifiers.org/uniprot/P62993"
-  x22 description "http://identifiers.org/omim/108355"
-  x24 hypernym "http://identifiers.org/uniprot/Q07889"
-  x24 description "http://identifiers.org/omim/182530"
-  x26 part "http://identifiers.org/chebi/CHEBI:17552",
-           "http://identifiers.org/uniprot/P01112"
-  x28 part "http://identifiers.org/chebi/CHEBI:15996",
-           "http://identifiers.org/uniprot/P01112"
-  x31 hypernym "http://identifiers.org/uniprot/P98077"
-  x31 description "http://identifiers.org/omim/605217"
-  x41 hypernym "http://identifiers.org/uniprot/P04049"
-  x41 description "http://identifiers.org/omim/164760"
-  x47 hypernym "http://identifiers.org/uniprot/Q02750",
-               "http://identifiers.org/uniprot/A4QPA9"
-  x47 description "http://identifiers.org/omim/176872"
-  x49 hypernym "http://identifiers.org/uniprot/Q02750",
-               "http://identifiers.org/uniprot/A4QPA9",
-               "http://identifiers.org/kegg.compound/C00562"
-  x49 description "http://identifiers.org/omim/176872"
-  x55 hypernym "http://identifiers.org/uniprot/P28482"
-  x55 description "http://identifiers.org/omim/176948"
-  v1 hypernym "http://identifiers.org/go/GO:0005154",
-              "http://identifiers.org/go/GO:0048408"
-  v1 hypernym "http://identifiers.org/reactome/REACT_9481"
-  v2 hypernym "http://identifiers.org/go/GO:0007171",
-              "http://identifiers.org/go/GO:0046983"
-  v2 hypernym "http://identifiers.org/reactome/REACT_9397"
-  v3 hypernym "http://identifiers.org/go/GO:0007171",
-              "http://identifiers.org/go/GO:0046777",
-              "http://identifiers.org/go/GO:0004713"
-  v3 hypernym "http://identifiers.org/reactome/REACT_9388"
-  v6 hypernym "http://identifiers.org/go/GO:0031623"
-  v7 hypernym "http://identifiers.org/go/GO:0031623"
-  v10 hypernym "http://identifiers.org/go/GO:0031623"
-  v100 description "http://identifiers.org/omim/164760"
-  v101 description "http://identifiers.org/omim/164760"
-end
-
-BIOMD0000000019 is "Schoeberl2002 - EGF MAPK"
-
-BIOMD0000000019 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617455076"
-BIOMD0000000019 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000019"
-BIOMD0000000019 description "http://identifiers.org/pubmed/11923843"
-BIOMD0000000019 taxon "http://identifiers.org/taxonomy/9606"
-BIOMD0000000019 hypernym "http://identifiers.org/reactome/REACT_9417.3",
-                         "http://identifiers.org/go/GO:0007173"
-BIOMD0000000019 version "http://identifiers.org/go/GO:0007265",
-                        "http://identifiers.org/go/GO:0000165"

BioModelsRAG/data/BIOMD0000000020.txt

@@ -1,101 +0,0 @@
-// Created by libAntimony v2.13.0
-model *hhsa_1952()
-
-  // Compartments and Species:
-  compartment unit_compartment;
-
-  // Assignment Rules:
-  i_Na := g_Na*m^3*h*(V - V_Na);
-  i_K := g_K*n^4*(V - V_K);
-  i_L := g_L*(V - V_L);
-  V_neg := -V;
-  E := V + E_R;
-  V_Na := E_Na - E_R;
-  V_K := E_K - E_R;
-  V_L := E_L - E_R;
-  alpha_m := 0.1*(V + 25)/(exp((V + 25)/10) - 1);
-  beta_m := 4*exp(V/18);
-  alpha_h := 0.07*exp(V/20);
-  beta_h := 1/(exp((V + 30)/10) + 1);
-  alpha_n := 0.01*(V + 10)/(exp((V + 10)/10) - 1);
-  beta_n := 0.125*exp(V/80);
-
-  // Rate Rules:
-  V' = (I - (i_Na + i_K + i_L))/Cm;
-  m' = alpha_m*(1 - m) - beta_m*m;
-  h' = alpha_h*(1 - h) - beta_h*h;
-  n' = alpha_n*(1 - n) - beta_n*n;
-
-  // Compartment initializations:
-  unit_compartment = 1;
-
-  // Variable initializations:
-  V = 0;
-  V has mV;
-  I = 0;
-  Cm = 1;
-  V_neg has mV;
-  E has mV;
-  E_R = -75;
-  E_R has mV;
-  g_Na = 120;
-  m = 0.052932;
-  h = 0.59612;
-  V_Na has mV;
-  g_K = 36;
-  n = 0.31768;
-  V_K has mV;
-  g_L = 0.3;
-  V_L has mV;
-  E_Na = -190;
-  E_Na has mV;
-  E_K = -63;
-  E_K has mV;
-  E_L = -85.613;
-  E_L has mV;
-
-  // Other declarations:
-  var V, i_Na, i_K, i_L, V_neg, E, m, h, V_Na, n, V_K, V_L, alpha_m, beta_m;
-  var alpha_h, beta_h, alpha_n, beta_n;
-  const unit_compartment, I, Cm, E_R, g_Na, g_K, g_L, E_Na, E_K, E_L;
-
-  // Unit definitions:
-  unit time_unit = 1e-3 second;
-  unit mV = 1e-3 volt;
-
-  // Display Names:
-  time_unit is "millisecond";
-  alpha_h is "auxiliary alpha_h";
-
-  // SBO terms:
-  V.sboTerm = 259
-  Cm.sboTerm = 258
-  V_neg.sboTerm = 259
-  E.sboTerm = 259
-  E_R.sboTerm = 259
-  g_Na.sboTerm = 257
-  V_Na.sboTerm = 259
-  g_K.sboTerm = 257
-  V_K.sboTerm = 259
-  g_L.sboTerm = 257
-  V_L.sboTerm = 259
-  E_Na.sboTerm = 259
-  E_K.sboTerm = 259
-  E_L.sboTerm = 259
-
-  // CV terms:
-  i_Na hypernym "http://identifiers.org/obo.go/GO:0005248"
-  i_K hypernym "http://identifiers.org/obo.go/GO:0008076"
-  i_L hypernym "http://identifiers.org/obo.go/GO:0022840"
-end
-
-hhsa_1952 is "hodgkin-huxley squid-axon 1952"
-
-hhsa_1952 model_entity_is "http://identifiers.org/biomodels.db/MODEL6617668482"
-hhsa_1952 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000020"
-hhsa_1952 description "http://identifiers.org/pubmed/12991237"
-hhsa_1952 hypernym "http://identifiers.org/obo.go/GO:0019227",
-                   "http://identifiers.org/obo.go/GO:0005248",
-                   "http://identifiers.org/obo.go/GO:0005249"
-hhsa_1952 taxon "http://identifiers.org/taxonomy/6618",
-                "http://identifiers.org/obo.go/GO:0042757"

BioModelsRAG/data/BIOMD0000000021.txt

@@ -1,214 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Leloup1999_CircClock_periodic()
-
-  // Compartments and Species:
-  compartment Cell, compartment_0000002;
-  species P0 in Cell, T0 in Cell, P1 in Cell, T1 in Cell, P2 in Cell, T2 in Cell;
-  species CC in Cell, Cn in compartment_0000002, Mp in Cell, Mt in Cell;
-
-  // Assignment Rules:
-  Pt := CC + Cn + P0 + P1 + P2;
-  Tt := CC + Cn + T0 + T1 + T2;
-
-  // Reactions:
-  P0_to_P1: P0 => P1; Cell*P0_to_P1_V_1P*P0/(P0_to_P1_K1_P + P0);
-  T0_to_T1: T0 => T1; Cell*T0_to_T1_V_1T*T0/(T0_to_T1_K_1T + T0);
-  P1_to_P0: P1 => P0; Cell*P1_to_P0_V_2P*P1/(P1_to_P0_K_2P + P1);
-  T1_to_T0: T1 => T0; Cell*T1_to_T0_V_2T*T1/(T1_to_T0_K_2T + T1);
-  P1_to_P2: P1 => P2; Cell*P1_to_P2_V_3P*P1/(P1_to_P2_K_3P + P1);
-  T1_to_T2: T1 => T2; Cell*T1_to_T2_V_3T*T1/(T1_to_T2_K_3T + T1);
-  P2_to_P1: P2 => P1; Cell*P2_to_P1_V_4P*P2/(P2_to_P1_K_4P + P2);
-  T2_to_T1: T2 => T1; Cell*T2_to_T1_V_4T*T2/(T2_to_T1_K_4T + T2);
-  P0_degradation: P0 => ; Cell*P0_degradation_k_d*P0;
-  T0_degradation: T0 => ; Cell*T0_degradation_k_d*T0;
-  P1_degradation: P1 => ; Cell*P1_degradation_k_d*P1;
-  T1_degradation: T1 => ; Cell*T1_degradation_k_d*T1;
-  P2_degradation: P2 => ; Cell*P2_degradation_k_d*P2 + Cell*P2_degradation_V_dP*P2/(P2_degradation_K_dP + P2);
-  T2_degradation: T2 => ; Cell*T2_degradation_k_d*T2 + Cell*V_dT*T2/(T2_degradation_K_dT + T2);
-  PT_complex_formation: P2 + T2 -> CC; Cell*PT_complex_formation_k3*P2*T2 - Cell*PT_complex_formation_k4*CC;
-  PT_complex_nucleation: CC -> Cn; Cell*PT_complex_nucleation_k1*CC - compartment_0000002*PT_complex_nucleation_k2*Cn;
-  PT_complex_degradation: CC => ; Cell*PT_complex_degradation_k_dC*CC;
-  PTnucl_complex_degradation: Cn => ; compartment_0000002*PTnucl_complex_degradation_k_dN*Cn;
-  Mp_production:  => Mp; Cell*Mp_production_v_sP*Mp_production_K_IP^Mp_production_n/(Mp_production_K_IP^Mp_production_n + Cn^Mp_production_n);
-  Mt_production:  => Mt; Cell*Mt_production_V_sT*Mt_production_K_IT^Mt_production_n/(Mt_production_K_IT^Mt_production_n + Cn^Mt_production_n);
-  P0_production:  => P0; Cell*P0_production_k_sP*Mp;
-  T0_production:  => T0; Cell*T0_production_k_sT*Mt;
-  Mp_degradation: Mp => ; Cell*Mp_degradation_k_d*Mp + Cell*Mp_degradation_V_mP*Mp/(Mp_degradation_K_mP + Mp);
-  Mt_degradation: Mt => ; Cell*Mt_degradation_k_d*Mt + Cell*V_mT*Mt/(Mt_degradation_K_mT + Mt);
-
-  // Species initializations:
-  P0 = 0;
-  T0 = 0;
-  P1 = 0;
-  T1 = 0;
-  P2 = 0;
-  T2 = 0;
-  CC = 0;
-  Cn = 0;
-  Mp = 0;
-  Mt = 0;
-
-  // Compartment initializations:
-  Cell = 1;
-  compartment_0000002 = 1;
-
-  // Variable initializations:
-  V_mT = 0.7;
-  V_dT = 2;
-  P0_to_P1_K1_P = 2;
-  P0_to_P1_V_1P = 8;
-  T0_to_T1_K_1T = 2;
-  T0_to_T1_V_1T = 8;
-  P1_to_P0_K_2P = 2;
-  P1_to_P0_V_2P = 1;
-  T1_to_T0_K_2T = 2;
-  T1_to_T0_V_2T = 1;
-  P1_to_P2_K_3P = 2;
-  P1_to_P2_V_3P = 8;
-  T1_to_T2_K_3T = 2;
-  T1_to_T2_V_3T = 8;
-  P2_to_P1_K_4P = 2;
-  P2_to_P1_V_4P = 1;
-  T2_to_T1_K_4T = 2;
-  T2_to_T1_V_4T = 1;
-  P0_degradation_k_d = 0.01;
-  T0_degradation_k_d = 0.01;
-  P1_degradation_k_d = 0.01;
-  T1_degradation_k_d = 0.01;
-  P2_degradation_k_d = 0.01;
-  P2_degradation_V_dP = 2;
-  P2_degradation_K_dP = 0.2;
-  T2_degradation_k_d = 0.01;
-  T2_degradation_K_dT = 0.2;
-  PT_complex_formation_k3 = 1.2;
-  PT_complex_formation_k4 = 0.6;
-  PT_complex_nucleation_k1 = 0.6;
-  PT_complex_nucleation_k2 = 0.2;
-  PT_complex_degradation_k_dC = 0.01;
-  PTnucl_complex_degradation_k_dN = 0.01;
-  Mp_production_v_sP = 1;
-  Mp_production_K_IP = 1;
-  Mp_production_n = 4;
-  Mt_production_V_sT = 1;
-  Mt_production_K_IT = 1;
-  Mt_production_n = 4;
-  P0_production_k_sP = 0.9;
-  T0_production_k_sT = 0.9;
-  Mp_degradation_k_d = 0.01;
-  Mp_degradation_V_mP = 0.7;
-  Mp_degradation_K_mP = 0.2;
-  Mt_degradation_k_d = 0.01;
-  Mt_degradation_K_mT = 0.2;
-
-  // Other declarations:
-  var Pt, Tt;
-  const Cell, compartment_0000002, V_mT, V_dT;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  time_unit is "hour (default)";
-  Cell is "cytoplasm";
-  compartment_0000002 is "nucleus";
-  P0 is "PER Protein (unphosphorylated)";
-  T0 is "TIM Protein (unphosphorylated)";
-  P1 is "PER Protein (mono-phosphorylated)";
-  T1 is "TIM Protein (mono-phosphorylated)";
-  P2 is "PER Protein (bi-phosphorylated)";
-  T2 is "TIM Protein (bi-phosphorylated)";
-  CC is "Cytosolic PER-TIM Complex";
-  Cn is "Nuclear PER-TIM Complex";
-  Mp is "PER mRNA";
-  Mt is "TIM mRNA";
-  Pt is "Total Per";
-  Tt is "Total Tim";
-  P0_to_P1 is "First Phosphorylation of PER";
-  T0_to_T1 is "First Phosphorylation of TIM";
-  P1_to_P0 is "Dephosphorylation of PER (1st P)";
-  T1_to_T0 is "Dephosphorylation of TIM (1st P)";
-  P1_to_P2 is "Second Phosphorylation of PER";
-  T1_to_T2 is "Second Phosphorylation of TIM";
-  P2_to_P1 is "Dephosphorylation of PER (2nd P)";
-  T2_to_T1 is "Dephosphorylation of TIM (2nd P)";
-  P0_degradation is "PER degradation";
-  T0_degradation is "TIM degradation";
-  P1_degradation is "PER-1 degradation";
-  T1_degradation is "TIM-1 degradation";
-  P2_degradation is "PER-2 degradation";
-  T2_degradation is "TIM-2 degradation";
-  PT_complex_formation is "PER-TIM complex formation";
-  PT_complex_nucleation is "PER-TIM complex nucleation";
-  PT_complex_degradation is "PER-TIM complex degradation (cytosol)";
-  PTnucl_complex_degradation is "PER-TIM complex degradation (nuclear)";
-  Mp_production is "PER mRNA production";
-  Mt_production is "TIM mRNA production";
-  P0_production is "PER production";
-  T0_production is "TIM production";
-  Mp_degradation is "PER mRNA degradation";
-  Mt_degradation is "TIM mRNA degradation";
-
-  // CV terms:
-  Cell identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000002 identity "http://identifiers.org/go/GO:0005634"
-  P0 hypernym "http://identifiers.org/uniprot/P07663"
-  T0 hypernym "http://identifiers.org/uniprot/P49021"
-  P1 hypernym "http://identifiers.org/uniprot/P07663"
-  T1 hypernym "http://identifiers.org/uniprot/P49021"
-  P2 hypernym "http://identifiers.org/uniprot/P07663"
-  T2 hypernym "http://identifiers.org/uniprot/P49021"
-  CC part "http://identifiers.org/uniprot/P49021",
-          "http://identifiers.org/uniprot/P07663"
-  Cn part "http://identifiers.org/uniprot/P49021",
-          "http://identifiers.org/uniprot/P07663"
-  Mp hypernym "http://identifiers.org/chebi/CHEBI:33699",
-              "http://identifiers.org/kegg.compound/C00046"
-  Mt hypernym "http://identifiers.org/chebi/CHEBI:33699",
-              "http://identifiers.org/kegg.compound/C00046"
-  P0_to_P1 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  T0_to_T1 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  P1_to_P0 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  T1_to_T0 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  P1_to_P2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  T1_to_T2 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-                    "http://identifiers.org/go/GO:0006468"
-  P2_to_P1 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  T2_to_T1 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                    "http://identifiers.org/go/GO:0006470"
-  P0_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  T0_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  P1_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  T1_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  P2_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  T2_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  PT_complex_formation hypernym "http://identifiers.org/go/GO:0006461"
-  PT_complex_nucleation hypernym "http://identifiers.org/go/GO:0006606"
-  PT_complex_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  PTnucl_complex_degradation hypernym "http://identifiers.org/go/GO:0030163"
-  Mp_production hypernym "http://identifiers.org/go/GO:0009299",
-                         "http://identifiers.org/go/GO:0006355"
-  Mt_production hypernym "http://identifiers.org/go/GO:0009299",
-                         "http://identifiers.org/go/GO:0006355"
-  P0_production hypernym "http://identifiers.org/go/GO:0006412"
-  T0_production hypernym "http://identifiers.org/go/GO:0006412"
-  Mp_degradation hypernym "http://identifiers.org/go/GO:0006402"
-  Mt_degradation hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-Leloup1999_CircClock_periodic is "Leloup1999_CircClock"
-
-Leloup1999_CircClock_periodic model_entity_is "http://identifiers.org/biomodels.db/MODEL6617834203"
-Leloup1999_CircClock_periodic model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000021"
-Leloup1999_CircClock_periodic description "http://identifiers.org/pubmed/10366496"
-Leloup1999_CircClock_periodic origin "http://identifiers.org/biomodels.db/BIOMD0000000171"
-Leloup1999_CircClock_periodic taxon "http://identifiers.org/taxonomy/7227"
-Leloup1999_CircClock_periodic identity "http://identifiers.org/kegg.pathway/dme04710"
-Leloup1999_CircClock_periodic hypernym "http://identifiers.org/go/GO:0042752"

