//Created by libAntimony v2.4
model novak_tyson_2004_version01__environment(time_)

  // Variable initializations:
  time_ = ;
end

model novak_tyson_2004_version01__ERG(ERG, k_15, k_16, J_15, epsilon, DRG, time_)

  // Rate Rules:
  ERG' = (epsilon * k_15) / (1 + power(DRG / J_15, 2)) - k_16 * ERG;

  // Variable initializations:
  ERG = ;
  k_15 = ;
  k_16 = ;
  J_15 = ;
  epsilon = ;
  DRG = ;
  time_ = ;
end

model novak_tyson_2004_version01__DRG(DRG, k_17_, k_17, k_18, epsilon, ERG, J_17, time_)

  // Rate Rules:
  DRG' = epsilon * (k_17_ * ERG + (power(DRG / J_17, 2) * k_17) / (1 + power(DRG / J_17, 2))) - k_18 * DRG;

  // Variable initializations:
  DRG = ;
  k_17_ = ;
  k_17 = ;
  k_18 = ;
  epsilon = ;
  ERG = ;
  J_17 = ;
  time_ = ;
end

model novak_tyson_2004_version01__Kip1(Kip1, k_5, k_24, k_24r, k_10, k_25, k_25r, k_30, V_6, V_8, epsilon, CycD, CycD_Kip1, CycE, CycA, CycE_Kip1, CycA_Kip1, Cdc20, time_)

  // Rate Rules:
  Kip1' = ((((epsilon * k_5 - V_6 * Kip1) - k_24 * CycD * Kip1) + k_24r * CycD_Kip1 + k_10 * CycD_Kip1) - k_25 * Kip1 * (CycE + CycA)) + k_25r * (CycE_Kip1 + CycA_Kip1) + V_8 * CycE_Kip1 + k_30 * Cdc20 * CycA_Kip1;

  // Variable initializations:
  Kip1 = ;
  k_5 = ;
  k_24 = ;
  k_24r = ;
  k_10 = ;
  k_25 = ;
  k_25r = ;
  k_30 = ;
  V_6 = ;
  V_8 = ;
  epsilon = ;
  CycD = ;
  CycD_Kip1 = ;
  CycE = ;
  CycA = ;
  CycE_Kip1 = ;
  CycA_Kip1 = ;
  Cdc20 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycA_Kip1(CycA_Kip1, k_25, k_25r, k_30, V_6, CycA, Kip1, Cdc20, time_)

  // Rate Rules:
  CycA_Kip1' = ((k_25 * CycA * Kip1 - k_25r * CycA_Kip1) - V_6 * CycA_Kip1) - k_30 * Cdc20 * CycA_Kip1;

  // Variable initializations:
  CycA_Kip1 = ;
  k_25 = ;
  k_25r = ;
  k_30 = ;
  V_6 = ;
  CycA = ;
  Kip1 = ;
  Cdc20 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycD_Kip1(CycD_Kip1, k_24, k_24r, k_10, V_6, CycD, Kip1, time_)

  // Rate Rules:
  CycD_Kip1' = ((k_24 * CycD * Kip1 - k_24r * CycD_Kip1) - V_6 * CycD_Kip1) - k_10 * CycD_Kip1;

  // Variable initializations:
  CycD_Kip1 = ;
  k_24 = ;
  k_24r = ;
  k_10 = ;
  V_6 = ;
  CycD = ;
  Kip1 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycE_Kip1(CycE_Kip1, k_25, k_25r, V_6, V_8, CycE, Kip1, time_)

  // Rate Rules:
  CycE_Kip1' = ((k_25 * CycE * Kip1 - k_25r * CycE_Kip1) - V_6 * CycE_Kip1) - V_8 * CycE_Kip1;

  // Variable initializations:
  CycE_Kip1 = ;
  k_25 = ;
  k_25r = ;
  V_6 = ;
  V_8 = ;
  CycE = ;
  Kip1 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycA(CycA, k_29, k_30, k_25, k_25r, V_6, epsilon, E2FA, Cdc20, Kip1, mass, CycA_Kip1, time_)

