//Created by libAntimony v2.4 model goldbeter_model_2008__environment(time_) // Variable initializations: time_ = ; end model goldbeter_model_2008__N(N, kc, KIF, F, epsilon, j, time_) // Rate Rules: N' = epsilon * (vsN - (vdN * (N / (KdN + N)) + kc * N * (power(KIF, j) / (power(KIF, j) + power(F, j))))); // Variable initializations: N = 0.5; KdN = 1.4; vsN = 0.23; vdN = 2.82; kc = ; KIF = ; F = ; epsilon = ; j = ; time_ = ; end model goldbeter_model_2008__Na(Na, Vtr, kc, N, Nan_, KIF, F, epsilon, j, time_) // Assignment Rules: Vtr := kt1 * Na - kt2 * Nan_; // Rate Rules: Na' = epsilon * (kc * N * (power(KIF, j) / (power(KIF, j) + power(F, j))) - (VdNa * (Na / (KdNa + Na)) + Vtr)); // Variable initializations: Na = 0.2; KdNa = 0.001; VdNa = 0.01; kt1 = 0.1; kt2 = 0.1; kc = ; N = ; Nan_ = ; KIF = ; F = ; epsilon = ; j = ; time_ = ; end model goldbeter_model_2008__Nan(Nan_, epsilon, Vtr, time_) // Rate Rules: Nan_' = epsilon * (Vtr - VdNan * (Nan_ / (KdNan + Nan_))); // Variable initializations: Nan_ = 0.0; KdNan = 0.001; VdNan = 0.1; epsilon = ; Vtr = ; time_ = ; end model goldbeter_model_2008__MF(MF, Nan_, epsilon, p, time_) // Rate Rules: MF' = epsilon * (vsF * (power(Nan_, p) / (power(KA, p) + power(Nan_, p))) - vmF * (MF / (KdMF + MF))); // Variable initializations: MF = 0.1; KdMF = 0.768; vsF = 3.0; vmF = 1.92; KA = 0.05; Nan_ = ; epsilon = ; p = ; time_ = ; end model goldbeter_model_2008__F(F, MF, epsilon, time_) // Rate Rules: F' = epsilon * (ksF * MF - vdF * (F / (KdF + F))); // Variable initializations: F = 0.001; KdF = 0.37; vdF = 0.39; ksF = 0.3; MF = ; epsilon = ; time_ = ; end model goldbeter_model_2008__K(K, V1, theta, time_) // Rate Rules: K' = theta * V1; // Variable initializations: K = 3.0; V1 = ; theta = ; time_ = ; end model goldbeter_model_2008__B(B, VK, VP, V2, Kt, AK, theta, time_) // Rate Rules: B' = theta * ((vsB + VP + V2) - (VK * (AK / Kt) + kd1 * B)); // Variable initializations: B = 0.1; kd1 = 0.0; vsB = 0.087; VK = ; VP = ; V2 = ; Kt = ; AK = ; theta = ; time_ = ; end model goldbeter_model_2008__Bp(Bp, VK, VP, Kt, AK, theta, time_) // Rate Rules: Bp' = theta * (VK * (AK / Kt) - (VP + kd2 * Bp)); // Variable initializations: Bp = 0.1; kd2 = 7.062; VK = ; VP = ; Kt = ; AK = ; theta = ; time_ = ; end model goldbeter_model_2008__BN(BN, V2, theta, time_) // Rate Rules: BN' = -(theta * V2); // Variable initializations: BN = 0.001; V2 = ; theta = ; time_ = ; end model goldbeter_model_2008__MAx(MAx, BN, theta, time_) // Rate Rules: MAx' = theta * ((v0 + vMB * (power(BN, n) / (power(KaB, n) + power(BN, n)))) - vmd * (MAx / (Kmd + MAx))); // Variable initializations: MAx = 0.1; v0 = 0.06; vMB = 1.64; vmd = 0.8; KaB = 0.7; Kmd = 0.48; n = 2.0; BN = ; theta = ; time_ = ; end model goldbeter_model_2008__A(A, V1, MAx, theta, time_) // Rate Rules: A' = theta * ((ksAx * MAx + V1) - vdAx * (A / (KdAx + A))); // Variable initializations: A = 0.1; ksAx = 0.02; vdAx = 0.6; KdAx = 0.63; V1 = ; MAx = ; theta = ; time_ = ; end model goldbeter_model_2008__Wnt_parameters(AK, V1, V2, VK, VP, Kt, K, A, B, Bp, BN) // Assignment Rules: AK := Kt - K; V1 := d1 * AK - a1 * A * K; V2 := kt4 * BN - kt3 * B; VK := VMK * (KID / (KID + D)) * (B / (K1 + B)); VP := VMP * (Bp / (K2 + Bp)); // Variable initializations: Kt = 3.0; d1 = 0.1; a1 = 1.8; K1 = 0.28; K2 = 0.03; D = 2.0; KID = 0.5; kt3 = 0.7; kt4 = 1.5; VMK = 5.08; VMP = 1.0; K = ; A = ; B = ; Bp = ; BN = ; end model goldbeter_model_2008__Rasa(Rasa, VaRas, VdRas, eta, time_) // Rate Rules: Rasa' = eta * (VaRas - VdRas); // Variable initializations: Rasa = 0.5; VaRas = ; VdRas = ; eta = ; time_ = ; end model goldbeter_model_2008__ERKa(ERKa, VaErk, VdErk, eta, time_) // Rate Rules: ERKa' = eta * (VaErk - VdErk); // Variable initializations: ERKa = 0.2; VaErk = ; VdErk = ; eta = ; time_ = ; end model goldbeter_model_2008__Xa(Xa, VaX, VdX, eta, time_) // Rate Rules: Xa' = eta * (VaX - VdX); // Variable initializations: Xa = 0.1; VaX = ; VdX = ; eta = ; time_ = ; end model goldbeter_model_2008__MDusp(MDusp, VsMDusp, VdMDusp, eta, time_) // Rate Rules: MDusp' = eta * (VsMDusp - VdMDusp); // Variable initializations: MDusp = 0.1; VsMDusp = ; VdMDusp = ; eta = ; time_ = ; end model goldbeter_model_2008__Dusp(Dusp, MDusp, eta, time_) // Rate Rules: Dusp' = eta * (ksDusp * MDusp - vdDusp * (Dusp / (KdDusp + Dusp))); // Variable initializations: Dusp = 0.1; ksDusp = 0.5; vdDusp = 2.0; KdDusp = 0.5; MDusp = ; eta = ; time_ = ; end model goldbeter_model_2008__FGF_parameters(VaRas, VdRas, VaErk, VdErk, VaX, VdX, VsMDusp, VdMDusp, Rasa, ERKa, Xa, Dusp, MDusp) // Assignment Rules: VaRas := VMaRas * (power(Fgf, r) / (power(KaFgf, r) + power(Fgf, r))) * (Rasi / (KaRas + Rasi)); VdRas := VMdRas * (Rasa / (KdRas + Rasa)); VaErk := VMaErk * (Rasa / Rast) * (ERKi / (KaErk + ERKi)); VdErk := kcDusp * Dusp * (ERKa / (KdErk + ERKa)); VaX := VMaX * (ERKa / ERKt) * (Xi / (KaX + Xi)); VdX := VMdX * (Xa / (KdX + Xa)); VsMDusp := VMsMDusp * (power(Xa, q) / (power(KaMDusp, q) + power(Xa, q))); VdMDusp := VMdMDusp * (MDusp / (KdMDusp + MDusp)); Rasi := Rast - Rasa; ERKi := ERKt - ERKa; Xi := Xt - Xa; // Variable initializations: Rast = 2.0; ERKt = 2.0; Xt = 2.0; kcDusp = 1.35; VMaRas = 4.968; VMdRas = 0.41; VMaErk = 3.30; VMaX = 1.6; VMdX = 0.5; VMsMDusp = 0.9; VMdMDusp = 0.5; Fgf = 1.0; KaFgf = 0.5; KaRas = 0.103; KdRas = 0.1; KdErk = 0.05; KaErk = 0.05; KaX = 0.05; KdX = 0.05; KaMDusp = 0.5; KdMDusp = 0.5; q = 2.0; r = 2.0; Rasa = ; ERKa = ; Xa = ; Dusp = ; MDusp = ; end model goldbeter_model_2008__model_parameters(kc, KIF, j, p, epsilon, theta, eta) // Variable initializations: kc = 3.45; KIF = 0.5; j = 2.0; p = 2.0; epsilon = 0.3; theta = 1.5; eta = 0.3; end model *goldbeter_model_2008____main() // Sub-modules, and any changes to those submodules: environment: goldbeter_model_2008__environment(time_); N: goldbeter_model_2008__N(N0, kc, KIF, F0, epsilon, j, time_); Na: goldbeter_model_2008__Na(Na0, Vtr, kc, N0, Nan_0, KIF, F0, epsilon, j, time_); Nan_: goldbeter_model_2008__Nan(Nan_0, epsilon, Vtr, time_); MF: goldbeter_model_2008__MF(MF0, Nan_0, epsilon, p, time_); F: goldbeter_model_2008__F(F0, MF0, epsilon, time_); K: goldbeter_model_2008__K(K0, V1, theta, time_); B: goldbeter_model_2008__B(B0, VK, VP, V2, Kt, AK, theta, time_); Bp: goldbeter_model_2008__Bp(Bp0, VK, VP, Kt, AK, theta, time_); BN: goldbeter_model_2008__BN(BN0, V2, theta, time_); MAx: goldbeter_model_2008__MAx(MAx0, BN0, theta, time_); A: goldbeter_model_2008__A(A0, V1, MAx0, theta, time_); Wnt_parameters: goldbeter_model_2008__Wnt_parameters(AK, V1, V2, VK, VP, Kt, K0, A0, B0, Bp0, BN0); Rasa: goldbeter_model_2008__Rasa(Rasa0, VaRas, VdRas, eta, time_); ERKa: goldbeter_model_2008__ERKa(ERKa0, VaErk, VdErk, eta, time_); Xa: goldbeter_model_2008__Xa(Xa0, VaX, VdX, eta, time_); MDusp: goldbeter_model_2008__MDusp(MDusp0, VsMDusp, VdMDusp, eta, time_); Dusp: goldbeter_model_2008__Dusp(Dusp0, MDusp0, eta, time_); FGF_parameters: goldbeter_model_2008__FGF_parameters(VaRas, VdRas, VaErk, VdErk, VaX, VdX, VsMDusp, VdMDusp, Rasa0, ERKa0, Xa0, Dusp0, MDusp0); model_parameters: goldbeter_model_2008__model_parameters(kc, KIF, j, p, epsilon, theta, eta); end