BioModelsRAG/data/BIOMD0000000022.txt

@@ -1,257 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Ueda2001_CircClock()
-
-  // Compartments and Species:
-  compartment Drosophilia, compartment_0000003, compartment_0000002;
-  species $EmptySet in Drosophilia, CCc in compartment_0000003, CCn in compartment_0000002;
-  species Clkc in compartment_0000003, Clkm in compartment_0000003, Perc in compartment_0000003;
-  species Perm in compartment_0000003, PTc in compartment_0000003, PTn in compartment_0000002;
-  species Timc in compartment_0000003, Timm in compartment_0000003, $species_0000012 in compartment_0000003;
-  species $species_0000013 in compartment_0000003;
-
-  // Reactions:
-  Reaction1: $EmptySet => Perm; compartment_0000003*(Reaction1_c1 + (Reaction1_B1 + (CCn/Reaction1_A1)^Reaction1_a)*Reaction1_s1/(1 + Reaction1_B1 + (CCn/Reaction1_A1)^Reaction1_a + (PTn/Reaction1_r1)^Reaction1_r));
-  Reaction2: Perm => $EmptySet; compartment_0000003*Reaction2_D0*Perm;
-  Reaction3: $EmptySet => Timm; compartment_0000003*(Reaction3_c2 + (Reaction3_B2 + (CCn/Reaction3_A2)^Reaction3_a)*Reaction3_s3/(1 + Reaction3_B2 + (CCn/Reaction3_A2)^Reaction3_a + (PTn/Reaction3_r2)^Reaction3_r));
-  Reaction4: Timm => $EmptySet; Drosophilia*Reaction4_D0*Timm;
-  Reaction5: $EmptySet => Clkm; compartment_0000003*(Reaction5_c3 + (Reaction5_B3 + (PTn/Reaction5_A3)^Reaction5_a)*Reaction5_s5/(1 + Reaction5_B3 + (PTn/Reaction5_A3)^Reaction5_a + (CCn/Reaction5_r3)^Reaction5_r));
-  Reaction6: Clkm => $EmptySet; Drosophilia*Clkm*Reaction6_D0;
-  Reaction7: CCc => CCn; compartment_0000003*(CCc*Reaction7_T3/(Reaction7_k3 + CCc));
-  Reaction8: CCn => CCc; compartment_0000002*(CCn*Reaction8_T4/(Reaction8_k4 + CCn));
-  Reaction9: PTn => PTc; compartment_0000002*(PTn*Reaction9_T2/(Reaction9_k2 + PTn));
-  Reaction10: PTc => PTn; compartment_0000003*(PTc*Reaction10_T1/(Reaction10_k1 + PTc));
-  Reaction11: $species_0000012 + Clkc -> CCc; compartment_0000003*(Clkc*Reaction11_v3*species_0000012 - Reaction11_parameter_0000073*CCc);
-  Reaction12: Perc + Timc -> PTc; compartment_0000003*(Perc*Timc*Reaction12_v1 - Reaction12_parameter_0000072*PTc);
-  Reaction16: $EmptySet => Timc; compartment_0000003*Reaction16_s4*Timm;
-  Reaction18: $EmptySet => Clkc; compartment_0000003*Clkm*Reaction18_s6;
-  Reaction19: $EmptySet => Perc; compartment_0000003*Reaction19_s2*Perm;
-  Reaction20: Perc => $EmptySet; Drosophilia*Reaction20_D0*Perc;
-  Reaction21: PTc => $EmptySet; compartment_0000003*Reaction21_D0*PTc;
-  Reaction23: PTn => $EmptySet; compartment_0000002*Reaction23_D0*PTn;
-  Reaction24: CCc => $EmptySet; compartment_0000003*CCc*Reaction24_D0;
-  Reaction25: Clkc => $EmptySet; compartment_0000003*Clkc*Reaction25_D0;
-  Reaction26: CCn => $EmptySet; compartment_0000002*CCn*Reaction26_D0;
-  Reaction27: Timc => $EmptySet; compartment_0000003*Reaction27_D0*Timc;
-  Reaction28: Perm => $EmptySet; compartment_0000003*(Reaction28_D1*Perm/(Reaction28_L1 + Perm));
-  Reaction29: Perc => $EmptySet; compartment_0000003*(Reaction29_D2*species_0000013*Perc/(Reaction29_L2 + Perc));
-  Reaction30: Timm => $EmptySet; compartment_0000003*(Reaction30_D3*Timm/(Reaction30_L3 + Timm));
-  Reaction31: Timc => $EmptySet; compartment_0000003*(Reaction31_D4*Timc/(Reaction31_L4 + Timc));
-  Reaction32: PTc => $EmptySet; compartment_0000003*(Reaction32_D5*PTc/(Reaction32_L5 + PTc));
-  Reaction33: PTn => $EmptySet; compartment_0000002*(Reaction33_D6*PTn/(Reaction33_L6 + PTn));
-  Reaction34: Clkm => $EmptySet; compartment_0000003*(Clkm*Reaction34_D7/(Clkm + Reaction34_L7));
-  Reaction35: Clkc => $EmptySet; compartment_0000003*(Clkc*Reaction35_D8/(Clkc + Reaction35_L8));
-  Reaction36: CCc => $EmptySet; compartment_0000003*(CCc*Reaction36_D9/(CCc + Reaction36_L9));
-  Reaction37: CCn => $EmptySet; compartment_0000002*(CCn*Reaction37_D10/(CCn + Reaction37_L10));
-
-  // Species initializations:
-  EmptySet = 0;
-  CCc = 0.3/compartment_0000003;
-  CCn = 0.4/compartment_0000002;
-  Clkc = 0.2/compartment_0000003;
-  Clkm = 0.1/compartment_0000003;
-  Perc = 0.6/compartment_0000003;
-  Perm = 0.5/compartment_0000003;
-  PTc = 0.9/compartment_0000003;
-  PTn = 1/compartment_0000002;
-  Timc = 0.8/compartment_0000003;
-  Timm = 0.7/compartment_0000003;
-  species_0000012 = 1/compartment_0000003;
-  species_0000013 = 1/compartment_0000003;
-
-  // Compartment initializations:
-  Drosophilia = 1;
-  compartment_0000003 = 1;
-  compartment_0000002 = 1;
-
-  // Variable initializations:
-  Reaction1_a = 1;
-  Reaction1_A1 = 0.45;
-  Reaction1_B1 = 0;
-  Reaction1_c1 = 0;
-  Reaction1_r1 = 1.02;
-  Reaction1_s1 = 1.45;
-  Reaction1_r = 4;
-  Reaction2_D0 = 0.012;
-  Reaction3_a = 1;
-  Reaction3_A2 = 0.45;
-  Reaction3_B2 = 0;
-  Reaction3_c2 = 0;
-  Reaction3_r2 = 1.02;
-  Reaction3_s3 = 1.45;
-  Reaction3_r = 4;
-  Reaction4_D0 = 0.012;
-  Reaction5_a = 1;
-  Reaction5_A3 = 0.8;
-  Reaction5_B3 = 0.6;
-  Reaction5_c3 = 0;
-  Reaction5_r3 = 0.89;
-  Reaction5_s5 = 1.63;
-  Reaction5_r = 4;
-  Reaction6_D0 = 0.012;
-  Reaction7_k3 = 2;
-  Reaction7_T3 = 1.63;
-  Reaction8_k4 = 2;
-  Reaction8_T4 = 0.52;
-  Reaction9_k2 = 2;
-  Reaction9_T2 = 0.72;
-  Reaction10_k1 = 2;
-  Reaction10_T1 = 1.73;
-  Reaction11_v3 = 1.63;
-  Reaction11_parameter_0000073 = 1.63;
-  Reaction12_v1 = 1.45;
-  Reaction12_parameter_0000072 = 1.45;
-  Reaction16_s4 = 0.48;
-  Reaction18_s6 = 0.47;
-  Reaction19_s2 = 0.48;
-  Reaction20_D0 = 0.012;
-  Reaction21_D0 = 0.012;
-  Reaction23_D0 = 0.012;
-  Reaction24_D0 = 0.012;
-  Reaction25_D0 = 0.012;
-  Reaction26_D0 = 0.012;
-  Reaction27_D0 = 0.012;
-  Reaction28_D1 = 0.94;
-  Reaction28_L1 = 0.3;
-  Reaction29_D2 = 0.44;
-  Reaction29_L2 = 0.2;
-  Reaction30_D3 = 0.94;
-  Reaction30_L3 = 0.3;
-  Reaction31_D4 = 0.44;
-  Reaction31_L4 = 0.2;
-  Reaction32_D5 = 0.44;
-  Reaction32_L5 = 0.2;
-  Reaction33_D6 = 0.29;
-  Reaction33_L6 = 0.2;
-  Reaction34_D7 = 0.54;
-  Reaction34_L7 = 0.13;
-  Reaction35_D8 = 0.6;
-  Reaction35_L8 = 0.2;
-  Reaction36_D9 = 0.6;
-  Reaction36_L9 = 0.2;
-  Reaction37_D10 = 0.3;
-  Reaction37_L10 = 0.2;
-
-  // Other declarations:
-  const Drosophilia, compartment_0000003, compartment_0000002;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  time_unit is "hour (default)";
-  compartment_0000003 is "cytoplasm";
-  compartment_0000002 is "nucleus";
-  CCc is "Clk-Cyc_cyt";
-  CCn is "Clk-Cyc_nuc";
-  Clkc is "Clk_cyt";
-  Clkm is "Clk_mRNA";
-  Perc is "Per_cyt";
-  Perm is "Per_mRNA";
-  PTc is "Per-Tim_cyt";
-  PTn is "Per-Tim_nuc";
-  Timc is "Tim_cyt";
-  Timm is "Tim_mRNA";
-  species_0000012 is "Cyc_cyt";
-  species_0000013 is "Dbt_cyt";
-  Reaction1 is "Per transcription";
-  Reaction2 is "non-specific Per mRNA degradation";
-  Reaction3 is "Tim transcription";
-  Reaction4 is "non-specific Tim mRNA degradation";
-  Reaction5 is "Clk transcription";
-  Reaction6 is "non-specific Clk mRNA degradation";
-  Reaction7 is "Clk-Cyc nuclear import";
-  Reaction8 is "Clk-Cyc nuclear export";
-  Reaction9 is "Per-Tim nuclear export";
-  Reaction10 is "Per-Tim nuclear import";
-  Reaction11 is "Clk Cyc equilibrium";
-  Reaction12 is "Per Tim equilibrium";
-  Reaction16 is "Tim translation";
-  Reaction18 is "Clk translation";
-  Reaction19 is "Per translation";
-  Reaction20 is "non-specific Per_cyt degradation";
-  Reaction21 is "non-specific Per-Tim_cyt degradation";
-  Reaction23 is "non-specific Per-Tim_nuc degradation";
-  Reaction24 is "non-specific Clk-Cyc_cyt degradation";
-  Reaction25 is "non-specific Clk_cyt degradation";
-  Reaction26 is "non-specific Clk-Cyc_nuc degradation";
-  Reaction27 is "non-specific Tim_cyt degradation";
-  Reaction28 is "Per mRNA degradation";
-  Reaction29 is "Dbt regulated Per_cyt degradation";
-  Reaction30 is "Tim mRNA degradation";
-  Reaction31 is "Tim_cyt degradation";
-  Reaction32 is "Per-Tim_cyt degradation";
-  Reaction33 is "Per-Tim_nuc degradation";
-  Reaction34 is "Clk mRNA degradation";
-  Reaction35 is "Clk_cyt degradation";
-  Reaction36 is "Clk-Cyc_cyt degradation";
-
-  // CV terms:
-  compartment_0000003 identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000002 identity "http://identifiers.org/go/GO:0005634"
-  CCc part "http://identifiers.org/uniprot/O61735",
-           "http://identifiers.org/uniprot/O61734"
-  CCn part "http://identifiers.org/uniprot/O61734",
-           "http://identifiers.org/uniprot/O61735"
-  Clkc identity "http://identifiers.org/uniprot/O61735"
-  Clkm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  Perc identity "http://identifiers.org/uniprot/P07663"
-  Perm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  PTc part "http://identifiers.org/uniprot/P07663",
-           "http://identifiers.org/uniprot/P49021"
-  PTn part "http://identifiers.org/uniprot/P07663",
-           "http://identifiers.org/uniprot/P49021"
-  Timc identity "http://identifiers.org/uniprot/P49021"
-  Timm hypernym "http://identifiers.org/chebi/CHEBI:33699",
-                "http://identifiers.org/kegg.compound/C00046"
-  species_0000012 identity "http://identifiers.org/uniprot/O61734"
-  species_0000013 identity "http://identifiers.org/uniprot/O76324"
-  Reaction1 hypernym "http://identifiers.org/go/GO:0006355",
-                     "http://identifiers.org/go/GO:0009299"
-  Reaction2 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction3 hypernym "http://identifiers.org/go/GO:0009299",
-                     "http://identifiers.org/go/GO:0006355"
-  Reaction4 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction5 hypernym "http://identifiers.org/go/GO:0009299",
-                     "http://identifiers.org/go/GO:0006355"
-  Reaction6 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction7 hypernym "http://identifiers.org/go/GO:0006606"
-  Reaction8 hypernym "http://identifiers.org/go/GO:0006611"
-  Reaction9 hypernym "http://identifiers.org/go/GO:0006611"
-  Reaction10 hypernym "http://identifiers.org/go/GO:0006606"
-  Reaction11 hypernym "http://identifiers.org/go/GO:0006461"
-  Reaction12 hypernym "http://identifiers.org/go/GO:0006461"
-  Reaction16 hypernym "http://identifiers.org/go/GO:0006412"
-  Reaction18 hypernym "http://identifiers.org/go/GO:0006412"
-  Reaction19 hypernym "http://identifiers.org/go/GO:0006412"
-  Reaction20 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction21 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction23 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction24 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction25 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction26 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction27 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction28 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction29 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction30 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction31 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction32 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction33 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction34 hypernym "http://identifiers.org/go/GO:0006402"
-  Reaction35 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction36 hypernym "http://identifiers.org/go/GO:0030163"
-  Reaction37 hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-Ueda2001_CircClock is "Ueda2001_CircClock"
-
-Ueda2001_CircClock model_entity_is "http://identifiers.org/biomodels.db/MODEL6617909980"
-Ueda2001_CircClock model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000022"
-Ueda2001_CircClock description "http://identifiers.org/pubmed/11403560"
-Ueda2001_CircClock origin "http://identifiers.org/pubmed/10531060"
-Ueda2001_CircClock hypernym "http://identifiers.org/kegg.pathway/dme04710"
-Ueda2001_CircClock taxon "http://identifiers.org/taxonomy/7227"
-Ueda2001_CircClock hypernym "http://identifiers.org/go/GO:0042752"

BioModelsRAG/data/BIOMD0000000023.txt

@@ -1,175 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Rohwer2001_Sucrose()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Fru in compartment_, Glc in compartment_, HexP in compartment_;
-  species Suc6P in compartment_, Suc in compartment_, $Sucvac in compartment_;
-  species $glycolysis in compartment_, $phos in compartment_, $UDP in compartment_;
-  species $ADP in compartment_, $ATP in compartment_, $Glcex in compartment_;
-  species $Fruex in compartment_;
-
-  // Reactions:
-  v1: $Fruex -> Fru; compartment_*(v1_Vmax1*Fruex/(v1_Km1Fruex*(1 + Fru/v1_Ki1Fru) + Fruex));
-  v2: $Glcex -> Glc; compartment_*(v2_Vmax2*Glcex/(v2_Km2Glcex*(1 + Glc/v2_Ki2Glc) + Glcex));
-  v3: $ATP + Glc -> HexP + $ADP; compartment_*(v3_Vmax3*(Glc/v3_Km3Glc)*(ATP/v3_Km3ATP)/((1 + ATP/v3_Km3ATP)*(1 + Glc/v3_Km3Glc + Fru/v3_Km4Fru + 0.113*HexP/v3_Ki3G6P + 0.0575*HexP/v3_Ki4F6P)));
-  v4: Fru + $ATP -> HexP + $ADP; compartment_*(v4_Vmax4*(Fru/v4_Km4Fru)*(ATP/v4_Km4ATP)/((1 + ATP/v4_Km4ATP)*(1 + Glc/v4_Km3Glc + Fru/v4_Km4Fru + 0.113*HexP/v4_Ki3G6P + 0.0575*HexP/v4_Ki4F6P)));
-  v5: Fru + $ATP -> HexP + $ADP; compartment_*((v5_Vmax5/(1 + Fru/v5_Ki5Fru))*(Fru/v5_Km5Fru)*(ATP/v5_Km5ATP)/(1 + Fru/v5_Km5Fru + ATP/v5_Km5ATP + Fru*ATP/(v5_Km5Fru*v5_Km5ATP) + ADP/v5_Ki5ADP));
-  v6: 2 HexP -> $UDP + Suc6P; compartment_*(v6_Vmax6f*(0.0575*HexP*0.8231*HexP - Suc6P*UDP/v6_Keq6)/(0.0575*HexP*0.8231*HexP*(1 + Suc6P/v6_Ki6Suc6P) + v6_Km6F6P*(1 + phos/v6_Ki6Pi)*(0.8231*HexP + v6_Ki6UDPGlc) + v6_Km6UDPGlc*0.0575*HexP + (v6_Vmax6f/(v6_Vmax6r*v6_Keq6))*(v6_Km6UDP*Suc6P*(1 + 0.8231*HexP/v6_Ki6UDPGlc) + UDP*(v6_Km6Suc6P*(1 + v6_Km6UDPGlc*0.0575*HexP/(v6_Ki6UDPGlc*v6_Km6F6P*(1 + phos/v6_Ki6Pi))) + Suc6P*(1 + 0.0575*HexP/v6_Ki6F6P)))));
-  v7: Suc6P -> Suc + $phos; compartment_*(v7_Vmax7*Suc6P/(v7_Km7Suc6P + Suc6P));
-  v8: HexP + Fru -> Suc + $UDP; compartment_*(-v8_Vmax8f*(Suc*UDP - Fru*0.8231*HexP/v8_Keq8)/(Suc*UDP*(1 + Fru/v8_Ki8Fru) + v8_Km8Suc*(UDP + v8_Ki8UDP) + v8_Km8UDP*Suc + (v8_Vmax8f/(v8_Vmax8r*v8_Keq8))*(v8_Km8UDPGlc*Fru*(1 + UDP/v8_Ki8UDP) + 0.8231*HexP*(v8_Km8Fru*(1 + v8_Km8UDP*Suc/(v8_Ki8UDP*v8_Km8Suc)) + Fru*(1 + Suc/v8_Ki8Suc)))));
-  v9: Suc -> Fru + Glc; compartment_*((v9_Vmax9/(1 + Glc/v9_Ki9Glc))*Suc/(v9_Km9Suc*(1 + Fru/v9_Ki9Fru) + Suc));
-  v10: HexP -> $glycolysis; compartment_*(v10_Vmax10*0.0575*HexP/(v10_Km10F6P + 0.0575*HexP));
-  v11: Suc -> $Sucvac; compartment_*(v11_Vmax11*Suc/(v11_Km11Suc + Suc));
-
-  // Species initializations:
-  Fru = 1;
-  Glc = 1;
-  HexP = 1;
-  Suc6P = 1;
-  Suc = 1;
-  Sucvac = 0;
-  glycolysis = 0;
-  phos = 5.1;
-  UDP = 0.2;
-  ADP = 0.2;
-  ATP = 1;
-  Glcex = 5;
-  Fruex = 5;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_Vmax1 = 0.286;
-  v1_Km1Fruex = 0.2;
-  v1_Ki1Fru = 1;
-  v2_Vmax2 = 0.286;
-  v2_Km2Glcex = 0.2;
-  v2_Ki2Glc = 1;
-  v3_Vmax3 = 0.197;
-  v3_Km3Glc = 0.07;
-  v3_Km3ATP = 0.25;
-  v3_Km4Fru = 10;
-  v3_Ki3G6P = 0.1;
-  v3_Ki4F6P = 10;
-  v4_Vmax4 = 0.197;
-  v4_Km4Fru = 10;
-  v4_Km4ATP = 0.25;
-  v4_Km3Glc = 0.07;
-  v4_Ki3G6P = 0.1;
-  v4_Ki4F6P = 10;
-  v5_Vmax5 = 0.164;
-  v5_Ki5Fru = 12;
-  v5_Km5Fru = 0.1;
-  v5_Km5ATP = 0.085;
-  v5_Ki5ADP = 2;
-  v6_Vmax6f = 0.379;
-  v6_Keq6 = 10;
-  v6_Ki6Suc6P = 0.07;
-  v6_Km6F6P = 0.6;
-  v6_Ki6Pi = 3;
-  v6_Ki6UDPGlc = 1.4;
-  v6_Km6UDPGlc = 1.8;
-  v6_Vmax6r = 0.2;
-  v6_Km6UDP = 0.3;
-  v6_Km6Suc6P = 0.1;
-  v6_Ki6F6P = 0.4;
-  v7_Vmax7 = 0.5;
-  v7_Km7Suc6P = 0.1;
-  v8_Vmax8f = 0.677;
-  v8_Keq8 = 5;
-  v8_Ki8Fru = 4;
-  v8_Km8Suc = 50;
-  v8_Ki8UDP = 0.3;
-  v8_Km8UDP = 0.3;
-  v8_Vmax8r = 0.3;
-  v8_Km8UDPGlc = 0.3;
-  v8_Km8Fru = 4;
-  v8_Ki8Suc = 40;
-  v9_Vmax9 = 0.372;
-  v9_Ki9Glc = 15;
-  v9_Km9Suc = 10;
-  v9_Ki9Fru = 15;
-  v10_Vmax10 = 0.1;
-  v10_Km10F6P = 0.2;
-  v11_Vmax11 = 1;
-  v11_Km11Suc = 100;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole (default)";
-  time_unit is "minute (default)";
-  compartment_ is "cell";
-
-  // CV terms:
-  compartment_ identity "http://identifiers.org/obo.go/GO:0005623"
-  Fru identity "http://identifiers.org/obo.chebi/CHEBI:15824",
-               "http://identifiers.org/kegg.compound/C00095"
-  Glc identity "http://identifiers.org/obo.chebi/CHEBI:17634",
-               "http://identifiers.org/kegg.compound/C00031"
-  HexP version "http://identifiers.org/obo.chebi/CHEBI:16218",
-               "http://identifiers.org/obo.chebi/CHEBI:15946",
-               "http://identifiers.org/obo.chebi/CHEBI:14314"
-  HexP version "http://identifiers.org/kegg.compound/C00029",
-               "http://identifiers.org/kegg.compound/C00668",
-               "http://identifiers.org/kegg.compound/C00085",
-               "http://identifiers.org/kegg.compound/C00103",
-               "http://identifiers.org/chebi/CHEBI:18066"
-  Suc6P identity "http://identifiers.org/obo.chebi/CHEBI:16308",
-                 "http://identifiers.org/kegg.compound/C02591"
-  Suc identity "http://identifiers.org/obo.chebi/CHEBI:17992",
-               "http://identifiers.org/kegg.compound/C00089"
-  Sucvac identity "http://identifiers.org/obo.chebi/CHEBI:17992",
-                  "http://identifiers.org/kegg.compound/C00089"
-  glycolysis identity "http://identifiers.org/kegg.compound/C05378",
-                      "http://identifiers.org/chebi/CHEBI:28013"
-  phos identity "http://identifiers.org/obo.chebi/CHEBI:18367",
-                "http://identifiers.org/kegg.compound/C00009"
-  UDP identity "http://identifiers.org/obo.chebi/CHEBI:17659",
-               "http://identifiers.org/kegg.compound/C00015"
-  ADP identity "http://identifiers.org/obo.chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  ATP identity "http://identifiers.org/obo.chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  Glcex identity "http://identifiers.org/obo.chebi/CHEBI:17634",
-                 "http://identifiers.org/kegg.compound/C00031"
-  Fruex identity "http://identifiers.org/obo.chebi/CHEBI:15824",
-                 "http://identifiers.org/kegg.compound/C00095"
-  v1 hypernym "http://identifiers.org/obo.go/GO:0015755"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0015758"
-  v3 hypernym "http://identifiers.org/ec-code/2.7.1.2"
-  v3 identity "http://identifiers.org/kegg.reaction/R00299"
-  v4 hypernym "http://identifiers.org/ec-code/2.7.1.4"
-  v4 identity "http://identifiers.org/kegg.reaction/R03920",
-              "http://identifiers.org/kegg.reaction/R00760"
-  v5 hypernym "http://identifiers.org/ec-code/2.7.1.4"
-  v5 identity "http://identifiers.org/kegg.reaction/R00760"
-  v6 hypernym "http://identifiers.org/ec-code/2.4.1.14"
-  v6 identity "http://identifiers.org/kegg.reaction/R00766"
-  v7 hypernym "http://identifiers.org/ec-code/3.1.3.24"
-  v7 identity "http://identifiers.org/kegg.reaction/R00805"
-  v8 hypernym "http://identifiers.org/ec-code/2.4.1.13"
-  v8 identity "http://identifiers.org/kegg.reaction/R00806"
-  v9 hypernym "http://identifiers.org/ec-code/3.2.1.26",
-              "http://identifiers.org/ec-code/3.2.1.48",
-              "http://identifiers.org/ec-code/3.2.1.20"
-  v9 identity "http://identifiers.org/kegg.reaction/R00802"
-  v10 hypernym "http://identifiers.org/obo.go/GO:0006096"
-  v11 hypernym "http://identifiers.org/obo.go/GO:0015770"
-end
-
-Rohwer2001_Sucrose is "Rohwer2001_Sucrose"
-
-Rohwer2001_Sucrose model_entity_is "http://identifiers.org/biomodels.db/MODEL6618063111"
-Rohwer2001_Sucrose model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000023"
-Rohwer2001_Sucrose description "http://identifiers.org/pubmed/11513743"
-Rohwer2001_Sucrose taxon "http://identifiers.org/taxonomy/4547"
-Rohwer2001_Sucrose hypernym "http://identifiers.org/obo.go/GO:0005986"
-Rohwer2001_Sucrose identity "http://identifiers.org/kegg.pathway/map00500"

BioModelsRAG/data/BIOMD0000000024.txt

@@ -1,67 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Scheper1999()
-
-  // Compartments and Species:
-  compartment compartment_0000004;
-  species $EmptySet in compartment_0000004, M in compartment_0000004, P in compartment_0000004;
-
-  // Reactions:
-  TC: $EmptySet => M; compartment_0000004*(TC_rM/(1 + (P/TC_k)^TC_n));
-  TL: $EmptySet => P; compartment_0000004*TL_rP*delay(M, TL_parameter_0000009)^TL_m;
-  Md: M => $EmptySet; compartment_0000004*Md_qM*M;
-  Pd: P => $EmptySet; compartment_0000004*Pd_qP*P;
-
-  // Species initializations:
-  EmptySet = 0;
-  M = 1e-15/compartment_0000004;
-  P = 1e-15/compartment_0000004;
-
-  // Compartment initializations:
-  compartment_0000004 = 1e-15;
-
-  // Variable initializations:
-  TC_rM = 1;
-  TC_k = 1;
-  TC_n = 2;
-  TL_rP = 1;
-  TL_m = 3;
-  TL_parameter_0000009 = 4;
-  Md_qM = 0.21;
-  Pd_qP = 0.21;
-
-  // Other declarations:
-  const compartment_0000004;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  compartment_0000004 is "cytoplasm";
-  M is "mRNA";
-  P is "protein";
-  TC is "mRNA production";
-  TL is "protein production";
-  Md is "messenger degradation";
-  Pd is "protein degradation";
-
-  // CV terms:
-  compartment_0000004 identity "http://identifiers.org/go/GO:0005737"
-  M hypernym "http://identifiers.org/chebi/CHEBI:33699",
-             "http://identifiers.org/kegg.compound/C00046"
-  P identity "http://identifiers.org/kegg.compound/C00017",
-             "http://identifiers.org/chebi/CHEBI:16541"
-  TC hypernym "http://identifiers.org/go/GO:0009299"
-  TL hypernym "http://identifiers.org/go/GO:0006412"
-  Md hypernym "http://identifiers.org/go/GO:0006402"
-  Pd hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-Scheper1999 is "Scheper1999_CircClock"
-
-Scheper1999 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618241436"
-Scheper1999 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000024"
-Scheper1999 description "http://identifiers.org/pubmed/9870936"
-Scheper1999 taxon "http://identifiers.org/taxonomy/10036",
-                  "http://identifiers.org/taxonomy/7227"
-Scheper1999 identity "http://identifiers.org/kegg.pathway/dme04711"
-Scheper1999 hypernym "http://identifiers.org/go/GO:0042752"

BioModelsRAG/data/BIOMD0000000025.txt

@@ -1,87 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Smolen2002()
-
-  // Compartments and Species:
-  compartment CELL;
-  species $EmptySet in CELL, Per in CELL, dClk in CELL, $dClkF in CELL;
-
-  // Assignment Rules:
-  dClkF := piecewise(0, (dClk - Per) < 0, dClk - Per);
-  dClkF_tau1 := piecewise(0, (delay(dClk, tau1) - delay(Per, tau1)) < 0, delay(dClk, tau1) - delay(Per, tau1));
-  dClkF_tau2 := piecewise(0, (delay(dClk, tau2) - delay(Per, tau2)) < 0, delay(dClk, tau2) - delay(Per, tau2));
-
-  // Reactions:
-  rPer: $EmptySet => Per; Vsp*(dClkF_tau1/(K1 + dClkF_tau1))*CELL;
-  rdClk: $EmptySet => dClk; CELL*Vsc*(K2/(K2 + dClkF_tau2));
-  rPerD: Per => $EmptySet; kdc*Per*CELL;
-  rdClkD: dClk => $EmptySet; kdp*dClk*CELL;
-
-  // Species initializations:
-  EmptySet = 0;
-  Per = 5e-16;
-  dClk = 1e-16;
-
-  // Compartment initializations:
-  CELL = 1e-15;
-  dClkF_tau1 has nM;
-
-  // Variable initializations:
-  tau1 = 10;
-  tau1 has time_unit;
-  dClkF_tau2 has nM;
-  tau2 = 10;
-  tau2 has time_unit;
-  Vsp = 0.5;
-  Vsp has nM_per_hr;
-  K1 = 0.3;
-  K1 has nM;
-  Vsc = 0.25;
-  Vsc has nM_per_hr;
-  K2 = 0.1;
-  K2 has nM;
-  kdc = 0.5;
-  kdc has per_hr;
-  kdp = 0.5;
-  kdp has per_hr;
-
-  // Other declarations:
-  var dClkF_tau1, dClkF_tau2;
-  const CELL, tau1, tau2, Vsp, K1, Vsc, K2, kdc, kdp;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-  unit nM = 1e-9 mole / litre;
-  unit nM_per_hr = 1e-9 mole / (litre * 3600 second);
-  unit per_hr = 1 / 3600 second;
-
-  // Display Names:
-  time_unit is "hour (new default)";
-  substance is "nanomole (new default)";
-  dClkF is "free dClk";
-  rPer is "Per production";
-  rdClk is "dClk production";
-  rPerD is "Per degradation";
-  rdClkD is "dClk degradation";
-
-  // CV terms:
-  CELL identity "http://identifiers.org/go/GO:0005623"
-  Per identity "http://identifiers.org/uniprot/P07663"
-  dClk part "http://identifiers.org/uniprot/P07663",
-            "http://identifiers.org/uniprot/O61735"
-  dClkF identity "http://identifiers.org/uniprot/O61735"
-  rPer hypernym "http://identifiers.org/go/GO:0006412"
-  rdClk hypernym "http://identifiers.org/go/GO:0006412"
-  rPerD hypernym "http://identifiers.org/go/GO:0030163"
-  rdClkD hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-Smolen2002 is "Smolen2002_CircClock"
-
-Smolen2002 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618294363"
-Smolen2002 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000025"
-Smolen2002 description "http://identifiers.org/pubmed/12414672"
-Smolen2002 origin "http://identifiers.org/pubmed/11517254"
-Smolen2002 taxon "http://identifiers.org/taxonomy/7227"
-Smolen2002 identity "http://identifiers.org/kegg.pathway/dme04710"
-Smolen2002 hypernym "http://identifiers.org/go/GO:0032922"