  // Rate Rules:
  CycA' = ((epsilon * k_29 * E2FA * mass - k_30 * Cdc20 * CycA) - k_25 * CycA * Kip1) + k_25r * CycA_Kip1 + V_6 * CycA_Kip1;

  // Variable initializations:
  CycA = ;
  k_29 = ;
  k_30 = ;
  k_25 = ;
  k_25r = ;
  V_6 = ;
  epsilon = ;
  E2FA = ;
  Cdc20 = ;
  Kip1 = ;
  mass = ;
  CycA_Kip1 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycB(CycB, k_1_, k_1, V_2, epsilon, J_1, time_)

  // Rate Rules:
  CycB' = epsilon * (k_1_ + (k_1 * power(CycB / J_1, 2)) / (1 + power(CycB / J_1, 2))) - V_2 * CycB;

  // Variable initializations:
  CycB = 0.6;
  k_1_ = ;
  k_1 = ;
  V_2 = ;
  epsilon = ;
  J_1 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycE(CycE, k_7_, k_7, k_25, k_25r, V_8, V_6, epsilon, E2FA, Kip1, CycE_Kip1, CycE_T, time_)

  // Assignment Rules:
  CycE_T := CycE + CycE_Kip1;

  // Rate Rules:
  CycE' = ((epsilon * (k_7_ + k_7 * E2FA) - V_8 * CycE) - k_25 * CycE * Kip1) + k_25r * CycE_Kip1 + V_6 * CycE_Kip1;

  // Variable initializations:
  CycE = ;
  k_7_ = ;
  k_7 = ;
  k_25 = ;
  k_25r = ;
  V_8 = ;
  V_6 = ;
  epsilon = ;
  E2FA = ;
  Kip1 = ;
  CycE_Kip1 = ;
  time_ = ;
end

model novak_tyson_2004_version01__CycD(CycD, k_9, k_24r, k_24, k_10, V_6, epsilon, DRG, Kip1, CycD_Kip1, CycD_T, time_)

  // Assignment Rules:
  CycD_T := CycD + CycD_Kip1;

  // Rate Rules:
  CycD' = ((epsilon * k_9 * DRG + V_6 * CycD_Kip1 + k_24r * CycD_Kip1) - k_24 * CycD_Kip1) - k_10 * CycD;

  // Variable initializations:
  CycD = ;
  k_9 = ;
  k_24r = ;
  k_24 = ;
  k_10 = ;
  V_6 = ;
  epsilon = ;
  DRG = ;
  Kip1 = ;
  CycD_Kip1 = ;
  time_ = ;
end

model novak_tyson_2004_version01__Cdc20(Cdc20, k_13, k_14, k_12, IEP, Cdc20_T, J_13, J_4, time_)

  // Rate Rules:
  Cdc20' = ((k_13 * IEP * (Cdc20_T - Cdc20)) / ((J_13 + Cdc20_T) - Cdc20) - (Cdc20 * k_14) / (J_4 + Cdc20)) - k_12 * Cdc20;

  // Variable initializations:
  Cdc20 = ;
  k_13 = ;
  k_14 = ;
  k_12 = ;
  IEP = ;
  Cdc20_T = ;
  J_13 = ;
  J_4 = ;
  time_ = ;
end

model novak_tyson_2004_version01__Cdc20_T(Cdc20_T, k_11_, k_11, k_12, CycB, epsilon, time_)

  // Rate Rules:
  Cdc20_T' = epsilon * (k_11_ + k_11 * CycB) - k_12 * Cdc20_T;

  // Variable initializations:
  Cdc20_T = ;
  k_11_ = ;
  k_11 = ;
  k_12 = ;
  CycB = ;
  epsilon = ;
  time_ = ;
end

model novak_tyson_2004_version01__IEP(IEP, k_31, k_32, CycB, PPX, J_31, J_32, time_)

