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BioModelsRAG/2data/BIOMD0000000001.txt

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+// 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

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+__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

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+// 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

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+// 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

@@ -0,0 +1,124 @@
+// 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

@@ -0,0 +1,102 @@
+// 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

@@ -0,0 +1,114 @@
+// 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

@@ -0,0 +1,66 @@
+// 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

@@ -0,0 +1,266 @@
+// 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

@@ -0,0 +1,121 @@
+// 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

@@ -0,0 +1,250 @@
+// 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

@@ -0,0 +1,140 @@
+// 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

@@ -0,0 +1,272 @@
+// 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

@@ -0,0 +1,161 @@
+// 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

@@ -0,0 +1,264 @@
+// 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

@@ -0,0 +1,1635 @@
+// 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

@@ -0,0 +1,411 @@
+// 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

@@ -0,0 +1,119 @@
+// 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

@@ -0,0 +1,218 @@
+// 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

@@ -0,0 +1,341 @@
+// 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

@@ -0,0 +1,652 @@
+// 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

@@ -0,0 +1,101 @@
+// 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

@@ -0,0 +1,214 @@
+// 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

@@ -0,0 +1,257 @@
+// 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

@@ -0,0 +1,175 @@
+// 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

@@ -0,0 +1,67 @@
+// 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

@@ -0,0 +1,87 @@
+// 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

@@ -0,0 +1,135 @@
+// 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

@@ -0,0 +1,78 @@
+// 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

@@ -0,0 +1,208 @@
+// 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

@@ -0,0 +1,112 @@
+// 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

@@ -0,0 +1,233 @@
+// 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

@@ -0,0 +1,80 @@
+// 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

@@ -0,0 +1,423 @@
+// 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

@@ -0,0 +1,278 @@
+// 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

@@ -0,0 +1,259 @@
+// 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

@@ -0,0 +1,103 @@
+// 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

@@ -0,0 +1,72 @@
+// 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

@@ -0,0 +1,89 @@
+// 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

@@ -0,0 +1,158 @@
+// 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

@@ -0,0 +1,95 @@
+// 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

@@ -0,0 +1,61 @@
+// 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

@@ -0,0 +1,127 @@
+// 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

@@ -0,0 +1,189 @@
+// 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

@@ -0,0 +1,88 @@
+// 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

@@ -0,0 +1,129 @@
+// 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

@@ -0,0 +1,97 @@
+// 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

@@ -0,0 +1,127 @@
+// 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

@@ -0,0 +1,80 @@
+// 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"