BioModelsRAG/data/BIOMD0000000026.txt

@@ -1,135 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Markevich2004_MAPK_orderedelementary()
-
-  // Compartments and Species:
-  compartment uVol;
-  species M in uVol, Mp in uVol, Mpp in uVol, MAPKK in uVol, MKP3 in uVol;
-  species M_MAPKK in uVol, Mp_MAPKK in uVol, Mpp_MKP3 in uVol, Mp_MKP3_dep in uVol;
-  species Mp_MKP3 in uVol, M_MKP3 in uVol;
-
-  // Reactions:
-  v1a: M + MAPKK -> M_MAPKK; uVol*(k1*M*MAPKK - k_1*M_MAPKK);
-  v1b: M_MAPKK => Mp + MAPKK; uVol*k2*M_MAPKK;
-  v2a: Mp + MAPKK -> Mp_MAPKK; uVol*(k3*Mp*MAPKK - k_3*Mp_MAPKK);
-  v2b: Mp_MAPKK => Mpp + MAPKK; uVol*k4*Mp_MAPKK;
-  v3a: Mpp + MKP3 -> Mpp_MKP3; uVol*(h1*Mpp*MKP3 - h_1*Mpp_MKP3);
-  v3b: Mpp_MKP3 => Mp_MKP3_dep; uVol*h2*Mpp_MKP3;
-  v3c: Mp_MKP3_dep -> Mp + MKP3; h3*Mp_MKP3_dep - h_3*Mp*MKP3;
-  v4a: Mp + MKP3 -> Mp_MKP3; uVol*(h4*Mp*MKP3 - h_4*Mp_MKP3);
-  v4b: Mp_MKP3 => M_MKP3; uVol*h5*Mp_MKP3;
-  v4c: M_MKP3 -> M + MKP3; uVol*(h6*M_MKP3 - h_6*M*MKP3);
-
-  // Species initializations:
-  M = 500/uVol;
-  Mp = 0;
-  Mpp = 0;
-  MAPKK = 50/uVol;
-  MKP3 = 100/uVol;
-  M_MAPKK = 0;
-  Mp_MAPKK = 0;
-  Mpp_MKP3 = 0;
-  Mp_MKP3_dep = 0;
-  Mp_MKP3 = 0;
-  M_MKP3 = 0;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  k1 = 0.02;
-  k_1 = 1;
-  k2 = 0.01;
-  k3 = 0.032;
-  k_3 = 1;
-  k4 = 15;
-  h1 = 0.045;
-  h_1 = 1;
-  h2 = 0.092;
-  h3 = 1;
-  h_3 = 0.01;
-  h4 = 0.01;
-  h_4 = 1;
-  h5 = 0.5;
-  h6 = 0.086;
-  h_6 = 0.0011;
-
-  // Other declarations:
-  const uVol, k1, k_1, k2, k3, k_3, k4, h1, h_1, h2, h3, h_3, h4, h_4, h5;
-  const h6, h_6;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  MKP3 is "MKP";
-  Mpp_MKP3 is "Mpp_MKP";
-  Mp_MKP3_dep is "Mp_MKP";
-  Mp_MKP3 is "Mp_MKP*";
-  M_MKP3 is "M_MKP";
-  v1a is "binding MAPK and PP-MAPKK";
-  v1b is "phosphorylation of MAPK";
-  v2a is "binding PP-MAPKK and P-MAPK";
-  v2b is "phosphorylation of P-MAPK";
-  v3a is "binding MKP and PP-MAPK";
-  v3b is "dephosphorylation of PP-MAPK";
-  v3c is "dissociation of MKP from P-MAPK";
-  v4a is "binding MKP and P-MAPK";
-  v4b is "dephosphorylation of P-MAPK";
-  v4c is "dissociation of MKP from MAPK";
-
-  // CV terms:
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  Mp hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  M_MAPKK part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  Mp_MAPKK part "http://identifiers.org/uniprot/Q05116",
-                "http://identifiers.org/uniprot/P26696"
-  Mpp_MKP3 part "http://identifiers.org/uniprot/Q90W58",
-                "http://identifiers.org/uniprot/P26696"
-  Mp_MKP3_dep part "http://identifiers.org/uniprot/Q90W58",
-                   "http://identifiers.org/uniprot/P26696"
-  Mp_MKP3 part "http://identifiers.org/uniprot/Q90W58",
-               "http://identifiers.org/uniprot/P26696"
-  M_MKP3 part "http://identifiers.org/uniprot/Q90W58",
-              "http://identifiers.org/uniprot/P26696"
-  v1a hypernym "http://identifiers.org/obo.go/GO:0031434",
-               "http://identifiers.org/obo.go/GO:0051019"
-  v1a homolog "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  v1b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/obo.go/GO:0006468",
-               "http://identifiers.org/obo.go/GO:0004708"
-  v1b homolog "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  v2a hypernym "http://identifiers.org/obo.go/GO:0031434",
-               "http://identifiers.org/obo.go/GO:0051019"
-  v2a homolog "http://identifiers.org/reactome/REACT_1780",
-              "http://identifiers.org/reactome/REACT_495"
-  v2b hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/obo.go/GO:0000187",
-               "http://identifiers.org/obo.go/GO:0006468",
-               "http://identifiers.org/obo.go/GO:0004708"
-  v2b homolog "http://identifiers.org/reactome/REACT_136",
-              "http://identifiers.org/reactome/REACT_2247"
-  v3a hypernym "http://identifiers.org/obo.go/GO:0031434",
-               "http://identifiers.org/obo.go/GO:0051019"
-  v3b hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/obo.go/GO:0000188",
-               "http://identifiers.org/obo.go/GO:0006470"
-  v3c hypernym "http://identifiers.org/obo.go/GO:0043241"
-  v4a hypernym "http://identifiers.org/obo.go/GO:0051019"
-  v4b hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  v4c hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-Markevich2004_MAPK_orderedelementary is "Markevich2004_MAPK_orderedElementary"
-
-Markevich2004_MAPK_orderedelementary model_entity_is "http://identifiers.org/biomodels.db/MODEL6618379269"
-Markevich2004_MAPK_orderedelementary model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000026"
-Markevich2004_MAPK_orderedelementary description "http://identifiers.org/pubmed/14744999"
-Markevich2004_MAPK_orderedelementary taxon "http://identifiers.org/taxonomy/8355"
-Markevich2004_MAPK_orderedelementary hypernym "http://identifiers.org/obo.go/GO:0000165"

BioModelsRAG/data/BIOMD0000000027.txt

@@ -1,78 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Markevich2004_MAPK_orderedMM()
-
-  // Compartments and Species:
-  compartment uVol;
-  species M in uVol, Mp in uVol, Mpp in uVol, $MAPKK in uVol, $MKP3 in uVol;
-
-  // Reactions:
-  v1: M => Mp; uVol*(k1cat*MAPKK*M/Km1/(1 + M/Km1 + Mp/Km2));
-  v2: Mp => Mpp; uVol*(k2cat*MAPKK*Mp/Km2/(1 + M/Km1 + Mp/Km2));
-  v3: Mpp => Mp; uVol*(k3cat*MKP3*Mpp/Km3/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-  v4: Mp => M; uVol*(k4cat*MKP3*Mp/Km4/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-
-  // Species initializations:
-  M = 500/uVol;
-  Mp = 0;
-  Mpp = 0;
-  MAPKK = 50/uVol;
-  MKP3 = 100/uVol;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  k1cat = 0.01;
-  Km1 = 50;
-  k2cat = 15;
-  Km2 = 500;
-  k3cat = 0.084;
-  Km3 = 22;
-  k4cat = 0.06;
-  Km4 = 18;
-  Km5 = 78;
-
-  // Other declarations:
-  const uVol, k1cat, Km1, k2cat, Km2, k3cat, Km3, k4cat, Km4, Km5;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  v1 is "phosphorylation of MAPK";
-  v2 is "phosphorylation of P-MAPK";
-  v3 is "dephosphorylation of PP-MAPK";
-  v4 is "dephosphorylation of P-MAPK";
-
-  // CV terms:
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  Mp hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  v1 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0006468"
-  v2 homolog "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/go/GO:0004708",
-              "http://identifiers.org/go/GO:0000187",
-              "http://identifiers.org/go/GO:0006468"
-  v3 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0000188",
-              "http://identifiers.org/go/GO:0006470"
-  v4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/go/GO:0006470"
-end
-
-Markevich2004_MAPK_orderedMM is "Markevich2004 - MAPK double phosphorylation,  ordered Michaelis-Menton"
-
-Markevich2004_MAPK_orderedMM model_entity_is "http://identifiers.org/biomodels.db/MODEL6618496308"
-Markevich2004_MAPK_orderedMM model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000027"
-Markevich2004_MAPK_orderedMM description "http://identifiers.org/pubmed/14744999"
-Markevich2004_MAPK_orderedMM hypernym "http://identifiers.org/go/GO:0000165"
-Markevich2004_MAPK_orderedMM taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000028.txt

@@ -1,208 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, MpY in cell, MpT in cell, Mpp in cell, MEK in cell, MKP3 in cell;
-  species MpY_MEK in cell, MpT_MEK in cell, M_MEK_Y in cell, M_MEK_T in cell;
-  species Mpp_MKP3 in cell, MpY_MKP3 in cell, MpT_MKP3_Y in cell, MpT_MKP3_T in cell;
-  species M_MKP3_T in cell, M_MKP3_Y in cell;
-
-  // Reactions:
-  reaction_0000001: M + MEK -> M_MEK_Y; cell*(k1*M*MEK - k_1*M_MEK_Y);
-  reaction_0000002: M_MEK_Y => MpY + MEK; cell*k2*M_MEK_Y;
-  reaction_0000003: MpY + MEK -> MpY_MEK; cell*(k3*MpY*MEK - k_3*MpY_MEK);
-  reaction_0000004: MpY_MEK => Mpp + MEK; cell*k4*MpY_MEK;
-  reaction_0000005: M + MEK -> M_MEK_T; cell*(k5*M*MEK - k_5*M_MEK_T);
-  reaction_0000006: M_MEK_T => MpT + MEK; cell*k6*M_MEK_T;
-  reaction_0000007: MpT + MEK -> MpT_MEK; cell*(k7*MpT*MEK - k_7*MpT_MEK);
-  reaction_0000008: MpT_MEK => Mpp + MEK; cell*k8*MpT_MEK;
-  reaction_0000009: Mpp + MKP3 -> Mpp_MKP3; cell*(h1*Mpp*MKP3 - h_1*Mpp_MKP3);
-  reaction_0000010: Mpp_MKP3 => MpT_MKP3_Y; cell*h2*Mpp_MKP3;
-  reaction_0000011: MpT_MKP3_Y -> MpT + MKP3; cell*(h3*MpT_MKP3_Y - h_3*MpT*MKP3);
-  reaction_0000012: MpT_MKP3_T => M_MKP3_T; cell*h5*MpT_MKP3_T;
-  reaction_0000013: MpT + MKP3 -> MpT_MKP3_T; cell*(h4*MpT*MKP3 - h_4*MpT_MKP3_T);
-  reaction_0000014: MpY_MKP3 => M_MKP3_Y; cell*h8*MpY_MKP3;
-  reaction_0000015: M_MKP3_T -> M + MKP3; cell*(h6*M_MKP3_T - h_6*M*MKP3);
-  reaction_0000017: MpY + MKP3 -> MpY_MKP3; cell*(h7*MpY*MKP3 - h_7*MpY_MKP3);
-  reaction_0000019: M_MKP3_Y -> M + MKP3; cell*(h9*M_MKP3_Y - h_9*M*MKP3);
-
-  // Species initializations:
-  M = 800;
-  MpY = 0;
-  MpT = 0;
-  Mpp = 0;
-  MEK = 180;
-  MKP3 = 100;
-  MpY_MEK = 0;
-  MpT_MEK = 0;
-  M_MEK_Y = 0;
-  M_MEK_T = 0;
-  Mpp_MKP3 = 0;
-  MpY_MKP3 = 0;
-  MpT_MKP3_Y = 0;
-  MpT_MKP3_T = 0;
-  M_MKP3_T = 0;
-  M_MKP3_Y = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  k1 = 0.005;
-  k_1 = 1;
-  k2 = 1.08;
-  k3 = 0.025;
-  k_3 = 1;
-  k4 = 0.007;
-  k5 = 0.05;
-  k_5 = 1;
-  k6 = 0.008;
-  k7 = 0.005;
-  k_7 = 1;
-  k8 = 0.45;
-  h1 = 0.045;
-  h_1 = 1;
-  h2 = 0.092;
-  h3 = 1;
-  h_3 = 0.01;
-  h4 = 0.01;
-  h_4 = 1;
-  h5 = 0.5;
-  h6 = 0.086;
-  h_6 = 0.0011;
-  h7 = 0.01;
-  h_7 = 1;
-  h8 = 0.47;
-  h9 = 0.14;
-  h_9 = 0.0018;
-
-  // Other declarations:
-  const cell, k1, k_1, k2, k3, k_3, k4, k5, k_5, k6, k7, k_7, k8, h1, h_1;
-  const h2, h3, h_3, h4, h_4, h5, h6, h_6, h7, h_7, h8, h9, h_9;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  M is "ERK";
-  MpY is "ERK-PY";
-  MpT is "ERK-PT";
-  Mpp is "ERK-PP";
-  MpY_MEK is "ERK-PY_MEK";
-  MpT_MEK is "ERK-PT_MEK";
-  M_MEK_Y is "ERK_MEK_Y";
-  M_MEK_T is "ERK_MEK_T";
-  Mpp_MKP3 is "ERK-PP_MKP3";
-  MpY_MKP3 is "ERK-PY_MKP3";
-  MpT_MKP3_Y is "ERK-PT_MKP3_Y";
-  MpT_MKP3_T is "ERK-PT_MKP3_T";
-  M_MKP3_T is "ERK_MKP3_T";
-  M_MKP3_Y is "ERK_MKP3_Y";
-  reaction_0000001 is "binding ERK and MEK";
-  reaction_0000002 is "tyr phosphorylation of ERK";
-  reaction_0000003 is "binding ERK-PY and MEK";
-  reaction_0000004 is "thr phosphorylation of ERK";
-  reaction_0000005 is "binding ERK and MEK";
-  reaction_0000006 is "thr phosphorylation of ERK";
-  reaction_0000007 is "binding ERK-PT and MEK";
-  reaction_0000008 is "tyr phosphorylation of ERK";
-  reaction_0000009 is "binding ERK-PP and MKP3";
-  reaction_0000010 is "dephosphorylation of tyr on ERK-PP";
-  reaction_0000011 is "dissociation ERK-PT and MKP3";
-  reaction_0000012 is "dephosphorylation of ERK-PT";
-  reaction_0000013 is "binding ERK-PT and MKP3";
-  reaction_0000014 is "dephosphorylation of ERK-PY";
-  reaction_0000015 is "dissociation ERK and MKP3";
-  reaction_0000017 is "binding ERK-PY and MKP3";
-  reaction_0000019 is "Dissociation ERK and MKP3";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  MpY hypernym "http://identifiers.org/uniprot/P26696"
-  MpT hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MEK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  MpY_MEK part "http://identifiers.org/uniprot/Q05116",
-               "http://identifiers.org/uniprot/P26696"
-  MpT_MEK part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  M_MEK_Y part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  M_MEK_T part "http://identifiers.org/uniprot/P26696",
-               "http://identifiers.org/uniprot/Q05116"
-  Mpp_MKP3 part "http://identifiers.org/uniprot/P26696",
-                "http://identifiers.org/uniprot/Q90W58"
-  MpY_MKP3 part "http://identifiers.org/uniprot/P26696",
-                "http://identifiers.org/uniprot/Q90W58"
-  MpT_MKP3_Y part "http://identifiers.org/uniprot/P26696",
-                  "http://identifiers.org/uniprot/Q90W58"
-  MpT_MKP3_T part "http://identifiers.org/uniprot/P26696",
-                  "http://identifiers.org/uniprot/Q90W58"
-  M_MKP3_T part "http://identifiers.org/uniprot/P26696",
-                "http://identifiers.org/uniprot/Q90W58"
-  M_MKP3_Y part "http://identifiers.org/uniprot/Q90W58",
-                "http://identifiers.org/uniprot/P26696"
-  reaction_0000001 homolog "http://identifiers.org/reactome/REACT_495",
-                           "http://identifiers.org/reactome/REACT_1780"
-  reaction_0000001 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000002 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000002 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0018108",
-                            "http://identifiers.org/obo.go/GO:0004708"
-  reaction_0000003 homolog "http://identifiers.org/reactome/REACT_495",
-                           "http://identifiers.org/reactome/REACT_1780"
-  reaction_0000003 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000004 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000004 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018107",
-                            "http://identifiers.org/obo.go/GO:0000187"
-  reaction_0000005 homolog "http://identifiers.org/reactome/REACT_495",
-                           "http://identifiers.org/reactome/REACT_1780"
-  reaction_0000005 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000006 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000006 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0018107",
-                            "http://identifiers.org/obo.go/GO:0004708"
-  reaction_0000007 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000007 hypernym "http://identifiers.org/obo.go/GO:0051019",
-                            "http://identifiers.org/obo.go/GO:0031434"
-  reaction_0000008 homolog "http://identifiers.org/reactome/REACT_2247",
-                           "http://identifiers.org/reactome/REACT_136"
-  reaction_0000008 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0000187",
-                            "http://identifiers.org/obo.go/GO:0018108",
-                            "http://identifiers.org/obo.go/GO:0004708"
-  reaction_0000009 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000010 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470",
-                            "http://identifiers.org/obo.go/GO:0000188"
-  reaction_0000011 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000012 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000013 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000014 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000015 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000017 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000019 hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-model_0000001 is "Markevich2004_MAPK_phosphoRandomElementary"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618552953"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000028"
-model_0000001 description "http://identifiers.org/pubmed/14744999"
-model_0000001 hypernym "http://identifiers.org/obo.go/GO:0000165"
-model_0000001 taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000029.txt

@@ -1,112 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, MpY in cell, MpT in cell, Mpp in cell, $MEK in cell;
-  species $MKP3 in cell;
-
-  // Reactions:
-  v1: M => MpY; cell*(kcat1*MEK*M/Km1/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v2: MpY => Mpp; cell*(kcat2*MEK*MpY/Km2/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v3: M => MpT; cell*(kcat3*MEK*M/Km3/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v4: MpT => Mpp; cell*(kcat4*MEK*MpT/Km4/(1 + M*((Km1 + Km3)/(Km1*Km3)) + MpY/Km2 + MpT/Km4));
-  v5: Mpp => MpT; cell*(kcat5*MKP3*Mpp/Km5/(1 + Mpp/Km5 + MpT/Km6 + MpY/Km7 + M/Km8));
-  v6: MpT => M; cell*(kcat6*MKP3*MpT/Km6/(1 + Mpp/Km5 + MpT/Km6 + MpY/Km7 + M/Km8));
-  v7: MpY => M; cell*(kcat7*MKP3*MpY/Km7/(1 + Mpp/Km5 + MpT/Km6 + MpY/Km7 + M/Km8));
-
-  // Species initializations:
-  M = 800;
-  MpY = 0;
-  MpT = 0;
-  Mpp = 0;
-  MEK = 180;
-  MKP3 = 100;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  Km1 = 410;
-  kcat1 = 1.08;
-  Km2 = 40;
-  kcat2 = 0.007;
-  Km3 = 20;
-  kcat3 = 0.008;
-  Km4 = 300;
-  kcat4 = 0.45;
-  Km5 = 22;
-  kcat5 = 0.084;
-  Km6 = 18;
-  kcat6 = 0.06;
-  Km7 = 34;
-  kcat7 = 0.108;
-  Km8 = 40;
-
-  // Other declarations:
-  const cell, Km1, kcat1, Km2, kcat2, Km3, kcat3, Km4, kcat4, Km5, kcat5;
-  const Km6, kcat6, Km7, kcat7, Km8;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  M is "ERK";
-  MpY is "ERK-PY";
-  MpT is "ERK-PT";
-  Mpp is "ERK-PP";
-  v1 is "phosphorylation of ERK on Tyr";
-  v2 is "phosphorylation of ERK-PY on Thr";
-  v3 is "phosphorylation of ERK on Thr";
-  v4 is "phosphorylation of ERK-PT on Tyr";
-  v5 is "dephosphorylation of ERK-PP on Tyr";
-  v6 is "dephosphorylation of ERK-PT";
-  v7 is "dephosphorylation of ERK-PY";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  MpY hypernym "http://identifiers.org/uniprot/P26696"
-  MpT hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MEK identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0018108",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v1 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v2 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0018107",
-              "http://identifiers.org/obo.go/GO:0000187",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v3 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0018107",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v3 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v4 homolog "http://identifiers.org/reactome/REACT_2247",
-             "http://identifiers.org/reactome/REACT_136"
-  v4 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0004708",
-              "http://identifiers.org/obo.go/GO:0000187",
-              "http://identifiers.org/obo.go/GO:0018108"
-  v5 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0000188",
-              "http://identifiers.org/obo.go/GO:0006470"
-  v6 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0006470"
-  v7 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0006470"
-end
-
-model_0000001 is "Markevich2004_MAPK_phosphoRandomMM"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618620128"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000029"
-model_0000001 description "http://identifiers.org/pubmed/14744999"
-model_0000001 hypernym "http://identifiers.org/obo.go/GO:0000165"
-model_0000001 taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000030.txt