  // Rate Rules:
  IEP' = (k_31 * CycB * (1 - IEP)) / ((J_31 + 1) - IEP) - (k_32 * PPX * IEP) / (J_32 + IEP);

  // Variable initializations:
  IEP = ;
  k_31 = ;
  k_32 = ;
  CycB = ;
  PPX = ;
  J_31 = ;
  J_32 = ;
  time_ = ;
end

model novak_tyson_2004_version01__PPX(PPX, k_33, k_34, epsilon, time_)

  // Rate Rules:
  PPX' = epsilon * k_33 - k_34 * PPX;

  // Variable initializations:
  PPX = ;
  k_33 = ;
  k_34 = ;
  epsilon = ;
  time_ = ;
end

model novak_tyson_2004_version01__E2F(E2F, k_22, k_23_, k_23, E2FT, CycA, CycB, time_)

  // Rate Rules:
  E2F' = k_22 * (E2FT - E2F) - (k_23_ + k_23 * (CycA + CycB)) * E2F;

  // Variable initializations:
  E2F = ;
  k_22 = ;
  k_23_ = ;
  k_23 = ;
  E2FT = ;
  CycA = ;
  CycB = ;
  time_ = ;
end

model novak_tyson_2004_version01__Cdh1(Cdh1, k_3_, k_3, V_4, Cdc20, J_3, J_4, time_)

  // Rate Rules:
  Cdh1' = ((k_3_ + k_3 * Cdc20) * (1 - Cdh1)) / ((J_3 + 1) - Cdh1) - (Cdh1 * V_4) / (J_4 + Cdh1);

  // Variable initializations:
  Cdh1 = ;
  k_3_ = ;
  k_3 = ;
  V_4 = ;
  Cdc20 = ;
  J_3 = ;
  J_4 = ;
  time_ = ;
end

model novak_tyson_2004_version01__GM(GM, k_27, k_28, Rb_hypo, Rb_T, mass, time_)

  // Assignment Rules:
  H := piecewise( 0 , Rb_hypo / Rb_T > 0.8 , 1 );

  // Rate Rules:
  GM' = k_27 * mass * H - k_28 * GM;

  // Variable initializations:
  GM = ;
  k_27 = ;
  k_28 = ;
  Rb_hypo = ;
  Rb_T = ;
  mass = ;
  time_ = ;
end

model novak_tyson_2004_version01__mass(mass, mu, epsilon, GM, time_)

  // Rate Rules:
  mass' = epsilon * mu * GM;

  // Variable initializations:
  mass = 1;
  mu = ;
  epsilon = ;
  GM = ;
  time_ = ;
end

model novak_tyson_2004_version01__PP1_A(PP1_A, PP1_T, K_21, phi_E, phi_B, CycE, CycA, CycB)

  // Assignment Rules:
  PP1_A := PP1_T / (1 + K_21 * (phi_E * (CycE + CycA) + phi_B * CycB));

  // Variable initializations:
  PP1_T = 1;
  K_21 = ;
  phi_E = ;
  phi_B = ;
  CycE = ;
  CycA = ;
  CycB = ;
end

model novak_tyson_2004_version01__Rb_hypo(Rb_hypo, k_20, k_19_, k_19, Rb_T, PP1_T, PP1_A, lambda_D, lambda_E, lambda_A, lambda_B, CycE, CycA, CycB, CycD_T)

  // Assignment Rules:
  Rb_hypo := Rb_T / (1 + (k_20 * (lambda_D * CycD_T + lambda_E * CycE + lambda_A * CycA + lambda_B * CycB)) / (k_19_ * (PP1_T - PP1_A) + k_19 * PP1_A));

  // Variable initializations:
  k_20 = ;
  k_19_ = ;
  k_19 = ;
  Rb_T = 10;
  PP1_T = ;
  PP1_A = ;
  lambda_D = ;
  lambda_E = ;
  lambda_A = ;
  lambda_B = ;
  CycE = ;
  CycA = ;
  CycB = ;
  CycD_T = ;
end

model novak_tyson_2004_version01__E2FA(E2FA, E2F, E2FT, E2F_Rb)

