// Created by libAntimony v2.13.0
model *Swat2004_Mammalian_G1_S_Transition()

  // Compartments and Species:
  compartment cell;
  species pRB in cell, pRBp in cell, E2F1 in cell, CycDi in cell, CycDa in cell;
  species AP1 in cell, pRBpp in cell, CycEi in cell, CycEa in cell;

  // Reactions:
  pRB_synthesis:  => pRB; cell*k1*(E2F1/(Km1 + E2F1))*(J11/(J11 + pRB))*(J61/(J61 + pRBp));
  pRB_phosphorylation: pRB => pRBp; cell*k16*pRB*CycDa;
  pRBp_dephosphorylation: pRBp => pRB; cell*k61*pRBp;
  pRB_degradation: pRB => ; cell*phi_pRB*pRB;
  E2F1_synthesis:  => E2F1; cell*(kp + (k2*(a^2 + E2F1^2)/(Km2^2 + E2F1^2))*(J12/(J12 + pRB))*(J62/(J62 + pRBp)));
  E2F1_degradation: E2F1 => ; cell*phi_E2F1*E2F1;
  CycD_synthesis:  => CycDi; cell*(k3*AP1 + k23*E2F1*(J13/(J13 + pRB))*(J63/(J63 + pRBp)));
  CycD_inibition: CycDa => CycDi; cell*k43*CycDa;
  CycD_activation: CycDi => CycDa; cell*k34*CycDi*(CycDa/(Km4 + CycDa));
  CycD_degradation: CycDi => ; cell*phi_CycDi*CycDi;
  CycD_degradation2: CycDa => ; cell*phi_CycDa*CycDa;
  AP1_synthesis:  => AP1; cell*(Fm + k25*E2F1*(J15/(J15 + pRB))*(J65/(J65 + pRBp)));
  Ap1_degradation: AP1 => ; cell*phi_AP1*AP1;
  pRBp_phosphorylation: pRBp => pRBpp; cell*k67*pRBp*CycEa;
  pRBpp_dephosphorylation: pRBpp => pRBp; cell*k76*pRBpp;
  pRBpp_degradation: pRBpp => ; cell*phi_pRBpp*pRBpp;
  pRBp_degradation: pRBp => ; cell*phi_pRBp*pRBp;
  CycE_synthesis:  => CycEi; cell*k28*E2F1*(J18/(J18 + pRB))*(J68/(J68 + pRBp));
  CycE_activation: CycEi => CycEa; cell*k89*CycEi*CycEa/(Km9 + CycEa);
  CycE_inibition: CycEa => CycEi; cell*k98*CycEa;
  CycE_degradation: CycEi => ; cell*phi_CycEi*CycEi;
  CycE_degradation2: CycEa => ; cell*phi_CycEa*CycEa;

  // Species initializations:
  pRB = 0.1;
  pRBp = 0.1;
  E2F1 = 0.1;
  CycDi = 0.1;
  CycDa = 0.1;
  AP1 = 0.1;
  pRBpp = 0.1;
  CycEi = 0.1;
  CycEa = 0.1;

  // Compartment initializations:
  cell = 1;

  // Variable initializations:
  k1 = 1;
  Km1 = 0.5;
  J11 = 0.5;
  J61 = 5;
  k16 = 0.4;
  k61 = 0.3;
  phi_pRB = 0.005;
  kp = 0.05;
  k2 = 1.6;
  a = 0.04;
  Km2 = 4;
  J12 = 5;
  J62 = 8;
  phi_E2F1 = 0.1;
  k3 = 0.05;
  k23 = 0.3;
  J13 = 0.002;
  J63 = 2;
  k34 = 0.04;
  Km4 = 0.3;
  phi_CycDi = 0.023;
  k43 = 0.01;
  phi_CycDa = 0.03;
  Fm = 0.005;
  k25 = 0.9;
  J15 = 0.001;
  J65 = 6;
  phi_AP1 = 0.01;
  k67 = 0.7;
  k76 = 0.1;
  phi_pRBpp = 0.04;
  phi_pRBp = 0.06;
  k28 = 0.06;
  J18 = 0.6;
  J68 = 7;
  k89 = 0.07;
  Km9 = 0.005;
  k98 = 0.01;
  phi_CycEi = 0.06;
  phi_CycEa = 0.05;

  // Other declarations:
  const cell, k1, Km1, J11, J61, k16, k61, phi_pRB, kp, k2, a, Km2, J12, J62;
  const phi_E2F1, k3, k23, J13, J63, k34, Km4, phi_CycDi, k43, phi_CycDa;
  const Fm, k25, J15, J65, phi_AP1, k67, k76, phi_pRBpp, phi_pRBp, k28, J18;
  const J68, k89, Km9, k98, phi_CycEi, phi_CycEa;