@@ -1,233 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment cell;
-  species M in cell, MpY in cell, MpT in cell, Mpp in cell, MAPKK in cell;
-  species MKP in cell, MpY_MAPKK in cell, MpT_MAPKK in cell, M_MAPKK_Y in cell;
-  species M_MAPKK_T in cell, Mpp_MKP_Y in cell, Mpp_MKP_T in cell, MpY_MKP_Y in cell;
-  species MpY_MKP_T in cell, MpT_MKP_Y in cell, MpT_MKP_T in cell, M_MKP_T in cell;
-  species M_MKP_Y in cell;
-
-  // Reactions:
-  reaction_0000001: M + MAPKK -> M_MAPKK_Y; cell*(k1*M*MAPKK - k_1*M_MAPKK_Y);
-  reaction_0000002: M_MAPKK_Y => MpY + MAPKK; cell*k2*M_MAPKK_Y;
-  reaction_0000003: MpY + MAPKK -> MpY_MAPKK; cell*(k3*MpY*MAPKK - k_3*MpY_MAPKK);
-  reaction_0000004: MpY_MAPKK => Mpp + MAPKK; cell*k4*MpY_MAPKK;
-  reaction_0000005: M + MAPKK -> M_MAPKK_T; cell*(k5*M*MAPKK - k_5*M_MAPKK_T);
-  reaction_0000006: M_MAPKK_T => MpT + MAPKK; cell*k6*M_MAPKK_T;
-  reaction_0000007: MpT + MAPKK -> MpT_MAPKK; cell*(k7*MpT*MAPKK - k_7*MpT_MAPKK);
-  reaction_0000008: MpT_MAPKK => Mpp + MAPKK; cell*k8*MpT_MAPKK;
-  reaction_0000009: Mpp + MKP -> Mpp_MKP_Y; cell*(h1*Mpp*MKP - h_1*Mpp_MKP_Y);
-  reaction_0000010: Mpp_MKP_Y => MpT_MKP_Y; cell*h2*Mpp_MKP_Y;
-  reaction_0000011: MpT_MKP_Y -> MpT + MKP; cell*(h3*MpT_MKP_Y - h_3*MpT*MKP);
-  reaction_0000013: MpT + MKP -> MpT_MKP_T; cell*(h4*MpT*MKP - h_4*MpT_MKP_T);
-  reaction_0000012: MpT_MKP_T => M_MKP_T; cell*h5*MpT_MKP_T;
-  reaction_0000015: M_MKP_T -> M + MKP; cell*(h6*M_MKP_T - h_6*M*MKP);
-  reaction_0000017: MpY + MKP -> MpY_MKP_Y; cell*(h7*MpY*MKP - h_7*MpY_MKP_Y);
-  reaction_0000014: MpY_MKP_Y => M_MKP_Y; cell*h8*MpY_MKP_Y;
-  reaction_0000019: M_MKP_Y -> M + MKP; cell*(h9*M_MKP_Y - h_9*M*MKP);
-  reaction_0000020: Mpp + MKP -> Mpp_MKP_T; cell*(h10*Mpp*MKP - h_10*Mpp_MKP_T);
-  reaction_0000021: Mpp_MKP_T => MpY_MKP_T; cell*h11*Mpp_MKP_T;
-  reaction_0000022: MpY_MKP_T -> MpY + MKP; cell*(h12*MpY_MKP_T - h_12*MpY*MKP);
-
-  // Species initializations:
-  M = 800;
-  MpY = 0;
-  MpT = 0;
-  Mpp = 0;
-  MAPKK = 180;
-  MKP = 100;
-  MpY_MAPKK = 0;
-  MpT_MAPKK = 0;
-  M_MAPKK_Y = 0;
-  M_MAPKK_T = 0;
-  Mpp_MKP_Y = 0;
-  Mpp_MKP_T = 0;
-  MpY_MKP_Y = 0;
-  MpY_MKP_T = 0;
-  MpT_MKP_Y = 0;
-  MpT_MKP_T = 0;
-  M_MKP_T = 0;
-  M_MKP_Y = 0;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  k1 = 0.02;
-  k_1 = 1;
-  k2 = 0.01;
-  k3 = 0.032;
-  k_3 = 1;
-  k4 = 15;
-  k5 = 0.02;
-  k_5 = 1;
-  k6 = 0.01;
-  k7 = 0.032;
-  k_7 = 1;
-  k8 = 15;
-  h1 = 0.045;
-  h_1 = 1;
-  h2 = 0.092;
-  h3 = 1;
-  h_3 = 0.01;
-  h4 = 0.01;
-  h_4 = 1;
-  h5 = 0.5;
-  h6 = 0.086;
-  h_6 = 0.0011;
-  h7 = 0.01;
-  h_7 = 1;
-  h8 = 0.47;
-  h9 = 0.14;
-  h_9 = 0.0018;
-  h10 = 0.045;
-  h_10 = 1;
-  h11 = 0.092;
-  h12 = 1;
-  h_12 = 0.01;
-
-  // Other declarations:
-  const cell, k1, k_1, k2, k3, k_3, k4, k5, k_5, k6, k7, k_7, k8, h1, h_1;
-  const h2, h3, h_3, h4, h_4, h5, h6, h_6, h7, h_7, h8, h9, h_9, h10, h_10;
-  const h11, h12, h_12;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  M is "MAPK";
-  MpY is "MAPK-PY";
-  MpT is "MAPK-PT";
-  Mpp is "MAPK-PP";
-  MpY_MAPKK is "MAPK-PY_MAPKK";
-  MpT_MAPKK is "MAPK-PT_MAPKK";
-  M_MAPKK_Y is "MAPK_MAPKK_Y";
-  M_MAPKK_T is "MAPK_MAPKK_T";
-  Mpp_MKP_Y is "MAPK-PP_MKP_T";
-  Mpp_MKP_T is "MAPK-PP_MKP_Y";
-  MpY_MKP_Y is "MAPK-PY_MKP_Y";
-  MpY_MKP_T is "MAPK-PY_MKP_T";
-  MpT_MKP_Y is "MAPK-PT_MKP_Y";
-  MpT_MKP_T is "MAPK-PT_MKP_T";
-  M_MKP_T is "MAPK_MKP_T";
-  M_MKP_Y is "MAPK_MKP_Y";
-  reaction_0000001 is "binding MAPKK on Tyr site of MAPK";
-  reaction_0000002 is "tyr phosphorylation of MAPK";
-  reaction_0000003 is "binding of MAPKK on MAPK-PY";
-  reaction_0000004 is "thr phosphorylation of MAPK";
-  reaction_0000005 is "binding of MAPKK on Thr site of MAPK";
-  reaction_0000006 is "thr phosphorylation of MAPK";
-  reaction_0000007 is "binding MAPK-PT and MAPKK";
-  reaction_0000008 is "tyr phosphorylation of MAPK";
-  reaction_0000009 is "binding of MKP on Tyr site of MAPK-PP";
-  reaction_0000010 is "dephosphorylation of Tyr on MAPKK-PP";
-  reaction_0000011 is "dissociation MAPK-PT and MKP";
-  reaction_0000013 is "binding of MKP on Thr site of MAPK-PT";
-  reaction_0000012 is "dephosphorylation of MAPK-PT";
-  reaction_0000015 is "dissociation MAPK and MKP";
-  reaction_0000017 is "binding of MKP on the Tyr site of MAPK-PY";
-  reaction_0000014 is "dephosphorylation of MAPK-PY";
-  reaction_0000019 is "Dissociation MAPK and MKP";
-  reaction_0000020 is "binding of MKP on Thr site of MAPK-PP";
-  reaction_0000021 is "dephosphorylation of Thr on MAPKK-PP";
-  reaction_0000022 is "dissociation MAPK-PY and MKP";
-
-  // CV terms:
-  cell identity "http://identifiers.org/obo.go/GO:0005623"
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  MpY hypernym "http://identifiers.org/uniprot/P26696"
-  MpT hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK identity "http://identifiers.org/uniprot/Q05116"
-  MKP identity "http://identifiers.org/uniprot/Q90W58"
-  MpY_MAPKK part "http://identifiers.org/uniprot/P26696",
-                 "http://identifiers.org/uniprot/Q05116"
-  MpT_MAPKK part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  M_MAPKK_Y part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  M_MAPKK_T part "http://identifiers.org/uniprot/Q05116",
-                 "http://identifiers.org/uniprot/P26696"
-  Mpp_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  Mpp_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpY_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpY_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpT_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  MpT_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-                 "http://identifiers.org/uniprot/P26696"
-  M_MKP_T part "http://identifiers.org/uniprot/Q90W58",
-               "http://identifiers.org/uniprot/P26696"
-  M_MKP_Y part "http://identifiers.org/uniprot/Q90W58",
-               "http://identifiers.org/uniprot/P26696"
-  reaction_0000001 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000001 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                            "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000002 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000002 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018108"
-  reaction_0000003 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000003 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                            "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000004 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000004 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018107",
-                            "http://identifiers.org/obo.go/GO:0000187"
-  reaction_0000005 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000005 hypernym "http://identifiers.org/obo.go/GO:0031434",
-                            "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000006 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000006 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018107"
-  reaction_0000007 homolog "http://identifiers.org/reactome/REACT_1780",
-                           "http://identifiers.org/reactome/REACT_495"
-  reaction_0000007 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000008 homolog "http://identifiers.org/reactome/REACT_136",
-                           "http://identifiers.org/reactome/REACT_2247"
-  reaction_0000008 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-                            "http://identifiers.org/obo.go/GO:0004708",
-                            "http://identifiers.org/obo.go/GO:0018108",
-                            "http://identifiers.org/obo.go/GO:0000187"
-  reaction_0000009 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000010 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0000188",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000011 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000013 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000012 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000015 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000017 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000014 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000019 hypernym "http://identifiers.org/obo.go/GO:0043241"
-  reaction_0000020 hypernym "http://identifiers.org/obo.go/GO:0051019"
-  reaction_0000021 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                            "http://identifiers.org/obo.go/GO:0000188",
-                            "http://identifiers.org/obo.go/GO:0006470"
-  reaction_0000022 hypernym "http://identifiers.org/obo.go/GO:0043241"
-end
-
-model_0000001 is "Markevich2004_MAPK_AllRandomElementary"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6618676537"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000030"
-model_0000001 description "http://identifiers.org/pubmed/14744999"
-model_0000001 hypernym "http://identifiers.org/obo.go/GO:0000165"
-model_0000001 taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000031.txt

@@ -1,80 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Markevich2004_MAPK_orderedMM2kinases()
-
-  // Compartments and Species:
-  compartment uVol;
-  species M in uVol, Mp in uVol, Mpp in uVol, $MAPKK1 in uVol, $MAPKK2 in uVol;
-  species $MKP3 in uVol;
-
-  // Reactions:
-  v1: M => Mp; uVol*(k1cat*MAPKK1*M/Km1/(1 + M/Km1));
-  v2: Mp => Mpp; uVol*(k2cat*MAPKK2*Mp/Km2/(1 + Mp/Km2));
-  v3: Mpp => Mp; uVol*(k3cat*MKP3*Mpp/Km3/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-  v4: Mp => M; uVol*(k4cat*MKP3*Mp/Km4/(1 + Mpp/Km3 + Mp/Km4 + M/Km5));
-
-  // Species initializations:
-  M = 500/uVol;
-  Mp = 0;
-  Mpp = 0;
-  MAPKK1 = 100/uVol;
-  MAPKK2 = 1/uVol;
-  MKP3 = 100/uVol;
-
-  // Compartment initializations:
-  uVol = 1;
-
-  // Variable initializations:
-  k1cat = 0.01;
-  Km1 = 50;
-  k2cat = 15;
-  Km2 = 500;
-  k3cat = 0.084;
-  Km3 = 5;
-  k4cat = 0.06;
-  Km4 = 18;
-  Km5 = 78;
-
-  // Other declarations:
-  const uVol, k1cat, Km1, k2cat, Km2, k3cat, Km3, k4cat, Km4, Km5;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  substance is "nanomole (default)";
-  v1 is "phosphorylation of MAPK";
-  v2 is "phosphorylation of P-MAPK";
-  v3 is "dephosphorylation of PP-MAPK";
-  v4 is "dephosphorylation of P-MAPK";
-
-  // CV terms:
-  M hypernym "http://identifiers.org/uniprot/P26696"
-  Mp hypernym "http://identifiers.org/uniprot/P26696"
-  Mpp hypernym "http://identifiers.org/uniprot/P26696"
-  MAPKK1 identity "http://identifiers.org/uniprot/Q05116"
-  MAPKK2 identity "http://identifiers.org/uniprot/Q05116"
-  MKP3 identity "http://identifiers.org/uniprot/Q90W58"
-  v1 homolog "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0006468",
-              "http://identifiers.org/obo.go/GO:0004708"
-  v2 homolog "http://identifiers.org/reactome/REACT_136",
-             "http://identifiers.org/reactome/REACT_2247"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-              "http://identifiers.org/obo.go/GO:0004708",
-              "http://identifiers.org/obo.go/GO:0000187"
-  v3 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0000188",
-              "http://identifiers.org/obo.go/GO:0006470"
-  v4 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-              "http://identifiers.org/obo.go/GO:0006470"
-end
-
-Markevich2004_MAPK_orderedMM2kinases is "Markevich2004_MAPK_orderedMM2kinases"
-
-Markevich2004_MAPK_orderedMM2kinases model_entity_is "http://identifiers.org/biomodels.db/MODEL6618738800"
-Markevich2004_MAPK_orderedMM2kinases model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000031"
-Markevich2004_MAPK_orderedMM2kinases description "http://identifiers.org/pubmed/14744999"
-Markevich2004_MAPK_orderedMM2kinases hypernym "http://identifiers.org/obo.go/GO:0000165"
-Markevich2004_MAPK_orderedMM2kinases taxon "http://identifiers.org/taxonomy/8355"

BioModelsRAG/data/BIOMD0000000032.txt

@@ -1,423 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Kofahl2004_PheromonePathway()
-
-  // Compartments and Species:
-  compartment Extracellular, compartment_;
-  species alpha in Extracellular, Ste2 in compartment_, Ste2a in compartment_;
-  species Gabc in compartment_, GaGTP in compartment_, Gbc in compartment_;
-  species GaGDP in compartment_, complexC in compartment_, complexD in compartment_;
-  species Ste5 in compartment_, Ste11 in compartment_, complexA in compartment_;
-  species Ste7 in compartment_, Fus3 in compartment_, complexB in compartment_;
-  species Ste20 in compartment_, complexE in compartment_, complexF in compartment_;
-  species complexG in compartment_, complexH in compartment_, complexI in compartment_;
-  species complexL in compartment_, Fus3PP in compartment_, complexK in compartment_;
-  species Ste12 in compartment_, Ste12a in compartment_, Bar1 in compartment_;
-  species Bar1a in compartment_, Bar1aex in Extracellular, Far1 in compartment_;
-  species Far1PP in compartment_, Far1U in compartment_, complexM in compartment_;
-  species complexN in compartment_, Cdc28 in compartment_, Sst2 in compartment_;
-  species $p in compartment_;
-
-  // Reactions:
-  v1: alpha -> ; Extracellular*alpha*Bar1aex*v1_k1;
-  v2: Ste2 -> Ste2a; compartment_*Ste2*alpha*v2_k2;
-  v3: Ste2a -> Ste2; compartment_*Ste2a*v3_k3;
-  v4: Ste2a -> $p; compartment_*Ste2a*v4_k4;
-  v5: Ste2 -> ; compartment_*Ste2*v5_k5;
-  v6: Gabc -> GaGTP + Gbc; compartment_*Ste2a*Gabc*v6_k6;
-  v7: GaGTP -> GaGDP; compartment_*GaGTP*v7_k7;
-  v8: GaGTP -> GaGDP; compartment_*GaGTP*Sst2*v8_k8;
-  v9: GaGDP + Gbc -> Gabc; compartment_*GaGDP*Gbc*v9_k9;
-  v10: Gbc + complexC -> complexD; compartment_*Gbc*complexC*v10_k10;
-  v11: complexD -> Gbc + complexC; compartment_*complexD*v11_k11;
-  v12: Ste11 + Ste5 -> complexA; compartment_*Ste5*Ste11*v12_k12;
-  v13: complexA -> Ste11 + Ste5; compartment_*complexA*v13_k13;
-  v14: Fus3 + Ste7 -> complexB; compartment_*Ste7*Fus3*v14_k14;
-  v15: complexB -> Fus3 + Ste7; compartment_*complexB*v15_k15;
-  v16: complexA + complexB -> complexC; compartment_*complexA*complexB*v16_k16;
-  v17: complexC -> Fus3 + Ste11 + Ste7 + Ste5; compartment_*complexC*v17_k17;
-  v18: complexD + Ste20 -> complexE; compartment_*complexD*Ste20*v18_k18;
-  v19: complexE -> complexD + Ste20; compartment_*complexE*v19_k19;
-  v20: complexE -> complexF; compartment_*complexE*v20_k20;
-  v21: complexE -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexE*v21_k21;
-  v22: complexF -> complexG; compartment_*complexF*v22_k22;
-  v23: complexF -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexF*v23_k23;
-  v24: complexG -> complexH; compartment_*complexG*v24_k24;
-  v25: complexG -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexG*v25_k25;
-  v26: complexH -> complexI; compartment_*complexH*v26_k26;
-  v27: complexH -> Gbc + Ste7 + Ste5 + Fus3 + Ste20 + Ste11; compartment_*complexH*v27_k27;
-  v28: complexI -> complexL + Fus3PP; compartment_*complexI*v28_k28;
-  v29: complexL + Fus3 -> complexK; compartment_*complexL*Fus3*v29_k29;
-  v30: complexK -> complexL + Fus3; compartment_*complexK*v30_k30;
-  v31: complexK -> complexI; compartment_*complexK*v31_k31;
-  v32: complexL -> Gbc + Ste7 + Ste5 + Ste20 + Ste11; compartment_*complexL*v32_k32;
-  v33: Fus3PP -> Fus3; compartment_*Fus3PP*v33_k33;
-  v34: Ste12 + Fus3PP -> Ste12a; compartment_*Ste12*Fus3PP*v34_k34;
-  v35: Ste12a -> Ste12 + Fus3PP; compartment_*Ste12a*v35_k35;
-  v36: Bar1 -> Bar1a; compartment_*Ste12a*Bar1*v36_k36;
-  v37: Bar1a -> Bar1; compartment_*Bar1a*v37_k37;
-  v38: Bar1a -> Bar1aex; compartment_*Bar1a*v38_k38;
-  v39: Far1 -> Far1PP; compartment_*(Far1*Fus3PP*Fus3PP/(100*100 + Fus3PP*Fus3PP))*v39_k39;
-  v40: Far1PP -> Far1; compartment_*Far1PP*v40_k40;
-  v41: Far1 -> Far1U; compartment_*Far1*Cdc28*v41_k41;
-  v42: Gbc + Far1PP -> complexM; compartment_*Gbc*Far1PP*v42_k42;
-  v43: complexM -> Gbc + Far1PP; compartment_*complexM*v43_k43;
-  v44: complexN -> Cdc28 + Far1PP; compartment_*complexN*v44_k44;
-  v45: Cdc28 + Far1PP -> complexN; compartment_*Far1PP*Cdc28*v45_k45;
-  v46: $p -> Sst2; compartment_*(Fus3PP^2/(4^2 + Fus3PP^2))*v46_k46;
-  v47: Sst2 -> $p; compartment_*Sst2*v47_k47;
-
-  // Species initializations:
-  alpha = 100;
-  Ste2 = 1666.6666667;
-  Ste2a = 0;
-  Gabc = 1666.6666667;
-  GaGTP = 0;
-  Gbc = 0;
-  GaGDP = 0;
-  complexC = 235.724935791903;
-  complexD = 0;
-  Ste5 = 158.33176608789;
-  Ste11 = 158.33176608789;
-  complexA = 105.943298120207;
-  Ste7 = 36.3997016405141;
-  Fus3 = 686.399701640513;
-  complexB = 77.8753625675829;
-  Ste20 = 1000;
-  complexE = 0;
-  complexF = 0;
-  complexG = 0;
-  complexH = 0;
-  complexI = 0;
-  complexL = 0;
-  Fus3PP = 0;
-  complexK = 0;
-  Ste12 = 200;
-  Ste12a = 0;
-  Bar1 = 200;
-  Bar1a = 0;
-  Bar1aex = 0;
-  Far1 = 500;
-  Far1PP = 0;
-  Far1U = 0;
-  complexM = 0;
-  complexN = 0;
-  Cdc28 = 300;
-  Sst2 = 0;
-  p = 0;
-
-  // Compartment initializations:
-  Extracellular = 1;
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1 = 0.03;
-  v1_k1 has min_inv_nM_inv;
-  v2_k2 = 0.0012;
-  v2_k2 has min_inv_nM_inv;
-  v3_k3 = 0.6;
-  v3_k3 has min_inv;
-  v4_k4 = 0.24;
-  v4_k4 has min_inv;
-  v5_k5 = 0.024;
-  v5_k5 has min_inv;
-  v6_k6 = 0.0036;
-  v6_k6 has min_inv_nM_inv;
-  v7_k7 = 0.24;
-  v7_k7 has min_inv;
-  v8_k8 = 0.033;
-  v8_k8 has min_inv_nM_inv;
-  v9_k9 = 2000;
-  v9_k9 has min_inv_nM_inv;
-  v10_k10 = 0.1;
-  v10_k10 has min_inv_nM_inv;
-  v11_k11 = 5;
-  v11_k11 has min_inv;
-  v12_k12 = 1;
-  v12_k12 has min_inv_nM_inv;
-  v13_k13 = 3;
-  v13_k13 has min_inv;
-  v14_k14 = 1;
-  v14_k14 has min_inv_nM_inv;
-  v15_k15 = 3;
-  v15_k15 has min_inv;
-  v16_k16 = 3;
-  v16_k16 has min_inv_nM_inv;
-  v17_k17 = 100;
-  v17_k17 has min_inv;
-  v18_k18 = 5;
-  v18_k18 has min_inv_nM_inv;
-  v19_k19 = 1;
-  v19_k19 has min_inv;
-  v20_k20 = 10;
-  v20_k20 has min_inv;
-  v21_k21 = 5;
-  v21_k21 has min_inv;
-  v22_k22 = 47;
-  v22_k22 has min_inv;
-  v23_k23 = 5;
-  v23_k23 has min_inv;
-  v24_k24 = 345;
-  v24_k24 has min_inv;
-  v25_k25 = 5;
-  v25_k25 has min_inv;
-  v26_k26 = 50;
-  v26_k26 has min_inv;
-  v27_k27 = 5;
-  v27_k27 has min_inv;
-  v28_k28 = 140;
-  v28_k28 has min_inv;
-  v29_k29 = 10;
-  v29_k29 has min_inv_nM_inv;
-  v30_k30 = 1;
-  v30_k30 has min_inv;
-  v31_k31 = 250;
-  v31_k31 has min_inv;
-  v32_k32 = 5;
-  v32_k32 has min_inv;
-  v33_k33 = 50;
-  v33_k33 has min_inv;
-  v34_k34 = 18;
-  v34_k34 has min_inv_nM_inv;
-  v35_k35 = 10;
-  v35_k35 has min_inv;
-  v36_k36 = 0.1;
-  v36_k36 has min_inv_nM_inv;
-  v37_k37 = 0.1;
-  v37_k37 has min_inv;
-  v38_k38 = 0.01;
-  v38_k38 has min_inv;
-  v39_k39 = 18;
-  v39_k39 has min_inv;
-  v40_k40 = 1;
-  v40_k40 has min_inv;
-  v41_k41 = 0.02;
-  v41_k41 has min_inv_nM_inv;
-  v42_k42 = 0.1;
-  v42_k42 has min_inv_nM_inv;
-  v43_k43 = 0.01;
-  v43_k43 has min_inv;
-  v44_k44 = 0.01;
-  v44_k44 has min_inv;
-  v45_k45 = 0.1;
-  v45_k45 has min_inv_nM_inv;
-  v46_k46 = 200;
-  v46_k46 has nM_min_inv;
-  v47_k47 = 1;
-  v47_k47 has min_inv;
-
-  // Other declarations:
-  const Extracellular, compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-9 mole;
-  unit time_unit = 60 second;
-  unit nanoMolar = 1e-9 mole / litre;
-  unit min_inv = 1 / 60 second;
-  unit min_inv_nM_inv = litre / (1e-9 mole * 60 second);
-  unit nM_min_inv = 1e-9 mole / (litre * 60 second);
-
-  // Display Names:
-  substance is "nanomole (default)";
-  time_unit is "minute (default)";
-  compartment_ is "cell";
-  alpha is "α-factor";
-  Ste2a is "Ste2active";
-  Gabc is "Gαβγ";
-  GaGTP is "GαGTP";
-  Gbc is "Gβγ";
-  GaGDP is "GαGDP";
-  Ste12a is "Ste12active";
-  Bar1a is "Bar1active";
-  Bar1aex is "Bar1activeEx";
-  Far1U is "Far1ubiquitin";
-  v1 is "alpha degradation";
-
-  // CV terms:
-  Extracellular hypernym "http://identifiers.org/go/GO:0005615"
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  Ste2 identity "http://identifiers.org/uniprot/P06842"
-  Ste2a identity "http://identifiers.org/uniprot/P06842"
-  Gabc part "http://identifiers.org/uniprot/P08539",
-            "http://identifiers.org/uniprot/P18851",
-            "http://identifiers.org/uniprot/P18852"
-  GaGTP identity "http://identifiers.org/uniprot/P08539"
-  Gbc part "http://identifiers.org/uniprot/P18851",
-           "http://identifiers.org/uniprot/P18852"
-  Gbc identity "http://identifiers.org/bind/50058"
-  GaGDP identity "http://identifiers.org/uniprot/P08539"
-  complexC part "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P32917"
-  complexC identity "http://identifiers.org/bind/133390"
-  complexD part "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P32917",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P18852"
-  Ste5 identity "http://identifiers.org/uniprot/P32917"
-  Ste11 identity "http://identifiers.org/uniprot/P23561"
-  complexA part "http://identifiers.org/uniprot/P32917",
-                "http://identifiers.org/uniprot/P23561"
-  Ste7 identity "http://identifiers.org/uniprot/P06784"
-  Fus3 identity "http://identifiers.org/uniprot/P16892"
-  complexB part "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P16892"
-  complexB identity "http://identifiers.org/bind/130661"
-  Ste20 identity "http://identifiers.org/uniprot/Q03497"
-  complexE part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  complexF part "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P32917",
-                "http://identifiers.org/uniprot/P23561"
-  complexG part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P32917"
-  complexH part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P32917"
-  complexI part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  complexL part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  Fus3PP identity "http://identifiers.org/uniprot/P16892"
-  complexK part "http://identifiers.org/uniprot/P18852",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P08539",
-                "http://identifiers.org/uniprot/P16892",
-                "http://identifiers.org/uniprot/P06784",
-                "http://identifiers.org/uniprot/Q03497",
-                "http://identifiers.org/uniprot/P23561",
-                "http://identifiers.org/uniprot/P32917"
-  Ste12 identity "http://identifiers.org/uniprot/P13574"
-  Ste12a identity "http://identifiers.org/uniprot/P13574"
-  Bar1 identity "http://identifiers.org/uniprot/P12630"
-  Bar1a identity "http://identifiers.org/uniprot/P12630"
-  Bar1aex identity "http://identifiers.org/uniprot/P12630"
-  Far1 identity "http://identifiers.org/uniprot/P21268"
-  Far1PP identity "http://identifiers.org/uniprot/P21268"
-  Far1U identity "http://identifiers.org/uniprot/P21268"
-  complexM part "http://identifiers.org/uniprot/P21268",
-                "http://identifiers.org/uniprot/P18851",
-                "http://identifiers.org/uniprot/P18852"
-  complexN part "http://identifiers.org/uniprot/P21268",
-                "http://identifiers.org/uniprot/P00546"
-  Cdc28 identity "http://identifiers.org/uniprot/P00546"
-  Sst2 identity "http://identifiers.org/uniprot/P11972"
-  v1 hypernym "http://identifiers.org/go/GO:0030163"
-  v2 identity "http://identifiers.org/intact/EBI-904275"
-  v2 hypernym "http://identifiers.org/go/GO:0004934"
-  v3 identity "http://identifiers.org/intact/EBI-904275"
-  v4 hypernym "http://identifiers.org/go/GO:0030163"
-  v5 hypernym "http://identifiers.org/go/GO:0030163"
-  v6 version "http://identifiers.org/intact/EBI-380703",
-             "http://identifiers.org/intact/EBI-48387",
-             "http://identifiers.org/intact/EBI-877237"
-  v6 hypernym "http://identifiers.org/go/GO:0004930"
-  v7 hypernym "http://identifiers.org/go/GO:0003924"
-  v8 hypernym "http://identifiers.org/go/GO:0005096"
-  v8 identity "http://identifiers.org/intact/EBI-904406"
-  v9 version "http://identifiers.org/intact/EBI-877243",
-             "http://identifiers.org/intact/EBI-380703"
-  v10 hypernym "http://identifiers.org/go/GO:0005078"
-  v10 identity "http://identifiers.org/intact/EBI-903953"
-  v11 hypernym "http://identifiers.org/go/GO:0043241"
-  v12 identity "http://identifiers.org/intact/EBI-877414"
-  v13 hypernym "http://identifiers.org/go/GO:0043241"
-  v14 hypernym "http://identifiers.org/go/GO:0051019"
-  v14 identity "http://identifiers.org/intact/EBI-877260"
-  v15 hypernym "http://identifiers.org/go/GO:0043241"
-  v16 hypernym "http://identifiers.org/go/GO:0005078"
-  v16 part "http://identifiers.org/intact/EBI-895753",
-           "http://identifiers.org/intact/EBI-877421",
-           "http://identifiers.org/intact/EBI-877417"
-  v17 hypernym "http://identifiers.org/go/GO:0043241"
-  v18 hypernym "http://identifiers.org/go/GO:0004674"
-  v18 identity "http://identifiers.org/intact/EBI-903992"
-  v19 hypernym "http://identifiers.org/go/GO:0043241"
-  v20 hypernym "http://identifiers.org/ec-code/2.7.11.1",
-               "http://identifiers.org/go/GO:0000185",
-               "http://identifiers.org/go/GO:0008349"
-  v21 hypernym "http://identifiers.org/go/GO:0043241"
-  v22 hypernym "http://identifiers.org/ec-code/2.7.11.25",
-               "http://identifiers.org/go/GO:0000186",
-               "http://identifiers.org/go/GO:0004709"
-  v23 hypernym "http://identifiers.org/go/GO:0043241"
-  v24 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0004708",
-               "http://identifiers.org/go/GO:0000187"
-  v25 hypernym "http://identifiers.org/go/GO:0043241"
-  v26 hypernym "http://identifiers.org/go/GO:0006468"
-  v27 hypernym "http://identifiers.org/go/GO:0043241"
-  v28 hypernym "http://identifiers.org/go/GO:0043241"
-  v29 hypernym "http://identifiers.org/go/GO:0051019"
-  v29 part "http://identifiers.org/intact/EBI-877260",
-           "http://identifiers.org/intact/EBI-877421"
-  v30 hypernym "http://identifiers.org/go/GO:0043241"
-  v31 hypernym "http://identifiers.org/ec-code/2.7.12.2",
-               "http://identifiers.org/go/GO:0004708",
-               "http://identifiers.org/go/GO:0000187"
-  v32 hypernym "http://identifiers.org/go/GO:0043241"
-  v33 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0016311",
-               "http://identifiers.org/go/GO:0000188"
-  v34 hypernym "http://identifiers.org/go/GO:0004707",
-               "http://identifiers.org/go/GO:0051019"
-  v35 hypernym "http://identifiers.org/go/GO:0043241"
-  v36 hypernym "http://identifiers.org/go/GO:0003700"
-  v37 hypernym "http://identifiers.org/go/GO:0043241"
-  v38 hypernym "http://identifiers.org/go/GO:0006611"
-  v39 hypernym "http://identifiers.org/ec-code/2.7.11.24",
-               "http://identifiers.org/go/GO:0004707"
-  v40 hypernym "http://identifiers.org/ec-code/3.1.3.16",
-               "http://identifiers.org/go/GO:0016311"
-  v41 hypernym "http://identifiers.org/go/GO:0016567"
-  v43 hypernym "http://identifiers.org/go/GO:0043241"
-  v44 hypernym "http://identifiers.org/go/GO:0043241"
-  v45 hypernym "http://identifiers.org/go/GO:0004861"
-  v46 hypernym "http://identifiers.org/ec-code/2.7.11.24",
-               "http://identifiers.org/go/GO:0004707"
-end
-
-Kofahl2004_PheromonePathway is "Kofahl2004_PheromonePathway"
-
-Kofahl2004_PheromonePathway model_entity_is "http://identifiers.org/biomodels.db/MODEL6618819961"
-Kofahl2004_PheromonePathway model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000032"
-Kofahl2004_PheromonePathway description "http://identifiers.org/pubmed/15300679"
-Kofahl2004_PheromonePathway hypernym "http://identifiers.org/go/GO:0019236"
-Kofahl2004_PheromonePathway taxon "http://identifiers.org/taxonomy/4932"
-Kofahl2004_PheromonePathway part "http://identifiers.org/go/GO:0000165"