  // Assignment Rules:
  E2FA := (E2F * (E2FT - E2F_Rb)) / E2FT;

  // Variable initializations:
  E2F = ;
  E2FT = 5;
  E2F_Rb = ;
end

model novak_tyson_2004_version01__E2F_Rb(E2F_Rb, E2FT, L, Rb_hypo)

  // Assignment Rules:
  E2F_Rb := (2 * E2FT * Rb_hypo) / (E2FT + Rb_hypo + L + root(power(E2FT + Rb_hypo + L, 2) - 4 * E2FT * Rb_hypo));

  // Variable initializations:
  E2FT = ;
  L = ;
  Rb_hypo = ;
end

model novak_tyson_2004_version01__V_2(V_2, k_2_, k_2, k_2__, Cdh1, Cdc20)

  // Assignment Rules:
  V_2 := k_2_ * (1 - Cdh1) + k_2 * Cdh1 + k_2__ * Cdc20;

  // Variable initializations:
  k_2_ = ;
  k_2 = ;
  k_2__ = ;
  Cdh1 = ;
  Cdc20 = ;
end

model novak_tyson_2004_version01__V_4(V_4, k_4, gamma_A, gamma_B, CycA, CycB)

  // Assignment Rules:
  V_4 := k_4 * (gamma_A * CycA + gamma_B * CycB);

  // Variable initializations:
  k_4 = ;
  gamma_A = ;
  gamma_B = ;
  CycA = ;
  CycB = ;
end

model novak_tyson_2004_version01__V_6(V_6, k_6_, k_6, eta_E, eta_A, eta_B, CycA, CycB, CycE)

  // Assignment Rules:
  V_6 := k_6_ + k_6 * (eta_E * CycE + eta_A * CycA + eta_B * CycB);

  // Variable initializations:
  k_6_ = ;
  k_6 = ;
  eta_E = ;
  eta_A = ;
  eta_B = ;
  CycA = ;
  CycB = ;
  CycE = ;
end

model novak_tyson_2004_version01__V_8(V_8, k_8_, k_8, psi_E, psi_B, J_8, CycE, CycA, CycB, CycE_T)

  // Assignment Rules:
  V_8 := (k_8_ * k_8 * (psi_E * (CycE + CycA) + psi_B * CycB) * 1) / (J_8 + CycE_T);

  // Variable initializations:
  k_8_ = ;
  k_8 = ;
  psi_E = ;
  psi_B = ;
  J_8 = ;
  CycE = ;
  CycA = ;
  CycB = ;
  CycE_T = ;
end

model novak_tyson_2004_version01__L(L, k_26r, k_26, k_20, lambda_D, lambda_E, lambda_A, lambda_B, CycD, CycE, CycA, CycB)

  // Assignment Rules:
  L := k_26r / k_26 + (k_20 / k_26) * (lambda_D * CycD + lambda_E * CycE + lambda_A * CycA + lambda_B * CycB);

  // Variable initializations:
  k_26r = ;
  k_26 = ;
  k_20 = ;
  lambda_D = ;
  lambda_E = ;
  lambda_A = ;
  lambda_B = ;
  CycD = ;
  CycE = ;
  CycA = ;
  CycB = ;
end

model novak_tyson_2004_version01__rate_constants(k_1_, k_1, k_2_, k_2, k_2__, k_3_, k_3, k_4, k_5, k_6_, k_6, k_7_, k_7, k_8_, k_8, k_9, k_10, k_11_, k_11, k_12, k_13, k_14, k_15, k_16, k_17_, k_17, k_18, k_19_, k_19, k_20, k_22, k_23_, k_23, k_24, k_24r, k_25, k_25r, k_26, k_26r, k_27, k_28, k_29, k_30, k_31, k_32, k_33, k_34, mu)