  // Unit definitions:
  unit time_unit = dimensionless;
  unit volume = dimensionless;
  unit substance = dimensionless;

  // Display Names:
  time_unit is "norm. time";
  volume is "norm. volume";
  substance is "norm substance";
  CycDi is "CycD/cdk4,6(i)";
  CycDa is "CycD/cdk4,6(a)";
  CycEi is "CycE/cdk2(i)";
  CycEa is "CycEa/cdk2(a)";
  pRB_synthesis is "pRB synthesis";
  pRB_phosphorylation is "pRB phosphorylation";
  pRBp_dephosphorylation is "pRBp dephosphorylation";
  pRB_degradation is "pRB degradation";
  E2F1_synthesis is "E2F1 synthesis";
  E2F1_degradation is "E2F1 degradation";
  CycD_synthesis is "CycD synthesis";
  CycD_inibition is "CycD inibition";
  CycD_activation is "CycD activation";
  CycD_degradation is "CycD degradation";
  CycD_degradation2 is "CycD degradation2";
  AP1_synthesis is "AP1 synthesis";
  Ap1_degradation is "Ap1 degradation";
  pRBp_phosphorylation is "pRBp phosphorylation";
  pRBpp_dephosphorylation is "pRBpp dephosphorylation";
  pRBpp_degradation is "pRBpp degradation";
  pRBp_degradation is "pRBp degradation";
  CycE_synthesis is "CycE synthesis";
  CycE_activation is "CycE activation";
  CycE_inibition is "CycE inibition";
  CycE_degradation is "CycE degradation";
  CycE_degradation2 is "CycE degradation2";

  // CV terms:
  pRB homolog "http://identifiers.org/uniprot/P06400"
  pRBp homolog "http://identifiers.org/uniprot/P06400"
  E2F1 homolog "http://identifiers.org/uniprot/Q01094"
  CycDi part "http://identifiers.org/uniprot/P30281",
             "http://identifiers.org/uniprot/P11802",
             "http://identifiers.org/uniprot/Q00534"
  CycDa part "http://identifiers.org/uniprot/Q00534",
             "http://identifiers.org/uniprot/P11802",
             "http://identifiers.org/uniprot/P30281"
  AP1 homolog "http://identifiers.org/uniprot/P01100"
  pRBpp homolog "http://identifiers.org/uniprot/P06400"
  CycEi part "http://identifiers.org/uniprot/P24864",
             "http://identifiers.org/uniprot/O96020",
             "http://identifiers.org/uniprot/P24941"
  CycEa part "http://identifiers.org/uniprot/P24864",
             "http://identifiers.org/uniprot/O96020",
             "http://identifiers.org/uniprot/P24941"
  pRB_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  pRB_phosphorylation hypernym "http://identifiers.org/obo.go/GO:0006468"
  pRBp_dephosphorylation hypernym "http://identifiers.org/obo.go/GO:0006470"
  pRB_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  E2F1_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  E2F1_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  CycD_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  CycD_inibition hypernym "http://identifiers.org/obo.go/GO:0031658"
  CycD_activation hypernym "http://identifiers.org/obo.go/GO:0031659"
  CycD_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  CycD_degradation2 hypernym "http://identifiers.org/obo.go/GO:0030163"
  AP1_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  Ap1_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  pRBp_phosphorylation hypernym "http://identifiers.org/obo.go/GO:0006468"
  pRBpp_dephosphorylation hypernym "http://identifiers.org/obo.go/GO:0006470"
  pRBpp_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  pRBp_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  CycE_synthesis hypernym "http://identifiers.org/obo.go/GO:0006412"
  CycE_activation hypernym "http://identifiers.org/obo.go/GO:0031659"
  CycE_inibition hypernym "http://identifiers.org/obo.go/GO:0031658"
  CycE_degradation hypernym "http://identifiers.org/obo.go/GO:0030163"
  CycE_degradation2 hypernym "http://identifiers.org/obo.go/GO:0030163"
end

Swat2004_Mammalian_G1_S_Transition is "Swat2004_Mammalian_G1_S_Transition"

Swat2004_Mammalian_G1_S_Transition model_entity_is "http://identifiers.org/biomodels.db/MODEL3897709120"
Swat2004_Mammalian_G1_S_Transition model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000228"
Swat2004_Mammalian_G1_S_Transition description "http://identifiers.org/pubmed/15231543"
Swat2004_Mammalian_G1_S_Transition parthood "http://identifiers.org/reactome/REACT_1783"
Swat2004_Mammalian_G1_S_Transition hypernym "http://identifiers.org/obo.go/GO:0000083"
Swat2004_Mammalian_G1_S_Transition taxon "http://identifiers.org/taxonomy/40674"