BioModelsRAG/data/BIOMD0000000033.txt

@@ -1,278 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Brown2004_NGF_EGF_signaling()
-
-  // Compartments and Species:
-  compartment cell;
-  species EGF in cell, NGF in cell, freeEGFReceptor in cell, boundEGFReceptor in cell;
-  species freeNGFReceptor in cell, boundNGFReceptor in cell, SosInactive in cell;
-  species SosActive in cell, P90RskInactive in cell, P90RskActive in cell;
-  species RasInactive in cell, RasActive in cell, $RasGapActive in cell, Raf1Inactive in cell;
-  species Raf1Active in cell, BRafInactive in cell, BRafActive in cell, MekInactive in cell;
-  species MekActive in cell, ErkInactive in cell, ErkActive in cell, PI3KInactive in cell;
-  species PI3KActive in cell, AktInactive in cell, AktActive in cell, C3GInactive in cell;
-  species C3GActive in cell, Rap1Inactive in cell, Rap1Active in cell, $RapGapActive in cell;
-  species $PP2AActive in cell, $Raf1PPtase in cell;
-
-  // Reactions:
-  EGFBindingReaction: EGF + freeEGFReceptor => boundEGFReceptor; cell*krbEGF*EGF*freeEGFReceptor;
-  EGFUnbindingReaction: boundEGFReceptor => EGF + freeEGFReceptor; cell*kruEGF*boundEGFReceptor;
-  NGFBindingReaction: NGF + freeNGFReceptor => boundNGFReceptor; krbNGF*NGF*freeNGFReceptor*cell;
-  NGFUnbindingReaction: boundNGFReceptor => NGF + freeNGFReceptor; kruNGF*boundNGFReceptor*cell;
-  SosActivationByEGFReaction: SosInactive -> SosActive; cell*(kEGF*boundEGFReceptor*SosInactive/(SosInactive + KmEGF));
-  SosActivationByNGFReaction: SosInactive -> SosActive; cell*(kNGF*boundNGFReceptor*SosInactive/(SosInactive + KmNGF));
-  SosDeactivationReaction: SosActive -> SosInactive; cell*(kdSos*P90RskActive*SosActive/(SosActive + KmdSos));
-  RasActivationReaction: RasInactive -> RasActive; cell*(kSos*SosActive*RasInactive/(RasInactive + KmSos));
-  RasDeactivationReaction: RasActive -> RasInactive; cell*(kRasGap*RasGapActive*RasActive/(RasActive + KmRasGap));
-  Raf1ByRasActivationReaction: Raf1Inactive -> Raf1Active; cell*(kRasToRaf1*RasActive*Raf1Inactive/(Raf1Inactive + KmRasToRaf1));
-  MekbyRaf1ActivationReaction: MekInactive -> MekActive; cell*(kpRaf1*Raf1Active*MekInactive/(MekInactive + KmpRaf1));
-  MekbyBRafActivationReaction: MekInactive -> MekActive; cell*(kpBRaf*BRafActive*MekInactive/(MekInactive + KmpBRaf));
-  ErkActivationReaction: ErkInactive -> ErkActive; cell*(kpMekCytoplasmic*MekActive*ErkInactive/(ErkInactive + KmpMekCytoplasmic));
-  MekDeactivationReaction: MekActive -> MekInactive; cell*(kdMek*PP2AActive*MekActive/(MekActive + KmdMek));
-  ErkDeactivationReaction: ErkActive -> ErkInactive; cell*(kdErk*PP2AActive*ErkActive/(ErkActive + KmdErk));
-  Raf1byPPtaseDeactivationReaction: Raf1Active -> Raf1Inactive; cell*(kdRaf1*Raf1PPtase*Raf1Active/(Raf1Active + KmdRaf1));
-  P90RskActivationReaction: P90RskInactive -> P90RskActive; cell*(kpP90Rsk*ErkActive*P90RskInactive/(P90RskInactive + KmpP90Rsk));
-  PI3KbyEGFRActivationReaction: PI3KInactive -> PI3KActive; cell*(kPI3K*boundEGFReceptor*PI3KInactive/(PI3KInactive + KmPI3K));
-  PI3KbyRasActivationReaction: PI3KInactive -> PI3KActive; cell*(kPI3KRas*RasActive*PI3KInactive/(PI3KInactive + KmPI3KRas));
-  AktActivationReaction: AktInactive -> AktActive; cell*(kAkt*PI3KActive*AktInactive/(AktInactive + KmAkt));
-  Raf1ByAktDeactivationReaction: Raf1Active -> Raf1Inactive; cell*(kdRaf1ByAkt*AktActive*Raf1Active/(Raf1Active + KmRaf1ByAkt));
-  C3GActivationReaction: C3GInactive -> C3GActive; cell*(kC3GNGF*boundNGFReceptor*C3GInactive/(C3GInactive + KmC3GNGF));
-  Rap1ActivationReaction: Rap1Inactive -> Rap1Active; cell*(kC3G*C3GActive*Rap1Inactive/(Rap1Inactive + KmC3G));
-  Rap1DeactivationReaction: Rap1Active -> Rap1Inactive; cell*(kRapGap*RapGapActive*Rap1Active/(Rap1Active + KmRapGap));
-  BRafByRap1ActivationReaction: BRafInactive -> BRafActive; cell*(kRap1ToBRaf*Rap1Active*BRafInactive/(BRafInactive + KmRap1ToBRaf));
-  BRafbyPPtaseDeactivationReaction: BRafActive -> BRafInactive; cell*(kdBRaf*Raf1PPtase*BRafActive/(BRafActive + KmdBRaf));
-
-  // Species initializations:
-  EGF = 10002000;
-  NGF = 456000;
-  freeEGFReceptor = 80000;
-  boundEGFReceptor = 0;
-  freeNGFReceptor = 10000;
-  boundNGFReceptor = 0;
-  SosInactive = 120000;
-  SosActive = 0;
-  P90RskInactive = 120000;
-  P90RskActive = 0;
-  RasInactive = 120000;
-  RasActive = 0;
-  RasGapActive = 120000;
-  Raf1Inactive = 120000;
-  Raf1Active = 0;
-  BRafInactive = 120000;
-  BRafActive = 0;
-  MekInactive = 600000;
-  MekActive = 0;
-  ErkInactive = 600000;
-  ErkActive = 0;
-  PI3KInactive = 120000;
-  PI3KActive = 0;
-  AktInactive = 120000;
-  AktActive = 0;
-  C3GInactive = 120000;
-  C3GActive = 0;
-  Rap1Inactive = 120000;
-  Rap1Active = 0;
-  RapGapActive = 120000;
-  PP2AActive = 120000;
-  Raf1PPtase = 120000;
-
-  // Compartment initializations:
-  cell = 1;
-
-  // Variable initializations:
-  krbEGF = 2.18503e-05;
-  kruEGF = 0.0121008;
-  krbNGF = 1.38209e-07;
-  kruNGF = 0.00723811;
-  kEGF = 694.731;
-  KmEGF = 6086070;
-  kNGF = 389.428;
-  KmNGF = 2112.66;
-  kdSos = 1611.97;
-  KmdSos = 896896;
-  kSos = 32.344;
-  KmSos = 35954.3;
-  kRasGap = 1509.36;
-  KmRasGap = 1432410;
-  kRasToRaf1 = 0.884096;
-  KmRasToRaf1 = 62464.6;
-  kpRaf1 = 185.759;
-  KmpRaf1 = 4768350;
-  kpBRaf = 125.089;
-  KmpBRaf = 157948;
-  kdMek = 2.83243;
-  KmdMek = 518753;
-  kpMekCytoplasmic = 9.85367;
-  KmpMekCytoplasmic = 1007340;
-  kdErk = 8.8912;
-  KmdErk = 3496490;
-  kpP90Rsk = 0.0213697;
-  KmpP90Rsk = 763523;
-  kPI3K = 10.6737;
-  KmPI3K = 184912;
-  kPI3KRas = 0.0771067;
-  KmPI3KRas = 272056;
-  kAkt = 0.0566279;
-  KmAkt = 653951;
-  kdRaf1ByAkt = 15.1212;
-  KmRaf1ByAkt = 119355;
-  kC3GNGF = 146.912;
-  KmC3GNGF = 12876.2;
-  kC3G = 1.40145;
-  KmC3G = 10965.6;
-  kRapGap = 27.265;
-  KmRapGap = 295990;
-  kRap1ToBRaf = 2.20995;
-  KmRap1ToBRaf = 1025460;
-  kdRaf1 = 0.126329;
-  KmdRaf1 = 1061.71;
-  kdBRaf = 441.287;
-  KmdBRaf = 10879500;
-
-  // Other declarations:
-  const cell, krbEGF, kruEGF, krbNGF, kruNGF, kEGF, KmEGF, kNGF, KmNGF, kdSos;
-  const KmdSos, kSos, KmSos, kRasGap, KmRasGap, kRasToRaf1, KmRasToRaf1, kpRaf1;
-  const KmpRaf1, kpBRaf, KmpBRaf, kdMek, KmdMek, kpMekCytoplasmic, KmpMekCytoplasmic;
-  const kdErk, KmdErk, kpP90Rsk, KmpP90Rsk, kPI3K, KmPI3K, kPI3KRas, KmPI3KRas;
-  const kAkt, KmAkt, kdRaf1ByAkt, KmRaf1ByAkt, kC3GNGF, KmC3GNGF, kC3G, KmC3G;
-  const kRapGap, KmRapGap, kRap1ToBRaf, KmRap1ToBRaf, kdRaf1, KmdRaf1, kdBRaf;
-  const KmdBRaf;
-
-  // Unit definitions:
-  unit substance = item;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "item (default)";
-  time_unit is "minute (default)";
-  EGFBindingReaction is "EGF binding";
-  EGFUnbindingReaction is "EFG unbinding";
-  NGFBindingReaction is "NGF binding";
-  NGFUnbindingReaction is "NGF unbinding";
-  SosActivationByEGFReaction is "SOS activation by EGF";
-  SosActivationByNGFReaction is "SOS activation by NGF";
-  SosDeactivationReaction is "SOS deactivation";
-  RasActivationReaction is "Ras activation";
-  RasDeactivationReaction is "Ras deactivation";
-  Raf1ByRasActivationReaction is "Raf1 activation by Ras";
-  MekbyRaf1ActivationReaction is "Mek activation by Raf1";
-  MekbyBRafActivationReaction is "Mek activation by B-Raf";
-  ErkActivationReaction is "Erk activation";
-  MekDeactivationReaction is "Mek deactivation";
-  ErkDeactivationReaction is "Erk deactivation";
-  Raf1byPPtaseDeactivationReaction is "Raf1 deactivation by PPase";
-  P90RskActivationReaction is "P90Rsk activation";
-  PI3KbyEGFRActivationReaction is "PI3K activation by EGFR";
-  PI3KbyRasActivationReaction is "PI3K activation by Ras";
-  AktActivationReaction is "Akt activation";
-  Raf1ByAktDeactivationReaction is "Raf1 deactivation by Akt";
-  C3GActivationReaction is "C3G activation";
-  Rap1ActivationReaction is "Rap1 activation";
-  Rap1DeactivationReaction is "Rap1 deactivation";
-  BRafByRap1ActivationReaction is "BRaf activation by Rap1";
-  BRafbyPPtaseDeactivationReaction is "BRaf deactivation by PPase";
-
-  // CV terms:
-  cell identity "http://identifiers.org/go/GO:0005623"
-  EGF identity "http://identifiers.org/uniprot/P07522"
-  NGF identity "http://identifiers.org/uniprot/P25427"
-  freeEGFReceptor identity "http://identifiers.org/uniprot/Q9QX70"
-  boundEGFReceptor part "http://identifiers.org/uniprot/Q9QX70",
-                        "http://identifiers.org/uniprot/P07522"
-  freeNGFReceptor identity "http://identifiers.org/uniprot/P35739"
-  boundNGFReceptor part "http://identifiers.org/uniprot/P35739",
-                        "http://identifiers.org/uniprot/P25427"
-  SosInactive hypernym "http://identifiers.org/ensembl/ENSRNOP00000009359",
-                       "http://identifiers.org/uniprot/Q9Z1I1"
-  SosActive hypernym "http://identifiers.org/ensembl/ENSRNOP00000009359",
-                     "http://identifiers.org/uniprot/Q9Z1I1"
-  P90RskInactive version "http://identifiers.org/uniprot/Q9Z1I2",
-                         "http://identifiers.org/uniprot/Q63531"
-  P90RskActive version "http://identifiers.org/uniprot/Q9Z1I2",
-                       "http://identifiers.org/uniprot/Q63531"
-  RasInactive hypernym "http://identifiers.org/interpro/IPR003577"
-  RasActive hypernym "http://identifiers.org/interpro/IPR003577"
-  RasGapActive identity "http://identifiers.org/uniprot/P50904"
-  Raf1Inactive hypernym "http://identifiers.org/uniprot/P11345"
-  Raf1Active hypernym "http://identifiers.org/uniprot/P11345"
-  BRafInactive hypernym "http://identifiers.org/uniprot/Q99MC6"
-  BRafActive hypernym "http://identifiers.org/uniprot/Q99MC6"
-  MekInactive hypernym "http://identifiers.org/uniprot/Q01986",
-                       "http://identifiers.org/uniprot/P36506"
-  MekActive hypernym "http://identifiers.org/uniprot/Q01986",
-                     "http://identifiers.org/uniprot/P36506"
-  ErkInactive hypernym "http://identifiers.org/uniprot/P21708",
-                       "http://identifiers.org/uniprot/P63086"
-  ErkActive hypernym "http://identifiers.org/uniprot/P21708",
-                     "http://identifiers.org/uniprot/P63086"
-  PI3KInactive part "http://identifiers.org/interpro/IPR015433"
-  PI3KInactive hypernym "http://identifiers.org/go/GO:0005942"
-  PI3KActive part "http://identifiers.org/interpro/IPR015433"
-  PI3KActive hypernym "http://identifiers.org/go/GO:0005942"
-  AktInactive version "http://identifiers.org/uniprot/P47196",
-                      "http://identifiers.org/uniprot/P47197",
-                      "http://identifiers.org/uniprot/Q63484"
-  AktActive version "http://identifiers.org/uniprot/P47196",
-                    "http://identifiers.org/uniprot/P47197",
-                    "http://identifiers.org/uniprot/Q63484"
-  C3GInactive hypernym "http://identifiers.org/uniprot/Q9QYV3"
-  C3GActive hypernym "http://identifiers.org/uniprot/Q9QYV3"
-  Rap1Inactive version "http://identifiers.org/uniprot/P10113",
-                       "http://identifiers.org/uniprot/Q62636"
-  Rap1Active version "http://identifiers.org/uniprot/P10113",
-                     "http://identifiers.org/uniprot/Q62636"
-  RapGapActive identity "http://identifiers.org/uniprot/P47736"
-  PP2AActive identity "http://identifiers.org/go/GO:0000159"
-  EGFBindingReaction identity "http://identifiers.org/go/GO:0048408"
-  EGFBindingReaction hypernym "http://identifiers.org/go/GO:0045741"
-  EGFUnbindingReaction hypernym "http://identifiers.org/go/GO:0007175"
-  NGFBindingReaction hypernym "http://identifiers.org/go/GO:0051396"
-  NGFBindingReaction identity "http://identifiers.org/go/GO:0048406"
-  NGFUnbindingReaction hypernym "http://identifiers.org/go/GO:0051395"
-  SosActivationByEGFReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                      "http://identifiers.org/go/GO:0004716"
-  SosActivationByNGFReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                      "http://identifiers.org/go/GO:0004716"
-  SosDeactivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37"
-  RasActivationReaction identity "http://identifiers.org/go/GO:0046579"
-  RasDeactivationReaction identity "http://identifiers.org/go/GO:0046580"
-  Raf1ByRasActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0008349",
-                                       "http://identifiers.org/go/GO:0000185"
-  MekbyRaf1ActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0004709",
-                                       "http://identifiers.org/go/GO:0000186"
-  MekbyBRafActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0004709",
-                                       "http://identifiers.org/go/GO:0000186"
-  ErkActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                 "http://identifiers.org/go/GO:0000187",
-                                 "http://identifiers.org/go/GO:0004708"
-  MekDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  ErkDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16",
-                                   "http://identifiers.org/go/GO:0000188"
-  Raf1byPPtaseDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16"
-  P90RskActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                    "http://identifiers.org/go/GO:0004707"
-  PI3KbyEGFRActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37"
-  PI3KbyRasActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                       "http://identifiers.org/go/GO:0008349"
-  AktActivationReaction hypernym "http://identifiers.org/go/GO:0045860"
-  Raf1ByAktDeactivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37"
-  C3GActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                 "http://identifiers.org/go/GO:0004716"
-  Rap1ActivationReaction identity "http://identifiers.org/go/GO:0046582"
-  BRafByRap1ActivationReaction hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                                        "http://identifiers.org/go/GO:0000185"
-  BRafbyPPtaseDeactivationReaction hypernym "http://identifiers.org/ec-code/3.1.3.16"
-end
-
-Brown2004_NGF_EGF_signaling is "Brown2004 - NGF and EGF signaling"
-
-Brown2004_NGF_EGF_signaling model_entity_is "http://identifiers.org/biomodels.db/MODEL6619514794"
-Brown2004_NGF_EGF_signaling model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000033"
-Brown2004_NGF_EGF_signaling description "http://identifiers.org/pubmed/16204838"
-Brown2004_NGF_EGF_signaling hypernym "http://identifiers.org/go/GO:0070371"
-Brown2004_NGF_EGF_signaling taxon "http://identifiers.org/taxonomy/131567"
-Brown2004_NGF_EGF_signaling property "http://identifiers.org/mamo/MAMO_0000046"
-Brown2004_NGF_EGF_signaling part "http://identifiers.org/go/GO:0048011",
-                                 "http://identifiers.org/go/GO:0007173"