  // Variable initializations:
  k_1_ = 0.1;
  k_1 = 0.6;
  k_2_ = 0.05;
  k_2 = 20;
  k_2__ = 1;
  k_3_ = 7.5;
  k_3 = 140;
  k_4 = 40;
  k_5 = 20;
  k_6_ = 10;
  k_6 = 100;
  k_7_ = 0;
  k_7 = 0.6;
  k_8_ = 0.1;
  k_8 = 2;
  k_9 = 2.5;
  k_10 = 5;
  k_11_ = 0;
  k_11 = 1.5;
  k_12 = 1.5;
  k_13 = 5;
  k_14 = 2.5;
  k_15 = 0.25;
  k_16 = 0.25;
  k_17_ = 0.35;
  k_17 = 10;
  k_18 = 10;
  k_19_ = 0;
  k_19 = 20;
  k_20 = 10;
  k_22 = 1;
  k_23_ = 0.005;
  k_23 = 1;
  k_24 = 1000;
  k_24r = 10;
  k_25 = 1000;
  k_25r = 10;
  k_26 = 10;
  k_26r = 200;
  k_27 = 0.2;
  k_28 = 0.2;
  k_29 = 0.05;
  k_30 = 20;
  k_31 = 0.7;
  k_32 = 1.8;
  k_33 = 0.05;
  k_34 = 0.05;
  mu = 0.061;
end

model novak_tyson_2004_version01__dimensionless_constants(J_1, J_3, J_4, J_8, J_13, J_14, J_15, J_17, J_31, J_32, K_21, phi_E, phi_B, gamma_A, gamma_B, eta_E, eta_A, eta_B, lambda_D, lambda_E, lambda_A, lambda_B, psi_E, psi_B, epsilon)

  // Variable initializations:
  J_1 = 0.1;
  J_3 = 0.01;
  J_4 = 0.01;
  J_8 = 0.1;
  J_13 = 0.005;
  J_14 = 0.005;
  J_15 = 0.1;
  J_17 = 0.3;
  J_31 = 0.01;
  J_32 = 0.01;
  K_21 = 1;
  phi_E = 25;
  phi_B = 2;
  gamma_A = 0.3;
  gamma_B = 1;
  eta_E = 0.5;
  eta_A = 0.5;
  eta_B = 1;
  lambda_D = 3.3;
  lambda_E = 5;
  lambda_A = 3;
  lambda_B = 5;
  psi_E = 1;
  psi_B = 0.05;
  epsilon = 1;
end

model *novak_tyson_2004_version01____main()