BioModelsRAG/data/BIOMD0000000034.txt

@@ -1,259 +0,0 @@
-// Created by libAntimony v2.13.0
-model *model_0000001()
-
-  // Compartments and Species:
-  compartment compartment_0000002, compartment_0000001;
-  species species_0000001 in compartment_0000001, species_0000002 in compartment_0000001;
-  species species_0000003 in compartment_0000001, species_0000004 in compartment_0000002;
-  species species_0000005 in compartment_0000002, species_0000006 in compartment_0000002;
-  species species_0000007 in compartment_0000001, species_0000008 in compartment_0000001;
-  species species_0000009 in compartment_0000001;
-
-  // Rate Rules:
-  parameter_0000001' = parameter_0000017*(species_0000008/(species_0000008 + parameter_0000011))*(parameter_0000005/(parameter_0000005 + species_0000001 + species_0000002 + species_0000003))*(1 - parameter_0000001) - parameter_0000014*parameter_0000001;
-  parameter_0000002' = parameter_0000018*(species_0000008/(species_0000008 + parameter_0000012))*(parameter_0000006/(parameter_0000006 + species_0000001 + species_0000002 + species_0000003))*(1 - parameter_0000002) - parameter_0000015*parameter_0000002;
-  parameter_0000003' = parameter_0000019*(species_0000008/(species_0000008 + parameter_0000013))*(parameter_0000007/(parameter_0000007 + species_0000001 + species_0000002 + species_0000003))*(1 - parameter_0000003) - parameter_0000016*parameter_0000003;
-  parameter_0000020' = (parameter_0000001^parameter_0000026 - parameter_0000020)/parameter_0000023;
-  parameter_0000021' = (parameter_0000002^parameter_0000026 - parameter_0000021)/parameter_0000024;
-  parameter_0000022' = (parameter_0000003^parameter_0000026 - parameter_0000022)/parameter_0000025;
-
-  // Reactions:
-  reaction_0000001:  => species_0000004; compartment_0000002*(parameter_0000027*parameter_0000021 + parameter_0000031);
-  reaction_0000002:  => species_0000007; compartment_0000001*(parameter_0000028*parameter_0000020 + parameter_0000032);
-  reaction_0000003:  => species_0000009; compartment_0000001*delay(parameter_0000029*parameter_0000022 + parameter_0000034, parameter_0000039);
-  reaction_0000004:  => species_0000008; compartment_0000001*(parameter_0000030*(species_0000009^2/(species_0000009^2 + parameter_0000010^2))*(parameter_0000008^2/(species_0000007^2 + parameter_0000008^2)) + parameter_0000033);
-  reaction_0000005: species_0000008 => ; compartment_0000001*parameter_0000036*species_0000008;
-  reaction_0000006: species_0000009 => ; compartment_0000001*parameter_0000038*species_0000009;
-  reaction_0000007: species_0000007 => ; compartment_0000001*parameter_0000037*species_0000007;
-  reaction_0000008: species_0000004 => species_0000005; compartment_0000002*(parameter_0000040*species_0000004/(parameter_0000041 + species_0000004));
-  reaction_0000009: species_0000005 => species_0000006; compartment_0000002*(parameter_0000040*species_0000005/(parameter_0000041 + species_0000005));
-  reaction_0000010: species_0000006 => species_0000001; compartment_0000002*(parameter_0000044*species_0000006/(parameter_0000045 + species_0000006));
-  reaction_0000011: species_0000001 => species_0000002; compartment_0000001*(parameter_0000042*species_0000001/(parameter_0000043 + species_0000001));
-  reaction_0000012: species_0000002 => species_0000003; compartment_0000001*(parameter_0000042*species_0000002/(parameter_0000043 + species_0000002));
-  reaction_0000013: species_0000003 => ; compartment_0000001*(parameter_0000046*species_0000003/(parameter_0000047 + species_0000003));
-  reaction_0000014: species_0000008 => ; compartment_0000001*parameter_0000048*species_0000008;
-  reaction_0000015: species_0000009 => ; compartment_0000001*parameter_0000048*species_0000009;
-  reaction_0000016: species_0000007 => ; compartment_0000001*parameter_0000048*species_0000007;
-  reaction_0000017: species_0000004 => ; compartment_0000002*parameter_0000048*species_0000004;
-  reaction_0000018: species_0000005 => ; compartment_0000002*parameter_0000048*species_0000005;
-  reaction_0000019: species_0000006 => ; compartment_0000002*parameter_0000048*species_0000006;
-  reaction_0000020: species_0000001 => ; compartment_0000001*parameter_0000048*species_0000001;
-  reaction_0000021: species_0000002 => ; compartment_0000001*parameter_0000048*species_0000002;
-  reaction_0000022: species_0000003 => ; compartment_0000001*parameter_0000048*species_0000003;
-
-  // Species initializations:
-  species_0000001 = 0.001;
-  species_0000002 = 0.001;
-  species_0000003 = 0.001;
-  species_0000004 = 0.001;
-  species_0000005 = 0.001;
-  species_0000006 = 0.001;
-  species_0000007 = 0.001;
-  species_0000008 = 0.001;
-  species_0000009 = 0.001;
-
-  // Compartment initializations:
-  compartment_0000002 = 1;
-  compartment_0000001 = 1;
-
-  // Variable initializations:
-  parameter_0000001 = ;
-  parameter_0000017 = 1.062;
-  parameter_0000011 = 0.083;
-  parameter_0000005 = 0.2;
-  parameter_0000014 = 0.2124;
-  parameter_0000002 = ;
-  parameter_0000018 = 1.062;
-  parameter_0000012 = 0.134;
-  parameter_0000006 = 0.24;
-  parameter_0000015 = 0.2124;
-  parameter_0000003 = ;
-  parameter_0000019 = 1.062;
-  parameter_0000013 = 0.248;
-  parameter_0000007 = 0.1;
-  parameter_0000016 = 0.2124;
-  parameter_0000008 = 0.54;
-  parameter_0000010 = 0.54;
-  parameter_0000020 = ;
-  parameter_0000026 = 5;
-  parameter_0000023 = 2.8249;
-  parameter_0000021 = ;
-  parameter_0000024 = 2.8249;
-  parameter_0000022 = ;
-  parameter_0000025 = 2.8249;
-  parameter_0000027 = 10.62;
-  parameter_0000028 = 76.464;
-  parameter_0000029 = 344.09;
-  parameter_0000030 = 1.062;
-  parameter_0000031 = 0.02124;
-  parameter_0000032 = 0.19116;
-  parameter_0000033 = 0.001062;
-  parameter_0000034 = 0.38232;
-  parameter_0000036 = 0.2124;
-  parameter_0000037 = 0.7434;
-  parameter_0000038 = 0.6903;
-  parameter_0000039 = 2.8249;
-  parameter_0000040 = 1.6992;
-  parameter_0000041 = 0.25;
-  parameter_0000042 = 0.3186;
-  parameter_0000043 = 0.001;
-  parameter_0000044 = 1.6992;
-  parameter_0000045 = 0.25;
-  parameter_0000046 = 5.31;
-  parameter_0000047 = 0.01;
-  parameter_0000048 = 0.00531;
-
-  // Other declarations:
-  var parameter_0000001, parameter_0000002, parameter_0000003, parameter_0000020;
-  var parameter_0000021, parameter_0000022;
-  const compartment_0000002, compartment_0000001, parameter_0000017, parameter_0000011;
-  const parameter_0000005, parameter_0000014, parameter_0000018, parameter_0000012;
-  const parameter_0000006, parameter_0000015, parameter_0000019, parameter_0000013;
-  const parameter_0000007, parameter_0000016, parameter_0000008, parameter_0000010;
-  const parameter_0000026, parameter_0000023, parameter_0000024, parameter_0000025;
-  const parameter_0000027, parameter_0000028, parameter_0000029, parameter_0000030;
-  const parameter_0000031, parameter_0000032, parameter_0000033, parameter_0000034;
-  const parameter_0000036, parameter_0000037, parameter_0000038, parameter_0000039;
-  const parameter_0000040, parameter_0000041, parameter_0000042, parameter_0000043;
-  const parameter_0000044, parameter_0000045, parameter_0000046, parameter_0000047;
-  const parameter_0000048;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-  unit substance = 1e-9 mole;
-
-  // Display Names:
-  time_unit is "hour";
-  substance is "nanomole";
-  compartment_0000002 is "cytoplasm";
-  compartment_0000001 is "nucleus";
-  species_0000001 is "P0nuc";
-  species_0000002 is "P1nuc";
-  species_0000003 is "P2nuc";
-  species_0000004 is "P0cyt";
-  species_0000005 is "P1cyt";
-  species_0000006 is "P2cyt";
-  species_0000007 is "VRI";
-  species_0000008 is "CLK";
-  species_0000009 is "PDP";
-  parameter_0000001 is "ACvri";
-  parameter_0000017 is "Fv";
-  parameter_0000011 is "Kcv";
-  parameter_0000005 is "Kpv";
-  parameter_0000014 is "Kvdeac";
-  parameter_0000002 is "ACper";
-  parameter_0000018 is "Fp";
-  parameter_0000012 is "Kcp";
-  parameter_0000006 is "Kpp";
-  parameter_0000015 is "Kpdeac";
-  parameter_0000003 is "ACpdp";
-  parameter_0000019 is "Fpd";
-  parameter_0000013 is "Kcpd";
-  parameter_0000007 is "Kppd";
-  parameter_0000016 is "Kpddeac";
-  parameter_0000008 is "Kvc";
-  parameter_0000010 is "Kpdc";
-  parameter_0000020 is "OPvri";
-  parameter_0000026 is "N";
-  parameter_0000023 is "Tvriop";
-  parameter_0000021 is "OPper";
-  parameter_0000024 is "Tperop";
-  parameter_0000022 is "OPpdp";
-  parameter_0000025 is "Tpdpop";
-  parameter_0000027 is "Vper";
-  parameter_0000028 is "Vvri";
-  parameter_0000029 is "Vpdp";
-  parameter_0000030 is "Vclk";
-  parameter_0000031 is "Rpbas";
-  parameter_0000032 is "Rvbas";
-  parameter_0000033 is "Rcbas";
-  parameter_0000034 is "Rpdbas";
-  parameter_0000036 is "Vdclk";
-  parameter_0000037 is "vdvri";
-  parameter_0000038 is "vdpdp";
-  parameter_0000039 is "Tdelay";
-  parameter_0000040 is "Vpcyt";
-  parameter_0000041 is "Kpcyt";
-  parameter_0000042 is "Vpnuc";
-  parameter_0000043 is "Kpnuc";
-  parameter_0000044 is "Vtrans";
-  parameter_0000045 is "Ktrans";
-  parameter_0000046 is "Vdegp";
-  parameter_0000047 is "Kdegp";
-  parameter_0000048 is "kd";
-  reaction_0000001 is "Per production";
-  reaction_0000002 is "Vri production";
-  reaction_0000003 is "Pdp production";
-  reaction_0000004 is "Clk production";
-  reaction_0000005 is "Clk specific degradation";
-  reaction_0000006 is "Pdp specific degradation";
-  reaction_0000007 is "Vri specific degradation";
-  reaction_0000008 is "first cytoplasmic Per phosphorylation";
-  reaction_0000009 is "second cytoplasmic Per phosphorylation";
-  reaction_0000010 is "Per nuclear transport";
-  reaction_0000011 is "first nuclear Per phosphorylation";
-  reaction_0000012 is "second nuclear Rer phosphorylation";
-  reaction_0000013 is "Per specific degradation";
-  reaction_0000014 is "Clk aspecific degradation";
-  reaction_0000015 is "Pdp aspecific degradation";
-  reaction_0000016 is "Vri aspecific degradation";
-  reaction_0000017 is "Per_cyt aspecific degradation";
-  reaction_0000018 is "Per-P_cyt aspecific degradation";
-  reaction_0000019 is "Per-PP_cyt aspecific degradation";
-  reaction_0000020 is "Per_nuc aspecific degradation";
-  reaction_0000021 is "Per-P_nuc aspecific degradation";
-  reaction_0000022 is "Per-PP_nuc aspecific degradation";
-
-  // CV terms:
-  compartment_0000002 identity "http://identifiers.org/go/GO:0005737"
-  compartment_0000001 identity "http://identifiers.org/go/GO:0005634"
-  species_0000001 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000002 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000003 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000004 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000005 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000006 hypernym "http://identifiers.org/uniprot/P07663"
-  species_0000007 identity "http://identifiers.org/uniprot/O18660"
-  species_0000008 part "http://identifiers.org/uniprot/O61735",
-                       "http://identifiers.org/uniprot/P07663"
-  species_0000009 identity "http://identifiers.org/uniprot/Q9TVS7"
-  reaction_0000001 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000002 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000003 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000004 part "http://identifiers.org/go/GO:0006412",
-                        "http://identifiers.org/go/GO:0006351"
-  reaction_0000005 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000006 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000007 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000008 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000009 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000010 hypernym "http://identifiers.org/go/GO:0006606"
-  reaction_0000011 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000012 hypernym "http://identifiers.org/ec-code/2.7.1.37",
-                            "http://identifiers.org/go/GO:0006468"
-  reaction_0000013 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000014 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000015 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000016 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000017 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000018 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000019 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000020 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000021 hypernym "http://identifiers.org/go/GO:0030163"
-  reaction_0000022 hypernym "http://identifiers.org/go/GO:0030163"
-end
-
-model_0000001 is "Smolen2004_CircClock"
-
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/MODEL6619579403"
-model_0000001 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000034"
-model_0000001 description "http://identifiers.org/pubmed/15111397"
-model_0000001 taxon "http://identifiers.org/taxonomy/7227"
-model_0000001 identity "http://identifiers.org/kegg.pathway/dme04710"
-model_0000001 hypernym "http://identifiers.org/go/GO:0042752"

BioModelsRAG/data/BIOMD0000000035.txt

@@ -1,103 +0,0 @@
-// Created by libAntimony v2.13.0
-model *vilarOscillator()
-
-  // Compartments and Species:
-  compartment deterministicOscillator;
-  substanceOnly species $EmptySet in deterministicOscillator, A in deterministicOscillator;
-  substanceOnly species C in deterministicOscillator, DA in deterministicOscillator;
-  substanceOnly species DAp in deterministicOscillator, DR in deterministicOscillator;
-  substanceOnly species DRp in deterministicOscillator, MA in deterministicOscillator;
-  substanceOnly species MR in deterministicOscillator, R in deterministicOscillator;
-
-  // Reactions:
-  Reaction1: A + R => C; A*R*Reaction1_gammaC;
-  Reaction2: A => $EmptySet; A*Reaction2_deltaA;
-  Reaction3: C => R; C*Reaction3_deltaA;
-  Reaction4: R => $EmptySet; R*Reaction4_deltaR;
-  Reaction5: A + DA => DAp; A*DA*Reaction5_gammaA;
-  Reaction6: DAp => A + DA; DAp*Reaction6_thetaA;
-  Reaction7: DA => DA + MA; DA*Reaction7_alphaA;
-  Reaction8: DAp => DAp + MA; DAp*Reaction8_alphaAp;
-  Reaction9: MA => $EmptySet; MA*Reaction9_deltaMA;
-  Reaction10: MA => A + MA; MA*Reaction10_betaA;
-  Reaction11: A + DR => DRp; A*DR*Reaction11_gammaR;
-  Reaction12: DRp => A + DR; DRp*Reaction12_thetaR;
-  Reaction13: DR => DR + MR; DR*Reaction13_alphaR;
-  Reaction14: DRp => DRp + MR; DRp*Reaction14_alphaRp;
-  Reaction15: MR => $EmptySet; MR*Reaction15_deltaMR;
-  Reaction16: MR => MR + R; MR*Reaction16_betaR;
-
-  // Species initializations:
-  EmptySet = 0;
-  A = 0;
-  C = 0;
-  DA = 1/deterministicOscillator;
-  DAp = 0;
-  DR = 1/deterministicOscillator;
-  DRp = 0;
-  MA = 0;
-  MR = 0;
-  R = 0;
-
-  // Compartment initializations:
-  deterministicOscillator = 1;
-
-  // Variable initializations:
-  Reaction1_gammaC = 2;
-  Reaction2_deltaA = 1;
-  Reaction3_deltaA = 1;
-  Reaction4_deltaR = 0.2;
-  Reaction5_gammaA = 1;
-  Reaction6_thetaA = 50;
-  Reaction7_alphaA = 50;
-  Reaction8_alphaAp = 500;
-  Reaction9_deltaMA = 10;
-  Reaction10_betaA = 50;
-  Reaction11_gammaR = 1;
-  Reaction12_thetaR = 100;
-  Reaction13_alphaR = 0.01;
-  Reaction14_alphaRp = 50;
-  Reaction15_deltaMR = 0.5;
-  Reaction16_betaR = 5;
-
-  // Other declarations:
-  const deterministicOscillator;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour";
-
-  // CV terms:
-  A hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  C hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  MA hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  MR hypernym "http://identifiers.org/chebi/CHEBI:33699"
-  R hypernym "http://identifiers.org/chebi/CHEBI:36080"
-  Reaction1 hypernym "http://identifiers.org/obo.go/GO:0006461"
-  Reaction2 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction3 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction4 hypernym "http://identifiers.org/obo.go/GO:0030163"
-  Reaction5 hypernym "http://identifiers.org/obo.go/GO:0016563"
-  Reaction6 hypernym "http://identifiers.org/obo.go/GO:0032986"
-  Reaction7 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction8 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction9 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction10 hypernym "http://identifiers.org/obo.go/GO:0006412"
-  Reaction11 hypernym "http://identifiers.org/obo.go/GO:0016563",
-                      "http://identifiers.org/obo.go/GO:0010843"
-  Reaction12 hypernym "http://identifiers.org/obo.go/GO:0032986"
-  Reaction13 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction14 hypernym "http://identifiers.org/obo.go/GO:0006351"
-  Reaction15 hypernym "http://identifiers.org/obo.go/GO:0006402"
-  Reaction16 hypernym "http://identifiers.org/obo.go/GO:0006412"
-end
-
-vilarOscillator is "Vilar2002_Oscillator"
-
-vilarOscillator model_entity_is "http://identifiers.org/biomodels.db/MODEL6619651140"
-vilarOscillator model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000035"
-vilarOscillator description "http://identifiers.org/pubmed/11972055"
-vilarOscillator hypernym "http://identifiers.org/obo.go/GO:0042752"
-vilarOscillator taxon "http://identifiers.org/taxonomy/131567"

BioModelsRAG/data/BIOMD0000000036.txt

@@ -1,72 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Tyson1999()
-
-  // Compartments and Species:
-  compartment default, CYTOPLASM;
-  species $EmptySet in default, M in CYTOPLASM, P in CYTOPLASM;
-
-  // Reactions:
-  TC: $EmptySet => M; CYTOPLASM*(TC_Vm/(1 + (P*(1 - 2/(1 + (1 + 8*TC_Keq*P)^0.5))/(2*TC_Pcrit))^2));
-  TL: $EmptySet => P; TL_V*M*CYTOPLASM;
-  mRNAD: M => $EmptySet; mRNAD_D*M*CYTOPLASM;
-  ProteinD: P => $EmptySet; ProteinD_D*P*CYTOPLASM;
-  DBT: P => $EmptySet; CYTOPLASM*((DBT_k1*P*(2/(1 + (1 + 8*DBT_Keq*P)^0.5)) + DBT_k2*P)/(DBT_J + P));
-
-  // Species initializations:
-  EmptySet = 0;
-  M = 1/CYTOPLASM;
-  P = 1/CYTOPLASM;
-
-  // Compartment initializations:
-  default = 1;
-  CYTOPLASM = 1;
-
-  // Variable initializations:
-  N_A = 6.0221367e+23;
-  TC_Vm = 1;
-  TC_Pcrit = 0.1;
-  TC_Keq = 200;
-  TL_V = 0.5;
-  mRNAD_D = 0.1;
-  ProteinD_D = 0.1;
-  DBT_k1 = 10;
-  DBT_k2 = 0.03;
-  DBT_J = 0.05;
-  DBT_Keq = 200;
-
-  // Other declarations:
-  const default, CYTOPLASM, N_A;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour";
-  P is "Pt";
-  TC is "transcription";
-  TL is "translation";
-  mRNAD is "mRNA degradation";
-  ProteinD is "protein degradation";
-  DBT is "Per phosphorylation and degradation";
-
-  // CV terms:
-  CYTOPLASM hypernym "http://identifiers.org/go/GO:0005737"
-  P identity "http://identifiers.org/uniprot/P07663"
-  TC hypernym "http://identifiers.org/go/GO:0006355",
-              "http://identifiers.org/go/GO:0009299"
-  TL hypernym "http://identifiers.org/go/GO:0006412"
-  mRNAD hypernym "http://identifiers.org/go/GO:0006402"
-  ProteinD hypernym "http://identifiers.org/go/GO:0030163"
-  DBT hypernym "http://identifiers.org/ec-code/2.7.1.37",
-               "http://identifiers.org/go/GO:0006468",
-               "http://identifiers.org/go/GO:0030163"
-end
-
-Tyson1999 is "Tyson1999_CircClock"
-
-Tyson1999 model_entity_is "http://identifiers.org/biomodels.db/MODEL6619720081"
-Tyson1999 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000036"
-Tyson1999 description "http://identifiers.org/pubmed/20540926"
-Tyson1999 identity "http://identifiers.org/kegg.pathway/dme04710"
-Tyson1999 taxon "http://identifiers.org/taxonomy/7227"
-Tyson1999 hypernym "http://identifiers.org/go/GO:0042752"

BioModelsRAG/data/BIOMD0000000037.txt

@@ -1,89 +0,0 @@
-// Created by libAntimony v2.13.0
-model *BIOMD0000000037()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species Pfr in compartment_, Pr in compartment_, Xi in compartment_, Xa in compartment_;
-  species prepreS in compartment_, preS in compartment_, Ya in compartment_;
-  species S in compartment_, $Gluc in compartment_, Yi in compartment_, V in compartment_;
-  species Pi in compartment_;
-
-  // Reactions:
-  Photoreceptor_activation: Pfr => Pr; compartment_*Pfr*Photoreceptor_activation_IfrSfrPfr;
-  Photoreceptor_inactivation: Pr => Pfr; Photoreceptor_inactivation_IrSrPr*Pr*compartment_;
-  Transducer_activation: Xi => Xa; Xi*Transducer_activation_kia*Pr*compartment_;
-  Transducer_inactivation: Xa => Xi; Transducer_inactivation_kai*Xa*compartment_;
-  preS_formation: prepreS => preS; prepreS*preS_formation_kx*Xa*compartment_;
-  S_generation: preS => S; preS*S_generation_ky*Ya*compartment_;
-  Glucose_sensor_inactivation: Ya + $Gluc => Yi; Glucose_sensor_inactivation_kG*Ya*Gluc*compartment_;
-  S_formation:  => S; compartment_*(S_formation_alpha1/(1 + V^3));
-  V_formation:  => V; compartment_*(V_formation_alpha2/(1 + S^3));
-  S_degradation: S => ; S_degradation_kd_s*S*compartment_;
-  V_degradation: V => ; compartment_*V*V_degradation_kd_v;
-  Photoreceptor_decay: Pr => Pi; compartment_*Photoreceptor_decay_kd*Pr;
-
-  // Species initializations:
-  Pfr = 10/compartment_;
-  Pr = 0;
-  Xi = 6/compartment_;
-  Xa = 0;
-  prepreS = 200/compartment_;
-  preS = 0;
-  Ya = 0.9/compartment_;
-  S = 0;
-  Gluc = 0;
-  Yi = 0;
-  V = 30/compartment_;
-  Pi = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  Photoreceptor_activation_IfrSfrPfr = 0.1;
-  Photoreceptor_inactivation_IrSrPr = 0;
-  Transducer_activation_kia = 0.1;
-  Transducer_inactivation_kai = 0.8;
-  preS_formation_kx = 0.2;
-  S_generation_ky = 1;
-  Glucose_sensor_inactivation_kG = 0.1;
-  S_formation_alpha1 = 30;
-  V_formation_alpha2 = 50;
-  S_degradation_kd_s = 1;
-  V_degradation_kd_v = 1;
-  Photoreceptor_decay_kd = 0.1;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit time_unit = 3600 second;
-
-  // Display Names:
-  time_unit is "hour";
-
-  // CV terms:
-  Pfr version "http://identifiers.org/chebi/CHEBI:35799",
-              "http://identifiers.org/interpro/IPR001294"
-  Pr version "http://identifiers.org/chebi/CHEBI:35799",
-             "http://identifiers.org/interpro/IPR001294"
-  Gluc identity "http://identifiers.org/chebi/CHEBI:17234",
-                "http://identifiers.org/kegg.compound/C00293"
-  Photoreceptor_activation hypernym "http://identifiers.org/go/GO:0031516"
-  Photoreceptor_inactivation hypernym "http://identifiers.org/go/GO:0031517"
-  S_formation hypernym "http://identifiers.org/go/GO:0009299",
-                       "http://identifiers.org/go/GO:0006412"
-  V_formation hypernym "http://identifiers.org/go/GO:0009299",
-                       "http://identifiers.org/go/GO:0006412"
-  S_degradation hypernym "http://identifiers.org/go/GO:0006402"
-  V_degradation hypernym "http://identifiers.org/go/GO:0006402"
-end
-
-BIOMD0000000037 is "Marwan2003 - Genetics, regulatory hierarchy between genes"
-
-BIOMD0000000037 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000037"
-BIOMD0000000037 model_entity_is "http://identifiers.org/biomodels.db/MODEL6621175859"
-BIOMD0000000037 description "http://identifiers.org/pubmed/12750324"
-BIOMD0000000037 hypernym "http://identifiers.org/go/GO:0010018",
-                         "http://identifiers.org/go/GO:0042173"
-BIOMD0000000037 taxon "http://identifiers.org/taxonomy/5791"

BioModelsRAG/data/BIOMD0000000038.txt

@@ -1,158 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Rohwer2000_Phosphotransferase_System()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species EI in compartment_, PyrPI in compartment_, EIP in compartment_;
-  species HPr in compartment_, EIPHPr in compartment_, HPrP in compartment_;
-  species EIIA in compartment_, HPrPIIA in compartment_, EIIAP in compartment_;
-  species EIICB in compartment_, EIIAPIICB in compartment_, EIICBP in compartment_;
-  species EIICBPGlc in compartment_, $PEP in compartment_, $Pyr in compartment_;
-  species $GlcP in compartment_, $Glc in compartment_;
-
-  // Reactions:
-  v1: $PEP + EI -> PyrPI; compartment_*(v1_k1f*PEP*EI - v1_k1r*PyrPI);
-  v2: PyrPI -> EIP + $Pyr; compartment_*(v2_k2f*PyrPI - v2_k2r*Pyr*EIP);
-  v3: HPr + EIP -> EIPHPr; compartment_*(v3_k3f*EIP*HPr - v3_k3r*EIPHPr);
-  v4: EIPHPr -> HPrP + EI; compartment_*(v4_k4f*EIPHPr - v4_k4r*EI*HPrP);
-  v5: HPrP + EIIA -> HPrPIIA; compartment_*(v5_k5f*HPrP*EIIA - v5_k5r*HPrPIIA);
-  v6: HPrPIIA -> EIIAP + HPr; compartment_*(v6_k6f*HPrPIIA - v6_k6r*HPr*EIIAP);
-  v7: EIICB + EIIAP -> EIIAPIICB; compartment_*(v7_k7f*EIIAP*EIICB - v7_k7r*EIIAPIICB);
-  v8: EIIAPIICB -> EIICBP + EIIA; compartment_*(v8_k8f*EIIAPIICB - v8_k8r*EIIA*EIICBP);
-  v9: EIICBP + $Glc -> EIICBPGlc; compartment_*(v9_k9f*EIICBP*Glc - v9_k9r*EIICBPGlc);
-  v10: EIICBPGlc -> EIICB + $GlcP; compartment_*(v10_k10f*EIICBPGlc - v10_k10r*EIICB*GlcP);
-
-  // Species initializations:
-  EI = 3;
-  PyrPI = 0;
-  EIP = 2;
-  HPr = 25;
-  EIPHPr = 0;
-  HPrP = 25;
-  EIIA = 20;
-  HPrPIIA = 0;
-  EIIAP = 20;
-  EIICB = 5;
-  EIIAPIICB = 0;
-  EIICBP = 5;
-  EIICBPGlc = 0;
-  PEP = 2800;
-  Pyr = 900;
-  GlcP = 50;
-  Glc = 500;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1f = 1960;
-  v1_k1r = 480000;
-  v2_k2f = 108000;
-  v2_k2r = 294;
-  v3_k3f = 14000;
-  v3_k3r = 14000;
-  v4_k4f = 84000;
-  v4_k4r = 3360;
-  v5_k5f = 21960;
-  v5_k5r = 21960;
-  v6_k6f = 4392;
-  v6_k6r = 3384;
-  v7_k7f = 880;
-  v7_k7r = 880;
-  v8_k8f = 2640;
-  v8_k8r = 960;
-  v9_k9f = 260;
-  v9_k9r = 389;
-  v10_k10f = 4800;
-  v10_k10r = 0.0054;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-  compartment_ is "cell";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005623"
-  EI hypernym "http://identifiers.org/uniprot/P08839"
-  PyrPI part "http://identifiers.org/uniprot/P08839",
-             "http://identifiers.org/kegg.compound/C00074",
-             "http://identifiers.org/chebi/CHEBI:18021"
-  PyrPI part "http://identifiers.org/chebi/CHEBI:18021",
-             "http://identifiers.org/uniprot/P08839",
-             "http://identifiers.org/kegg.compound/C00615"
-  EIP hypernym "http://identifiers.org/uniprot/P08839"
-  HPr identity "http://identifiers.org/uniprot/P07006"
-  EIPHPr part "http://identifiers.org/uniprot/P07006",
-              "http://identifiers.org/uniprot/P08839"
-  HPrP part "http://identifiers.org/uniprot/P07006",
-            "http://identifiers.org/kegg.compound/C00615"
-  EIIA identity "http://identifiers.org/uniprot/P69783"
-  HPrPIIA part "http://identifiers.org/uniprot/P07006",
-               "http://identifiers.org/uniprot/P69783"
-  EIIAP identity "http://identifiers.org/uniprot/P69783"
-  EIICB identity "http://identifiers.org/uniprot/P69786"
-  EIIAPIICB identity "http://identifiers.org/uniprot/P69786",
-                     "http://identifiers.org/uniprot/P69783"
-  EIICBP identity "http://identifiers.org/uniprot/P69786"
-  EIICBPGlc part "http://identifiers.org/chebi/CHEBI:17234",
-                 "http://identifiers.org/uniprot/P69786",
-                 "http://identifiers.org/kegg.compound/C00293"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021",
-               "http://identifiers.org/kegg.compound/C00074"
-  Pyr identity "http://identifiers.org/chebi/CHEBI:15361",
-               "http://identifiers.org/kegg.compound/C00022"
-  GlcP identity "http://identifiers.org/chebi/CHEBI:14314",
-                "http://identifiers.org/kegg.compound/C00092"
-  Glc identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  v1 hypernym "http://identifiers.org/ec-code/2.7.3.9",
-              "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0008965",
-              "http://identifiers.org/go/GO:0016772"
-  v1 identity "http://identifiers.org/kegg.reaction/R02628"
-  v2 hypernym "http://identifiers.org/ec-code/2.7.3.9",
-              "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0008965",
-              "http://identifiers.org/go/GO:0018106"
-  v2 identity "http://identifiers.org/kegg.reaction/R02628"
-  v3 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0018106"
-  v3 identity "http://identifiers.org/intact/EBI-902828"
-  v4 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0018106"
-  v4 identity "http://identifiers.org/intact/EBI-902828"
-  v5 hypernym "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0016772"
-  v5 identity "http://identifiers.org/intact/EBI-903339"
-  v6 hypernym "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0016772"
-  v6 identity "http://identifiers.org/intact/EBI-903339"
-  v7 hypernym "http://identifiers.org/go/GO:0018106",
-              "http://identifiers.org/go/GO:0016772"
-  v7 identity "http://identifiers.org/intact/EBI-903826"
-  v8 identity "http://identifiers.org/intact/EBI-903826"
-  v8 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0018106"
-  v9 hypernym "http://identifiers.org/go/GO:0016772",
-              "http://identifiers.org/go/GO:0046835"
-  v10 hypernym "http://identifiers.org/go/GO:0016772",
-               "http://identifiers.org/go/GO:0046835"
-end
-
-Rohwer2000_Phosphotransferase_System is "Rohwer2000_Phosphotransferase_System"
-
-Rohwer2000_Phosphotransferase_System model_entity_is "http://identifiers.org/biomodels.db/MODEL6621395815"
-Rohwer2000_Phosphotransferase_System model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000038"
-Rohwer2000_Phosphotransferase_System description "http://identifiers.org/pubmed/10889194"
-Rohwer2000_Phosphotransferase_System identity "http://identifiers.org/kegg.pathway/eco02060"
-Rohwer2000_Phosphotransferase_System hypernym "http://identifiers.org/go/GO:0009401",
-                                              "http://identifiers.org/go/GO:0010827"
-Rohwer2000_Phosphotransferase_System taxon "http://identifiers.org/taxonomy/562"
-Rohwer2000_Phosphotransferase_System property "http://identifiers.org/mamo/MAMO_0000046"