  // Sub-modules, and any changes to those submodules:
  environment: novak_tyson_2004_version01__environment(time_);
  ERG: novak_tyson_2004_version01__ERG(ERG0, k_15, k_16, J_15, epsilon, DRG0, time_);
  DRG: novak_tyson_2004_version01__DRG(DRG0, k_17_, k_17, k_18, epsilon, ERG0, J_17, time_);
  Kip1: novak_tyson_2004_version01__Kip1(Kip10, k_5, k_24, k_24r, k_10, k_25, k_25r, k_30, V_60, V_80, epsilon, CycD0, CycD_Kip10, CycE0, CycA0, CycE_Kip10, CycA_Kip10, Cdc200, time_);
  CycA_Kip1: novak_tyson_2004_version01__CycA_Kip1(CycA_Kip10, k_25, k_25r, k_30, V_60, CycA0, Kip10, Cdc200, time_);
  CycD_Kip1: novak_tyson_2004_version01__CycD_Kip1(CycD_Kip10, k_24, k_24r, k_10, V_60, CycD0, Kip10, time_);
  CycE_Kip1: novak_tyson_2004_version01__CycE_Kip1(CycE_Kip10, k_25, k_25r, V_60, V_80, CycE0, Kip10, time_);
  CycA: novak_tyson_2004_version01__CycA(CycA0, k_29, k_30, k_25, k_25r, V_60, epsilon, E2FA0, Cdc200, Kip10, mass0, CycA_Kip10, time_);
  CycB: novak_tyson_2004_version01__CycB(CycB0, k_1_, k_1, V_20, epsilon, J_1, time_);
  CycE: novak_tyson_2004_version01__CycE(CycE0, k_7_, k_7, k_25, k_25r, V_80, V_60, epsilon, E2FA0, Kip10, CycE_Kip10, CycE_T, time_);
  CycD: novak_tyson_2004_version01__CycD(CycD0, k_9, k_24r, k_24, k_10, V_60, epsilon, DRG0, Kip10, CycD_Kip10, CycD_T, time_);
  Cdc20: novak_tyson_2004_version01__Cdc20(Cdc200, k_13, k_14, k_12, IEP0, Cdc20_T0, J_13, J_4, time_);
  Cdc20_T: novak_tyson_2004_version01__Cdc20_T(Cdc20_T0, k_11_, k_11, k_12, CycB0, epsilon, time_);
  IEP: novak_tyson_2004_version01__IEP(IEP0, k_31, k_32, CycB0, PPX0, J_31, J_32, time_);
  PPX: novak_tyson_2004_version01__PPX(PPX0, k_33, k_34, epsilon, time_);
  E2F: novak_tyson_2004_version01__E2F(E2F0, k_22, k_23_, k_23, E2FT, CycA0, CycB0, time_);
  Cdh1: novak_tyson_2004_version01__Cdh1(Cdh10, k_3_, k_3, V_40, Cdc200, J_3, J_4, time_);
  GM: novak_tyson_2004_version01__GM(GM0, k_27, k_28, Rb_hypo0, Rb_T, mass0, time_);
  mass: novak_tyson_2004_version01__mass(mass0, mu, epsilon, GM0, time_);
  PP1_A: novak_tyson_2004_version01__PP1_A(PP1_A0, PP1_T, K_21, phi_E, phi_B, CycE0, CycA0, CycB0);
  Rb_hypo: novak_tyson_2004_version01__Rb_hypo(Rb_hypo0, k_20, k_19_, k_19, Rb_T, PP1_T, PP1_A0, lambda_D, lambda_E, lambda_A, lambda_B, CycE0, CycA0, CycB0, CycD_T);
  E2FA: novak_tyson_2004_version01__E2FA(E2FA0, E2F0, E2FT, E2F_Rb0);
  E2F_Rb: novak_tyson_2004_version01__E2F_Rb(E2F_Rb0, E2FT, L0, Rb_hypo0);
  V_2: novak_tyson_2004_version01__V_2(V_20, k_2_, k_2, k_2__, Cdh10, Cdc200);
  V_4: novak_tyson_2004_version01__V_4(V_40, k_4, gamma_A, gamma_B, CycA0, CycB0);
  V_6: novak_tyson_2004_version01__V_6(V_60, k_6_, k_6, eta_E, eta_A, eta_B, CycA0, CycB0, CycE0);
  V_8: novak_tyson_2004_version01__V_8(V_80, k_8_, k_8, psi_E, psi_B, J_8, CycE0, CycA0, CycB0, CycE_T);
  L: novak_tyson_2004_version01__L(L0, k_26r, k_26, k_20, lambda_D, lambda_E, lambda_A, lambda_B, CycD0, CycE0, CycA0, CycB0);
  rate_constants: novak_tyson_2004_version01__rate_constants(k_1_, k_1, k_2_, k_2, k_2__, k_3_, k_3, k_4, k_5, k_6_, k_6, k_7_, k_7, k_8_, k_8, k_9, k_10, k_11_, k_11, k_12, k_13, k_14, k_15, k_16, k_17_, k_17, k_18, k_19_, k_19, k_20, k_22, k_23_, k_23, k_24, k_24r, k_25, k_25r, k_26, k_26r, k_27, k_28, k_29, k_30, k_31, k_32, k_33, k_34, mu);
  dimensionless_constants: novak_tyson_2004_version01__dimensionless_constants(J_1, J_3, J_4, J_8, J_13, J_14, J_15, J_17, J_31, J_32, K_21, phi_E, phi_B, gamma_A, gamma_B, eta_E, eta_A, eta_B, lambda_D, lambda_E, lambda_A, lambda_B, psi_E, psi_B, epsilon);
end