BioModelsRAG/data/BIOMD0000000039.txt

@@ -1,95 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins()
-
-  // Compartments and Species:
-  compartment Cytosol, Endoplasmic_Reticulum, Mitochondria;
-  species Ca_cyt in Cytosol, CaER in Endoplasmic_Reticulum, CaM in Mitochondria;
-  species CaPr in Cytosol, Pr in Cytosol;
-
-  // Reactions:
-  v1: 0.25 CaER => Ca_cyt; Cytosol*(v1_Kch*Ca_cyt^2*(CaER - Ca_cyt)/(v1_K1^2 + Ca_cyt^2));
-  v3: 0.25 CaER => Ca_cyt; Cytosol*v3_Kleak*(CaER - Ca_cyt);
-  v5: Ca_cyt => 0.25 CaER; Endoplasmic_Reticulum*v5_Kpump*Ca_cyt;
-  v7: 0.25 CaM => Ca_cyt; Cytosol*CaM*(v7_Kout*Ca_cyt^2/(v7_K3^2 + Ca_cyt^2) + v7_Km);
-  v9: Ca_cyt => 0.25 CaM; Mitochondria*(v9_Kin*Ca_cyt^8/(v9_K2^8 + Ca_cyt^8));
-  v11: CaPr => Pr + Ca_cyt; Cytosol*v11_Kminus*CaPr;
-  v12: Pr + Ca_cyt => CaPr; Cytosol*v12_Kplus*Ca_cyt*Pr;
-
-  // Species initializations:
-  Ca_cyt = 0.35;
-  CaER = 0.76;
-  CaM = 0.29;
-  CaPr = 85.45;
-  Pr = 34.55;
-
-  // Compartment initializations:
-  Cytosol = 1;
-  Endoplasmic_Reticulum = 1;
-  Mitochondria = 1;
-
-  // Variable initializations:
-  v1_Kch = 4100;
-  v1_K1 = 5;
-  v3_Kleak = 0.05;
-  v5_Kpump = 20;
-  v7_Kout = 125;
-  v7_K3 = 5;
-  v7_Km = 0.00625;
-  v9_Kin = 300;
-  v9_K2 = 0.8;
-  v11_Kminus = 0.01;
-  v12_Kplus = 0.1;
-
-  // Other declarations:
-  const Cytosol, Endoplasmic_Reticulum, Mitochondria;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole (default)";
-  v1 is "Jch";
-  v3 is "Jleak";
-  v5 is "Jpump";
-  v7 is "Jout";
-  v9 is "Jin";
-  v11 is "dissociation of CaPr";
-  v12 is "binding of Ca on Pr";
-
-  // CV terms:
-  Cytosol identity "http://identifiers.org/go/GO:0005829"
-  Endoplasmic_Reticulum identity "http://identifiers.org/go/GO:0005790"
-  Mitochondria identity "http://identifiers.org/go/GO:0005739"
-  Ca_cyt identity "http://identifiers.org/chebi/CHEBI:29108"
-  CaER identity "http://identifiers.org/chebi/CHEBI:29108"
-  CaM identity "http://identifiers.org/chebi/CHEBI:29108"
-  CaPr part "http://identifiers.org/chebi/CHEBI:29108",
-            "http://identifiers.org/kegg.compound/C00017"
-  Pr hypernym "http://identifiers.org/kegg.compound/C00017",
-              "http://identifiers.org/chebi/CHEBI:16541"
-  v1 hypernym "http://identifiers.org/go/GO:0051482",
-              "http://identifiers.org/go/GO:0006816"
-  v3 hypernym "http://identifiers.org/go/GO:0006816",
-              "http://identifiers.org/go/GO:0007204"
-  v5 hypernym "http://identifiers.org/go/GO:0051481",
-              "http://identifiers.org/go/GO:0006816"
-  v7 identity "http://identifiers.org/go/GO:0006816",
-              "http://identifiers.org/go/GO:0007204"
-  v9 hypernym "http://identifiers.org/go/GO:0006816",
-              "http://identifiers.org/go/GO:0051481"
-  v11 hypernym "http://identifiers.org/go/GO:0007204"
-  v12 hypernym "http://identifiers.org/go/GO:0005509",
-               "http://identifiers.org/go/GO:0051481"
-end
-
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins is "Marhl2000_CaOscillations"
-
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins model_entity_is "http://identifiers.org/biomodels.db/MODEL6621933497"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000039"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins description "http://identifiers.org/pubmed/11004387"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins origin "http://identifiers.org/pubmed/17029696",
-                                                                              "http://identifiers.org/pubmed/12362939"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins taxon "http://identifiers.org/taxonomy/8355"
-Marhl_Calcium_Oscillations_role_of_mitochondria_and_cytosolic_proteins identity "http://identifiers.org/kegg.pathway/hsa04020",
-                                                                                "http://identifiers.org/go/GO:0019722",
-                                                                                "http://identifiers.org/go/GO:0048016"

BioModelsRAG/data/BIOMD0000000040.txt

@@ -1,61 +0,0 @@
-// Created by libAntimony v2.13.0
-
-// Warnings from automatic translation:
-//    Unable to set the stoichiometry math for the product Br in reaction Reaction5 because stoichiometry math is not a defined concept in Antimony.
-
-model *Field1974_Oregonator()
-
-  // Compartments and Species:
-  compartment BZ;
-  species Br in BZ, $BrO3 in BZ, Ce in BZ, HBrO2 in BZ, $HOBr in BZ;
-
-  // Reactions:
-  Reaction1: Br + $BrO3 => HBrO2 + $HOBr; Br*BrO3*Reaction1_k1*BZ;
-  Reaction2: Br + HBrO2 => 2 $HOBr; Br*HBrO2*Reaction2_k2*BZ;
-  Reaction3: $BrO3 + HBrO2 => Ce + 2 HBrO2; BrO3*HBrO2*Reaction3_k3*BZ;
-  Reaction4: 2 HBrO2 => $BrO3 + $HOBr; HBrO2^2*Reaction4_k4*BZ;
-  Reaction5: Ce => Br; Ce*Reaction5_k5*BZ;
-
-  // Species initializations:
-  Br = 1e-07;
-  BrO3 = 0.06;
-  Ce = 0.05;
-  HBrO2 = 5e-11;
-  HOBr = 0;
-
-  // Compartment initializations:
-  BZ = 1;
-
-  // Variable initializations:
-  f = 1;
-  Reaction1_k1 = 1.34;
-  Reaction2_k2 = 1600000000;
-  Reaction3_k3 = 8000;
-  Reaction4_k4 = 40000000;
-  Reaction5_k5 = 1;
-
-  // Other declarations:
-  const BZ, f;
-
-  // Display Names:
-  Br is "Br-";
-  BrO3 is "BrO3-";
-  Ce is "Ce4+";
-  Reaction1 is "M1";
-  Reaction2 is "M2";
-  Reaction3 is "M3";
-  Reaction4 is "M4";
-  Reaction5 is "M5";
-
-  // CV terms:
-  Br identity "http://identifiers.org/chebi/CHEBI:15858"
-  BrO3 identity "http://identifiers.org/chebi/CHEBI:29223"
-end
-
-Field1974_Oregonator is "Field1974_Oregonator"
-
-Field1974_Oregonator model_entity_is "http://identifiers.org/biomodels.db/MODEL6622000424"
-Field1974_Oregonator model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000040"
-Field1974_Oregonator description "http://identifiers.org/doi/10.1063/1.1681288"
-Field1974_Oregonator taxon "http://identifiers.org/taxonomy/131567"
-Field1974_Oregonator hypernym "http://identifiers.org/go/GO:0007622"

BioModelsRAG/data/BIOMD0000000041.txt

@@ -1,127 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Kongas___Van_Beek()
-
-  // Compartments and Species:
-  compartment IMS, CYT;
-  species ADPi in IMS, ATPi in IMS, Cri in IMS, PCri in IMS, PCr in CYT, ADP in CYT;
-  species ATP in CYT, Cr in CYT, Pi in IMS, P in CYT;
-
-  // Reactions:
-  OxPhos: ADPi + Pi -> ATPi; IMS*(OxPhos_V_1*ADPi*Pi/(OxPhos_Ka_1*OxPhos_Kb_1*(1 + ADPi/OxPhos_Ka_1 + Pi/OxPhos_Kb_1 + ADPi*Pi/(OxPhos_Ka_1*OxPhos_Kb_1))));
-  MiCK: ATPi + Cri -> ADPi + PCri; IMS*((MiCK_Vf_2*ATPi*Cri/(MiCK_Kia_2*MiCK_Kb_2) - MiCK_Vb_2*ADPi*PCri/(MiCK_Kic_2*MiCK_Kd_2))/(1 + Cri/MiCK_Kib_2 + PCri/MiCK_Kid_2 + ATPi*(1/MiCK_Kia_2 + Cri/(MiCK_Kia_2*MiCK_Kb_2)) + ADPi*(1/MiCK_Kic_2 + Cri/(MiCK_Kic_2*MiCK_Kib_2) + PCri/(MiCK_Kid_2*(MiCK_Kic_2*MiCK_Kd_2/MiCK_Kid_2)))));
-  MMCK: ATP + Cr -> PCr + ADP; CYT*((MMCK_Vf_3*ATP*Cr/(MMCK_Kia_3*MMCK_Kb_3) - MMCK_Vb_3*ADP*PCr/(MMCK_Kic_3*MMCK_Kd_3))/(1 + Cr/MMCK_Kib_3 + PCr/MMCK_Kid_3 + ATP*(1/MMCK_Kia_3 + Cr/(MMCK_Kia_3*MMCK_Kb_3)) + ADP*(1/MMCK_Kic_3 + Cr/(MMCK_Kic_3*MMCK_Kib_3) + PCr/(MMCK_Kid_3*(MMCK_Kic_3*MMCK_Kd_3/MMCK_Kid_3)))));
-  ATPase: ATP => ADP + P; CYT*ATPase_v_4*ATP;
-  Pi_diffusion: Pi -> P; IMS*Pi_diffusion_k2_5*Pi - CYT*Pi_diffusion_k2_5*P;
-  Cr_diffusion: Cri -> Cr; IMS*Cr_diffusion_k1_6*Cri - CYT*Cr_diffusion_k1_6*Cr;
-  ADP_diffusion: ADPi -> ADP; IMS*ADP_diffusion_k1_7*ADPi - CYT*ADP_diffusion_k1_7*ADP;
-  PCr_diffusion: PCri -> PCr; IMS*PCr_diffusion_k1_8*PCri - CYT*PCr_diffusion_k1_8*PCr;
-  ATP_diffusion: ATPi -> ATP; IMS*ATP_diffusion_k1_9*ATPi - CYT*ATP_diffusion_k1_9*ATP;
-
-  // Species initializations:
-  ADPi = 0;
-  ATPi = 0;
-  Cri = 0;
-  PCri = 0;
-  PCr = 0;
-  ADP = 0;
-  ATP = 9700;
-  Cr = 26000;
-  Pi = 32000;
-  P = 0;
-
-  // Compartment initializations:
-  IMS = 0.0625;
-  CYT = 0.75;
-
-  // Variable initializations:
-  OxPhos_V_1 = 4600;
-  OxPhos_Ka_1 = 800;
-  OxPhos_Kb_1 = 20;
-  MiCK_Vf_2 = 2658;
-  MiCK_Kia_2 = 750;
-  MiCK_Kb_2 = 5200;
-  MiCK_Vb_2 = 11160;
-  MiCK_Kic_2 = 204.8;
-  MiCK_Kd_2 = 500;
-  MiCK_Kib_2 = 28800;
-  MiCK_Kid_2 = 1600;
-  MMCK_Vf_3 = 6966;
-  MMCK_Kia_3 = 900;
-  MMCK_Kb_3 = 15500;
-  MMCK_Vb_3 = 29250;
-  MMCK_Kic_3 = 222.4;
-  MMCK_Kd_3 = 1670;
-  MMCK_Kib_3 = 34900;
-  MMCK_Kid_3 = 4730;
-  ATPase_v_4 = 4600;
-  Pi_diffusion_k2_5 = 18.4;
-  Cr_diffusion_k1_6 = 14.6;
-  ADP_diffusion_k1_7 = 8.16;
-  PCr_diffusion_k1_8 = 14.6;
-  ATP_diffusion_k1_9 = 8.16;
-
-  // Other declarations:
-  const IMS, CYT;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-  Pi is "Pii";
-  P is "Pi";
-  OxPhos is "Vsyn";
-  MiCK is "Vmick";
-  MMCK is "Vmmck";
-  ATPase is "Vhyd";
-  Pi_diffusion is "Jpi";
-  Cr_diffusion is "Jcr";
-  ADP_diffusion is "Jadp";
-  PCr_diffusion is "Jpcr";
-  ATP_diffusion is "Jatp";
-
-  // CV terms:
-  IMS hypernym "http://identifiers.org/go/GO:0005758"
-  CYT hypernym "http://identifiers.org/go/GO:0005829"
-  ADPi identity "http://identifiers.org/chebi/CHEBI:16761",
-                "http://identifiers.org/kegg.compound/C00008"
-  ATPi identity "http://identifiers.org/chebi/CHEBI:15422",
-                "http://identifiers.org/kegg.compound/C00002"
-  Cri identity "http://identifiers.org/chebi/CHEBI:16919",
-               "http://identifiers.org/kegg.compound/C00300"
-  PCri identity "http://identifiers.org/chebi/CHEBI:17287",
-                "http://identifiers.org/kegg.compound/C02305"
-  PCr identity "http://identifiers.org/chebi/CHEBI:17287",
-               "http://identifiers.org/kegg.compound/C02305"
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  Cr identity "http://identifiers.org/chebi/CHEBI:16919",
-              "http://identifiers.org/kegg.compound/C00300"
-  Pi identity "http://identifiers.org/chebi/CHEBI:18367",
-              "http://identifiers.org/kegg.compound/C00009"
-  P identity "http://identifiers.org/chebi/CHEBI:18367",
-             "http://identifiers.org/kegg.compound/C00009"
-  OxPhos hypernym "http://identifiers.org/go/GO:0006119"
-  MiCK hypernym "http://identifiers.org/ec-code/2.7.3.2",
-                "http://identifiers.org/go/GO:0004111"
-  MMCK hypernym "http://identifiers.org/ec-code/2.7.3.2",
-                "http://identifiers.org/go/GO:0004111"
-  ATPase hypernym "http://identifiers.org/go/GO:0016887"
-  Pi_diffusion hypernym "http://identifiers.org/go/GO:0006817"
-  Cr_diffusion hypernym "http://identifiers.org/go/GO:0015881"
-  ADP_diffusion hypernym "http://identifiers.org/go/GO:0015866"
-  PCr_diffusion hypernym "http://identifiers.org/go/GO:0015881"
-  ATP_diffusion hypernym "http://identifiers.org/go/GO:0015867"
-end
-
-Kongas___Van_Beek is "Kongas2007 - Creatine Kinase in energy metabolic signaling in muscle"
-
-Kongas___Van_Beek model_entity_is "http://identifiers.org/biomodels.db/MODEL6622188656"
-Kongas___Van_Beek model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000041"
-Kongas___Van_Beek description "http://identifiers.org/doi/10.1038/npre.2007.1317.1"
-Kongas___Van_Beek origin "http://identifiers.org/pubmed/10751324"
-Kongas___Van_Beek hypernym "http://identifiers.org/go/GO:0006600",
-                           "http://identifiers.org/go/GO:0046034"
-Kongas___Van_Beek taxon "http://identifiers.org/taxonomy/9984"

BioModelsRAG/data/BIOMD0000000042.txt

@@ -1,189 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Glycolysis_Nielsen()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species ATP in compartment_, ADP in compartment_, AMP in compartment_, GLC in compartment_;
-  species F6P in compartment_, FBP in compartment_, GAP in compartment_, NAD in compartment_;
-  species NADH in compartment_, DPG in compartment_, PEP in compartment_;
-  species PYR in compartment_, ACA in compartment_, EtOH in compartment_;
-  species P in compartment_;
-
-  // Reactions:
-  ATPflow:  -> ATP; compartment_*(3.5 - ATP)*flow;
-  ADPflow:  -> ADP; compartment_*(1.1 - ADP)*flow;
-  NADHflow:  -> NADH; compartment_*(0.24 - NADH)*flow;
-  NADflow:  -> NAD; compartment_*(4 - NAD)*flow;
-  GLCflow:  -> GLC; compartment_*(50 - GLC)*flow;
-  F6Pflow: F6P => ; compartment_*F6P*flow;
-  FBPflow: FBP => ; compartment_*FBP*flow;
-  GAPflow: GAP => ; compartment_*GAP*flow;
-  DPGflow: DPG => ; compartment_*DPG*flow;
-  PEPflow: PEP => ; compartment_*PEP*flow;
-  PYRflow: PYR => ; compartment_*PYR*flow;
-  ACAflow: ACA => ; compartment_*ACA*flow;
-  EtOHflow: EtOH => ; compartment_*EtOH*flow;
-  AMPflow: AMP => ; compartment_*AMP*flow;
-  Pflow: P => ; compartment_*P*flow;
-  reaction_1: GLC + ATP => F6P + ADP; compartment_*(V1*ATP*GLC/((K1GLC + GLC)*(K1ATP + ATP)));
-  reaction_2: F6P + ATP => FBP + ADP; compartment_*(V2*ATP*F6P^2/((K2*(1 + k2*(ATP/AMP)^2) + F6P^2)*(K2ATP + ATP)));
-  reaction_3: FBP -> 2 GAP; compartment_*(k3f*FBP - k3b*GAP^2);
-  reaction_4: GAP + NAD => DPG + NADH; compartment_*(V4*NAD*GAP/((K4GAP + GAP)*(K4NAD + NAD)));
-  reaction_5: DPG + ADP -> PEP + ATP; compartment_*(k5f*DPG*ADP - k5b*PEP*ATP);
-  reaction_6: PEP + ADP => PYR + ATP; compartment_*(V6*ADP*PEP/((K6PEP + PEP)*(K6ADP + ADP)));
-  reaction_7: PYR => ACA; compartment_*(V7*PYR/(K7PYR + PYR));
-  reaction_8: ACA + NADH -> EtOH + NAD; compartment_*(k8f*NADH*ACA - k8b*NAD*EtOH);
-  reaction_9: AMP + ATP -> 2 ADP; compartment_*(k9f*AMP*ATP - k9b*ADP^2);
-  reaction_10: F6P => P; compartment_*k10*F6P;
-
-  // Species initializations:
-  ATP = 4.49064/compartment_;
-  ADP = 0.108367/compartment_;
-  AMP = 0.00261149/compartment_;
-  GLC = 0.0112817/compartment_;
-  F6P = 0.65939/compartment_;
-  FBP = 0.00770135/compartment_;
-  GAP = 0.00190919/compartment_;
-  NAD = 3.62057/compartment_;
-  NADH = 0.616118/compartment_;
-  DPG = 0.299109/compartment_;
-  PEP = 0.0021125/compartment_;
-  PYR = 0.00422702/compartment_;
-  ACA = 0.0738334/compartment_;
-  EtOH = 0.33981/compartment_;
-  P = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  V1 = 0.5;
-  K1GLC = 0.1;
-  K1ATP = 0.063;
-  V2 = 1.5;
-  K2 = 0.0016;
-  k2 = 0.017;
-  K2ATP = 0.01;
-  k3f = 1;
-  k3b = 50;
-  V4 = 10;
-  K4GAP = 1;
-  K4NAD = 1;
-  k5f = 1;
-  k5b = 0.5;
-  V6 = 10;
-  K6PEP = 0.2;
-  K6ADP = 0.3;
-  V7 = 2;
-  K7PYR = 0.3;
-  k8f = 1;
-  k8b = 0.000143;
-  k9f = 10;
-  k9b = 10;
-  k10 = 0.05;
-  flow = 0.011;
-
-  // Other declarations:
-  const compartment_, V1, K1GLC, K1ATP, V2, K2, k2, K2ATP, k3f, k3b, V4, K4GAP;
-  const K4NAD, k5f, k5b, V6, K6PEP, K6ADP, V7, K7PYR, k8f, k8b, k9f, k9b;
-  const k10, flow;
-
-  // Unit definitions:
-  unit substance = 1e-3 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "millimole";
-  time_unit is "minute";
-
-  // CV terms:
-  compartment_ hypernym "http://identifiers.org/go/GO:0005737"
-  ATP identity "http://identifiers.org/chebi/CHEBI:15422",
-               "http://identifiers.org/kegg.compound/C00002"
-  ADP identity "http://identifiers.org/chebi/CHEBI:16761",
-               "http://identifiers.org/kegg.compound/C00008"
-  AMP identity "http://identifiers.org/chebi/CHEBI:16027",
-               "http://identifiers.org/kegg.compound/C00020"
-  GLC identity "http://identifiers.org/chebi/CHEBI:17234",
-               "http://identifiers.org/kegg.compound/C00293"
-  F6P identity "http://identifiers.org/chebi/CHEBI:20935",
-               "http://identifiers.org/kegg.compound/C05345"
-  FBP identity "http://identifiers.org/chebi/CHEBI:16905",
-               "http://identifiers.org/kegg.compound/C05378"
-  GAP identity "http://identifiers.org/chebi/CHEBI:29052",
-               "http://identifiers.org/kegg.compound/C00118"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  DPG identity "http://identifiers.org/chebi/CHEBI:16001",
-               "http://identifiers.org/kegg.compound/C00236"
-  PEP identity "http://identifiers.org/chebi/CHEBI:18021",
-               "http://identifiers.org/kegg.compound/C00074"
-  PYR identity "http://identifiers.org/chebi/CHEBI:15361",
-               "http://identifiers.org/kegg.compound/C00022"
-  ACA identity "http://identifiers.org/chebi/CHEBI:15343",
-               "http://identifiers.org/kegg.compound/C00084"
-  EtOH identity "http://identifiers.org/chebi/CHEBI:16236",
-                "http://identifiers.org/kegg.compound/C00469"
-  ATPflow hypernym "http://identifiers.org/go/GO:0006754"
-  ADPflow hypernym "http://identifiers.org/go/GO:0006172"
-  NADHflow hypernym "http://identifiers.org/go/GO:0006735"
-  NADflow hypernym "http://identifiers.org/go/GO:0009435"
-  GLCflow hypernym "http://identifiers.org/go/GO:0046323"
-  F6Pflow hypernym "http://identifiers.org/go/GO:0006002"
-  FBPflow hypernym "http://identifiers.org/go/GO:0030388"
-  GAPflow hypernym "http://identifiers.org/go/GO:0019683"
-  PYRflow hypernym "http://identifiers.org/go/GO:0042867"
-  ACAflow hypernym "http://identifiers.org/go/GO:0046187"
-  EtOHflow hypernym "http://identifiers.org/go/GO:0006068"
-  AMPflow hypernym "http://identifiers.org/go/GO:0006196"
-  reaction_1 homolog "http://identifiers.org/reactome/REACT_1164"
-  reaction_1 part "http://identifiers.org/ec-code/2.7.1.2",
-                  "http://identifiers.org/ec-code/5.3.1.9"
-  reaction_1 part "http://identifiers.org/kegg.reaction/R00771",
-                  "http://identifiers.org/kegg.reaction/R00299"
-  reaction_2 homolog "http://identifiers.org/reactome/REACT_1840"
-  reaction_2 hypernym "http://identifiers.org/ec-code/2.7.1.11",
-                      "http://identifiers.org/kegg.reaction/R00756"
-  reaction_3 homolog "http://identifiers.org/reactome/REACT_1693"
-  reaction_3 part "http://identifiers.org/kegg.reaction/R01070",
-                  "http://identifiers.org/kegg.reaction/R01015"
-  reaction_3 part "http://identifiers.org/ec-code/5.3.1.1",
-                  "http://identifiers.org/ec-code/4.1.2.13"
-  reaction_4 homolog "http://identifiers.org/reactome/REACT_587"
-  reaction_4 hypernym "http://identifiers.org/ec-code/1.2.1.12",
-                      "http://identifiers.org/kegg.reaction/R01061"
-  reaction_5 part "http://identifiers.org/ec-code/5.4.2.1",
-                  "http://identifiers.org/ec-code/2.7.2.3",
-                  "http://identifiers.org/ec-code/4.2.1.11"
-  reaction_5 part "http://identifiers.org/kegg.reaction/R00658",
-                  "http://identifiers.org/kegg.reaction/R01512",
-                  "http://identifiers.org/kegg.reaction/R01518"
-  reaction_5 part "http://identifiers.org/reactome/REACT_1771",
-                  "http://identifiers.org/reactome/REACT_1400"
-  reaction_6 version "http://identifiers.org/ec-code/2.7.1.40",
-                     "http://identifiers.org/kegg.reaction/R00200"
-  reaction_6 homolog "http://identifiers.org/reactome/REACT_1911"
-  reaction_7 hypernym "http://identifiers.org/ec-code/4.1.1.1",
-                      "http://identifiers.org/kegg.reaction/R00224"
-  reaction_8 hypernym "http://identifiers.org/ec-code/1.1.1.71",
-                      "http://identifiers.org/kegg.reaction/R00754"
-  reaction_8 homolog "http://identifiers.org/reactome/REACT_799"
-  reaction_9 hypernym "http://identifiers.org/ec-code/2.7.4.3",
-                      "http://identifiers.org/kegg.reaction/R00127"
-  reaction_10 hypernym "http://identifiers.org/go/GO:0006001"
-  reaction_10 homolog "http://identifiers.org/reactome/REACT_1571"
-end
-
-Glycolysis_Nielsen is "Nielsen1998_Glycolysis"
-
-Glycolysis_Nielsen model_entity_is "http://identifiers.org/biomodels.db/MODEL6622455387"
-Glycolysis_Nielsen model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000042"
-Glycolysis_Nielsen description "http://identifiers.org/pubmed/17029704"
-Glycolysis_Nielsen origin "http://identifiers.org/pubmed/6454892",
-                          "http://identifiers.org/pubmed/8061224"
-Glycolysis_Nielsen homolog "http://identifiers.org/reactome/REACT_1383"
-Glycolysis_Nielsen taxon "http://identifiers.org/taxonomy/4932"
-Glycolysis_Nielsen identity "http://identifiers.org/kegg.pathway/sce00010"
-Glycolysis_Nielsen hypernym "http://identifiers.org/go/GO:0006096"

BioModelsRAG/data/BIOMD0000000043.txt

@@ -1,88 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular;
-  species EC in extracellular, Z in cytosol, Rho in cytosol, Y in intravesicular;
-  species Fraction_Inactive_Channels in cytosol;
-
-  // Reactions:
-  vin: EC => Z; cytosol*(vin_v0 + vin_v1*beta);
-  v2: Z => Y; intravesicular*(v2_Vm2*Z^2/(v2_K2^2 + Z^2));
-  v3: Y => Z; cytosol*(beta*(Rho*(a/d)*Z^4/(1 + (a/d)*Z^4))*v3_Vm3*Y^2/(v3_Ky^2 + Y^2));
-  v4: Y => Z; cytosol*v4_Kf*Y;
-  v5: Z => EC; extracellular*v5_K*Z;
-  v6: Rho => Fraction_Inactive_Channels; cytosol*v6_Kd*Z^4*Rho;
-  v7: Fraction_Inactive_Channels => Rho; cytosol*v7_Kr*(1 - Rho);
-
-  // Species initializations:
-  EC = 0;
-  Z = 0;
-  Rho = 0;
-  Y = 0.36;
-  Fraction_Inactive_Channels = 0;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular = 1;
-
-  // Variable initializations:
-  a = 40000;
-  d = 100;
-  beta = 1;
-  vin_v0 = 1;
-  vin_v1 = 1;
-  v2_Vm2 = 6.5;
-  v2_K2 = 0.1;
-  v3_Vm3 = 50;
-  v3_Ky = 0.2;
-  v4_Kf = 1;
-  v5_K = 10;
-  v6_Kd = 5000;
-  v7_Kr = 5;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular, a, d, beta;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005615"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  intravesicular hypernym "http://identifiers.org/obo.go/GO:0005790"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Rho hypernym "http://identifiers.org/interpro/IPR016093",
-               "http://identifiers.org/interpro/IPR000493"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Fraction_Inactive_Channels hypernym "http://identifiers.org/interpro/IPR000493",
-                                      "http://identifiers.org/pirsf/PIRSF002433"
-  vin hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v3 hypernym "http://identifiers.org/obo.go/GO:0007204"
-  v4 hypernym "http://identifiers.org/obo.go/GO:0007204"
-  v5 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v6 hypernym "http://identifiers.org/obo.go/GO:0005220"
-  v7 hypernym "http://identifiers.org/obo.go/GO:0005220"
-end
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition is "Borghans1997 - Calcium Oscillation - Model 1"
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition model_entity_is "http://identifiers.org/biomodels.db/MODEL6622689184"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000043"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition description "http://identifiers.org/pubmed/17029867"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition hypernym "http://identifiers.org/obo.go/GO:0048016",
-                                                                               "http://identifiers.org/obo.go/GO:0019722"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition identity "http://identifiers.org/kegg.pathway/rno04020"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_channel_inhibition taxon "http://identifiers.org/taxonomy/10114"

BioModelsRAG/data/BIOMD0000000044.txt

@@ -1,129 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular;
-  species EC in extracellular, Z in cytosol, A in cytosol, Y in intravesicular;
-
-  // Reactions:
-  vin: EC => Z; cytosol*(vin_v0 + vin_v1*beta);
-  v2: Z => Y; intravesicular*(v2_Vm2*Z^2/(v2_K2^2 + Z^2));
-  v3: Y => Z; cytosol*v3_Vm3*A^4*Y^2*Z^4/((v3_Ka^4 + A^4)*(v3_Ky^2 + Y^2)*(v3_Kz^4 + Z^4));
-  v4: Y => Z; cytosol*v4_Kf*Y;
-  v5: Z => EC; extracellular*v5_K*Z;
-  v6:  => A; cytosol*beta*v6_Vp;
-  v7: A => ; cytosol*v7_Vd*A^2*Z^v7_n/((v7_Kp^2 + A^2)*(v7_Kd^v7_n + Z^v7_n));
-  v8: A => ; cytosol*v8_epsilon*A;
-
-  // Species initializations:
-  EC = 1000;
-  Z = 0;
-  A = 0.45;
-  Y = 0.36;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular = 1;
-
-  // Variable initializations:
-  beta = 0.5;
-  vin_v0 = 2;
-  vin_v1 = 1;
-  v2_Vm2 = 6.5;
-  v2_K2 = 0.1;
-  v3_Vm3 = 19.5;
-  v3_Ka = 0.2;
-  v3_Ky = 0.2;
-  v3_Kz = 0.3;
-  v4_Kf = 1;
-  v5_K = 10;
-  v6_Vp = 2.5;
-  v7_Vd = 80;
-  v7_Kp = 1;
-  v7_Kd = 0.4;
-  v7_n = 4;
-  v8_epsilon = 0.1;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular, beta;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-  v6 is "Agonist stimulated production of IP3";
-  v7 is "Ca dependent IP3 degradation";
-  v8 is "Ca independent IP3 degradation";
-
-  // SBO terms:
-  extracellular.sboTerm = 290
-  cytosol.sboTerm = 290
-  intravesicular.sboTerm = 290
-  EC.sboTerm = 327
-  Z.sboTerm = 327
-  A.sboTerm = 327
-  Y.sboTerm = 327
-  beta.sboTerm = 498
-  vin.sboTerm = 185
-  vin_v0.sboTerm = 485
-  vin_v1.sboTerm = 162
-  v2.sboTerm = 185
-  v2_Vm2.sboTerm = 186
-  v2_K2.sboTerm = 424
-  v3.sboTerm = 185
-  v3_Vm3.sboTerm = 186
-  v3_Ka.sboTerm = 194
-  v3_Ky.sboTerm = 424
-  v3_Kz.sboTerm = 423
-  v4.sboTerm = 185
-  v4_Kf.sboTerm = 35
-  v5.sboTerm = 185
-  v5_K.sboTerm = 35
-  v6.sboTerm = 393
-  v6_Vp.sboTerm = 48
-  v7.sboTerm = 179
-  v7_Vd.sboTerm = 324
-  v7_Kp.sboTerm = 424
-  v7_Kd.sboTerm = 194
-  v7_n.sboTerm = 190
-  v8.sboTerm = 179
-  v8_epsilon.sboTerm = 498
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005615"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  intravesicular hypernym "http://identifiers.org/obo.go/GO:0005790"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  A identity "http://identifiers.org/chebi/CHEBI:16595",
-             "http://identifiers.org/kegg.compound/C01245"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  vin hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v2 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v3 hypernym "http://identifiers.org/obo.go/GO:0006816",
-              "http://identifiers.org/obo.go/GO:0051482"
-  v4 hypernym "http://identifiers.org/obo.go/GO:0007204"
-  v5 hypernym "http://identifiers.org/obo.go/GO:0051481"
-  v6 hypernym "http://identifiers.org/obo.go/GO:0006021",
-              "http://identifiers.org/obo.go/GO:0007200"
-  v7 hypernym "http://identifiers.org/obo.go/GO:0019310"
-  v8 hypernym "http://identifiers.org/obo.go/GO:0019310"
-end
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 is "Borghans1997 - Calcium Oscillation - Model 2"
-
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 model_entity_is "http://identifiers.org/biomodels.db/MODEL6622948601"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000044"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 description "http://identifiers.org/pubmed/17029867"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 hypernym "http://identifiers.org/obo.go/GO:0019722",
-                                                                                         "http://identifiers.org/obo.go/GO:0048016"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 parthood "http://identifiers.org/kegg.pathway/rno04020"
-Goldbeter_Calcium_Oscillation_based_on_CICR_AND_CA_Activated_degradation_of_IP3 taxon "http://identifiers.org/taxonomy/10114"

BioModelsRAG/data/BIOMD0000000045.txt

@@ -1,97 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model()
-
-  // Compartments and Species:
-  compartment extracellular, cytosol, intravesicular1, intravesicular2;
-  species EC in extracellular, Z in cytosol, Y in intravesicular2, X in intravesicular1;
-
-  // Reactions:
-  vin: EC => Z; cytosol*(vin_v0 + vin_v1*beta);
-  v2i: Z => Y; intravesicular2*v2i_Vm2i*Z^2/(v2i_K2i^2 + Z^2);
-  v3i: Y => Z; cytosol*v3i_Vm3i*Y^2*Z^2/((v3i_K3y^2 + Y^2)*(v3i_K3z^2 + Z^2));
-  v4: Y => Z; cytosol*v4_Kf*Y;
-  v5: Z => EC; extracellular*v5_K*Z;
-  v6: X => Z; cytosol*v6_Kf*X;
-  v2s: Z => X; intravesicular1*v2s_Vm2s*Z^2/(v2s_K2s^2 + Z^2);
-  v3s: X => Z; cytosol*beta*v3s_Vm3s*X^2/(v3s_K3s^2 + X^2);
-
-  // Species initializations:
-  EC = 0;
-  Z = 0;
-  Y = 0;
-  X = 0.5;
-
-  // Compartment initializations:
-  extracellular = 1;
-  cytosol = 1;
-  intravesicular1 = 1;
-  intravesicular2 = 1;
-
-  // Variable initializations:
-  beta = 1;
-  vin_v0 = 0.015;
-  vin_v1 = 0.012;
-  v2i_Vm2i = 3.1;
-  v2i_K2i = 0.005;
-  v3i_Vm3i = 25;
-  v3i_K3y = 0.065;
-  v3i_K3z = 0.022;
-  v4_Kf = 0.5;
-  v5_K = 1;
-  v6_Kf = 0.5;
-  v2s_Vm2s = 1.5;
-  v2s_K2s = 0.0265;
-  v3s_Vm3s = 0.169;
-  v3s_K3s = 0.1;
-
-  // Other declarations:
-  const extracellular, cytosol, intravesicular1, intravesicular2, beta;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  extracellular hypernym "http://identifiers.org/obo.go/GO:0005615"
-  cytosol hypernym "http://identifiers.org/obo.go/GO:0005829"
-  intravesicular1 hypernym "http://identifiers.org/obo.go/GO:0005790"
-  EC identity "http://identifiers.org/chebi/CHEBI:29108",
-              "http://identifiers.org/kegg.compound/C00076"
-  Z identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  Y identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  X identity "http://identifiers.org/chebi/CHEBI:29108",
-             "http://identifiers.org/kegg.compound/C00076"
-  vin hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v2i hypernym "http://identifiers.org/obo.go/GO:0051481",
-               "http://identifiers.org/obo.go/GO:0006816"
-  v3i hypernym "http://identifiers.org/obo.go/GO:0005219",
-               "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0007204"
-  v4 hypernym "http://identifiers.org/obo.go/GO:0006816",
-              "http://identifiers.org/obo.go/GO:0007204"
-  v5 hypernym "http://identifiers.org/obo.go/GO:0051481",
-              "http://identifiers.org/obo.go/GO:0006816"
-  v6 hypernym "http://identifiers.org/obo.go/GO:0006816",
-              "http://identifiers.org/obo.go/GO:0007204"
-  v2s hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0051481"
-  v3s hypernym "http://identifiers.org/obo.go/GO:0006816",
-               "http://identifiers.org/obo.go/GO:0051482"
-end
-
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model is "Borghans1997 - Calcium Oscillation - Model 3"
-
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model model_entity_is "http://identifiers.org/biomodels.db/MODEL6623009547"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000045"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model description "http://identifiers.org/pubmed/17029867"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model hypernym "http://identifiers.org/obo.go/GO:0048016",
-                                                                       "http://identifiers.org/obo.go/GO:0019722"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model taxon "http://identifiers.org/taxonomy/10114"
-Goldbeter_Calcium_Oscillation_based_onCICR_AND_two_pool_model identity "http://identifiers.org/kegg.pathway/rno04020"

BioModelsRAG/data/BIOMD0000000046.txt

@@ -1,127 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Olsen2003_peroxidase()
-
-  // Compartments and Species:
-  compartment compartment_;
-  species NADH in compartment_, O2 in compartment_, H2O2 in compartment_;
-  species per3 in compartment_, coI in compartment_, ArH in compartment_;
-  species coII in compartment_, Ar in compartment_, NADrad in compartment_;
-  species super in compartment_, coIII in compartment_, per2 in compartment_;
-  species $NAD2 in compartment_, $NAD in compartment_, $O2g in compartment_;
-  species $NADHres in compartment_;
-
-  // Reactions:
-  v1: NADH + O2 => H2O2 + $NAD; compartment_*v1_k1*NADH*O2;
-  v2: per3 + H2O2 => coI; compartment_*v2_k2*H2O2*per3;
-  v3: ArH + coI => Ar + coII; compartment_*v3_k3*coI*ArH;
-  v4: coII + ArH => per3 + Ar; compartment_*v4_k4*coII*ArH;
-  v5: NADrad + O2 => $NAD + super; compartment_*v5_k5*NADrad*O2;
-  v6: per3 + super => coIII; compartment_*v6_k6*super*per3;
-  v7: 2 super => H2O2 + O2; compartment_*v7_k7*super*super;
-  v8: NADrad + coIII => $NAD + coI; compartment_*v8_k8*coIII*NADrad;
-  v9: 2 NADrad => $NAD2; compartment_*v9_k9*NADrad*NADrad;
-  v10: per3 + NADrad => per2 + $NAD; compartment_*v10_k10*per3*NADrad;
-  v11: per2 + O2 => coIII; compartment_*v11_k11*per2*O2;
-  v12: $NADHres => NADH; compartment_*v12_k12;
-  v131: $O2g => O2; compartment_*v131_k13f*O2g;
-  v132: O2 => $O2g; compartment_*v132_k13b*O2;
-  v14: NADH + Ar => NADrad + ArH; compartment_*v14_k14*Ar*NADH;
-
-  // Species initializations:
-  NADH = 0;
-  O2 = 0;
-  H2O2 = 0;
-  per3 = 1.4;
-  coI = 0;
-  ArH = 500;
-  coII = 0;
-  Ar = 0;
-  NADrad = 0;
-  super = 0;
-  coIII = 0;
-  per2 = 0;
-  NAD2 = 0;
-  NAD = 0;
-  O2g = 12;
-  NADHres = 0;
-
-  // Compartment initializations:
-  compartment_ = 1;
-
-  // Variable initializations:
-  v1_k1 = 3e-06;
-  v2_k2 = 18;
-  v3_k3 = 0.15;
-  v4_k4 = 0.0052;
-  v5_k5 = 20;
-  v6_k6 = 17;
-  v7_k7 = 20;
-  v8_k8 = 40;
-  v9_k9 = 60;
-  v10_k10 = 1.8;
-  v11_k11 = 0.1;
-  v12_k12 = 0.08;
-  v131_k13f = 0.006;
-  v132_k13b = 0.006;
-  v14_k14 = 0.7;
-
-  // Other declarations:
-  const compartment_;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-
-  // Display Names:
-  substance is "micromole";
-
-  // CV terms:
-  NADH identity "http://identifiers.org/chebi/CHEBI:16908",
-                "http://identifiers.org/kegg.compound/C00004"
-  O2 identity "http://identifiers.org/chebi/CHEBI:15379",
-              "http://identifiers.org/kegg.compound/C00007"
-  H2O2 identity "http://identifiers.org/chebi/CHEBI:16240",
-                "http://identifiers.org/kegg.compound/C00027"
-  per3 hypernym "http://identifiers.org/interpro/IPR000823",
-                "http://identifiers.org/pirsf/PIRSF000293"
-  coI hypernym "http://identifiers.org/interpro/IPR000823",
-               "http://identifiers.org/pirsf/PIRSF000293"
-  ArH version "http://identifiers.org/chebi/CHEBI:30763",
-              "http://identifiers.org/chebi/CHEBI:16796"
-  ArH version "http://identifiers.org/kegg.compound/C00156",
-              "http://identifiers.org/kegg.compound/C01598"
-  coII hypernym "http://identifiers.org/interpro/IPR000823",
-                "http://identifiers.org/pirsf/PIRSF000293"
-  Ar version "http://identifiers.org/chebi/CHEBI:17879",
-             "http://identifiers.org/chebi/CHEBI:16796"
-  Ar version "http://identifiers.org/kegg.compound/C00156",
-             "http://identifiers.org/kegg.compound/C01598"
-  NADrad hypernym "http://identifiers.org/chebi/CHEBI:15846",
-                  "http://identifiers.org/kegg.compound/C00003"
-  super identity "http://identifiers.org/chebi/CHEBI:18421",
-                 "http://identifiers.org/kegg.compound/C00704"
-  coIII hypernym "http://identifiers.org/interpro/IPR000823",
-                 "http://identifiers.org/pirsf/PIRSF000293"
-  per2 hypernym "http://identifiers.org/interpro/IPR000823",
-                "http://identifiers.org/pirsf/PIRSF000293"
-  NAD2 part "http://identifiers.org/chebi/CHEBI:15846"
-  NAD2 part "http://identifiers.org/kegg.compound/C00003"
-  NAD identity "http://identifiers.org/chebi/CHEBI:15846",
-               "http://identifiers.org/kegg.compound/C00003"
-  O2g identity "http://identifiers.org/chebi/CHEBI:15379",
-               "http://identifiers.org/kegg.compound/C00007"
-  NADHres identity "http://identifiers.org/chebi/CHEBI:16908",
-                   "http://identifiers.org/kegg.compound/C00004"
-  v1 identity "http://identifiers.org/kegg.reaction/R07171"
-  v1 hypernym "http://identifiers.org/ec-code/1.6.3.1"
-  v7 identity "http://identifiers.org/kegg.reaction/R00275"
-  v7 hypernym "http://identifiers.org/ec-code/1.15.1.1"
-end
-
-Olsen2003_peroxidase is "Olsen2003_peroxidase"
-
-Olsen2003_peroxidase model_entity_is "http://identifiers.org/biomodels.db/MODEL6623265463"
-Olsen2003_peroxidase model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000046"
-Olsen2003_peroxidase description "http://identifiers.org/pubmed/12823550"
-Olsen2003_peroxidase origin "http://identifiers.org/pubmed/11901676"
-Olsen2003_peroxidase taxon "http://identifiers.org/taxonomy/3704"
-Olsen2003_peroxidase hypernym "http://identifiers.org/go/GO:0016692"

BioModelsRAG/data/BIOMD0000000047.txt

@@ -1,80 +0,0 @@
-// Created by libAntimony v2.13.0
-model *Oxhamre_Bacteria_induced_Ca_oscillations()
-
-  // Compartments and Species:
-  compartment Cytosol, Endoplasmic_Reticulum;
-  species CaER in Endoplasmic_Reticulum, Ca_Cyt in Cytosol;
-
-  // Assignment Rules:
-  n := n0*(exp(-kbN*time) + kappa*(1 - exp(-kbN*time)));
-  p1 := p11 + p12*n/(K1 + n);
-  p2 := Ca_Cyt/(K2 + Ca_Cyt);
-
-  // Rate Rules:
-  p3' = -(k31*Ca_Cyt*p3) + k31*K3*(1 - p3);
-
-  // Reactions:
-  Jch: CaER => Ca_Cyt; Jch_Fch_0*p1*p2*p3;
-  Jleak: CaER => Ca_Cyt; Jleak_Fleak;
-  Jpump: Ca_Cyt => CaER; Jpump_Fpump_0*Ca_Cyt/(Jpump_Kpump + Ca_Cyt);
-
-  // Species initializations:
-  CaER = 0;
-  Ca_Cyt = 0;
-
-  // Compartment initializations:
-  Cytosol = 1;
-  Endoplasmic_Reticulum = 1;
-
-  // Variable initializations:
-  n0 = 1;
-  kbN = 0.5;
-  kappa = 5;
-  p11 = 0.2;
-  p12 = 0.8;
-  K1 = 5;
-  K2 = 0.7;
-  p3 = 0.95;
-  k31 = 0.5;
-  K3 = 0.7;
-  Jch_Fch_0 = 8;
-  Jleak_Fleak = 0.5;
-  Jpump_Fpump_0 = 2;
-  Jpump_Kpump = 0.1;
-
-  // Other declarations:
-  var n, p1, p2, p3;
-  const Cytosol, Endoplasmic_Reticulum, n0, kbN, kappa, p11, p12, K1, K2;
-  const k31, K3;
-
-  // Unit definitions:
-  unit substance = 1e-6 mole;
-  unit time_unit = 60 second;
-
-  // Display Names:
-  substance is "micromole (default)";
-  time_unit is "minute (default)";
-
-  // CV terms:
-  Cytosol hypernym "http://identifiers.org/go/GO:0005829"
-  Endoplasmic_Reticulum hypernym "http://identifiers.org/go/GO:0005790"
-  CaER hypernym "http://identifiers.org/chebi/CHEBI:29108"
-  Ca_Cyt hypernym "http://identifiers.org/chebi/CHEBI:29108"
-  Jch hypernym "http://identifiers.org/go/GO:0006816",
-               "http://identifiers.org/go/GO:0051482"
-  Jleak hypernym "http://identifiers.org/go/GO:0007204",
-                 "http://identifiers.org/go/GO:0006816"
-  Jpump hypernym "http://identifiers.org/go/GO:0051481",
-                 "http://identifiers.org/go/GO:0006816"
-end
-
-Oxhamre_Bacteria_induced_Ca_oscillations is "Oxhamre2005_Ca_oscillation"
-
-Oxhamre_Bacteria_induced_Ca_oscillations model_entity_is "http://identifiers.org/biomodels.db/MODEL6623415355"
-Oxhamre_Bacteria_induced_Ca_oscillations model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000047"
-Oxhamre_Bacteria_induced_Ca_oscillations description "http://identifiers.org/pubmed/15596518"
-Oxhamre_Bacteria_induced_Ca_oscillations origin "http://identifiers.org/pubmed/11874447"
-Oxhamre_Bacteria_induced_Ca_oscillations identity "http://identifiers.org/kegg.pathway/rno04020"
-Oxhamre_Bacteria_induced_Ca_oscillations taxon "http://identifiers.org/taxonomy/10114"
-Oxhamre_Bacteria_induced_Ca_oscillations hypernym "http://identifiers.org/go/GO:0048016",
-                                                  "http://identifiers.org/go/GO:0019722"