//Created by libAntimony v2.4 model fujita_2010__environment(time_) // Variable initializations: time_ = ; end model fujita_2010__NGF(NGF) // Variable initializations: NGF = 30.0; end model fujita_2010__pro_TrkA(pro_TrkA) // Variable initializations: pro_TrkA = 8.52065e0; end model fujita_2010__TrkA(TrkA, NGF_TrkA, NGF, pro_TrkA, k2_NGF_TrkA, k1_NGF_TrkA, TrkA_turnover, time_) // Rate Rules: TrkA' = (k2_NGF_TrkA * NGF_TrkA + TrkA_turnover * (pro_TrkA - TrkA)) - k1_NGF_TrkA * NGF * TrkA; // Variable initializations: TrkA = 8.52065e0; NGF_TrkA = ; NGF = ; pro_TrkA = ; k2_NGF_TrkA = ; k1_NGF_TrkA = ; TrkA_turnover = ; time_ = ; end model fujita_2010__NGF_TrkA(NGF_TrkA, TrkA, NGF, k2_NGF_TrkA, k1_NGF_TrkA, k1_TrkA_phosphorylation, time_) // Rate Rules: NGF_TrkA' = k1_NGF_TrkA * NGF * TrkA - (k2_NGF_TrkA * NGF_TrkA + k1_TrkA_phosphorylation * NGF_TrkA); // Variable initializations: NGF_TrkA = 0.0; TrkA = ; NGF = ; k2_NGF_TrkA = ; k1_NGF_TrkA = ; k1_TrkA_phosphorylation = ; time_ = ; end model fujita_2010__pTrkA(pTrkA, NGF_TrkA, pTrkA_Akt, Akt, k1_pTrkA_degradation, k1_Akt_phosphorylation, k1_TrkA_phosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, time_) // Rate Rules: pTrkA' = (k1_TrkA_phosphorylation * NGF_TrkA + k1_Akt_phosphorylation * pTrkA_Akt + k2_pTrkA_Akt * pTrkA_Akt) - (k1_pTrkA_degradation * pTrkA + k1_pTrkA_Akt * pTrkA * Akt); // Variable initializations: pTrkA = 0.0; NGF_TrkA = ; pTrkA_Akt = ; Akt = ; k1_pTrkA_degradation = ; k1_Akt_phosphorylation = ; k1_TrkA_phosphorylation = ; k1_pTrkA_Akt = ; k2_pTrkA_Akt = ; time_ = ; end model fujita_2010__pTrkA_Akt(pTrkA_Akt, pTrkA, Akt, k1_Akt_phosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, time_) // Rate Rules: pTrkA_Akt' = k1_pTrkA_Akt * pTrkA * Akt - (k2_pTrkA_Akt * pTrkA_Akt + k1_Akt_phosphorylation * pTrkA_Akt); // Variable initializations: pTrkA_Akt = 0.0; pTrkA = ; Akt = ; k1_Akt_phosphorylation = ; k1_pTrkA_Akt = ; k2_pTrkA_Akt = ; time_ = ; end model fujita_2010__Akt(Akt, pTrkA, pTrkA_Akt, pAkt, k1_pAkt_dephosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, time_) // Rate Rules: Akt' = (k2_pTrkA_Akt * pTrkA_Akt + k1_pAkt_dephosphorylation * pAkt) - k1_pTrkA_Akt * pTrkA * Akt; // Variable initializations: Akt = 1.15595e0; pTrkA = ; pTrkA_Akt = ; pAkt = ; k1_pAkt_dephosphorylation = ; k1_pTrkA_Akt = ; k2_pTrkA_Akt = ; time_ = ; end model fujita_2010__pAkt(pAkt, S6, pTrkA_Akt, pAkt_S6, k1_Akt_phosphorylation, k1_pAkt_S6, k2_pAkt_S6, k1_S6_phosphorylation, k1_pAkt_dephosphorylation, time_) // Rate Rules: pAkt' = (k1_Akt_phosphorylation * pTrkA_Akt + k2_pAkt_S6 * pAkt_S6 + k1_S6_phosphorylation * pAkt_S6) - (k1_pAkt_dephosphorylation * pAkt + k1_pAkt_S6 * pAkt * S6); // Variable initializations: pAkt = 0.0; S6 = ; pTrkA_Akt = ; pAkt_S6 = ; k1_Akt_phosphorylation = ; k1_pAkt_S6 = ; k2_pAkt_S6 = ; k1_S6_phosphorylation = ; k1_pAkt_dephosphorylation = ; time_ = ; end model fujita_2010__pAkt_S6(pAkt_S6, S6, pAkt, k1_pAkt_S6, k2_pAkt_S6, k1_S6_phosphorylation, time_) // Rate Rules: pAkt_S6' = k1_pAkt_S6 * pAkt * S6 - (k2_pAkt_S6 * pAkt_S6 + k1_S6_phosphorylation * pAkt_S6); // Variable initializations: pAkt_S6 = 0.0; S6 = ; pAkt = ; k1_pAkt_S6 = ; k2_pAkt_S6 = ; k1_S6_phosphorylation = ; time_ = ; end model fujita_2010__S6(S6, pAkt_S6, pS6, pAkt, k1_pAkt_S6, k2_pAkt_S6, k1_pS6_dephosphorylation, time_) // Rate Rules: S6' = (k2_pAkt_S6 * pAkt_S6 + k1_pS6_dephosphorylation * pS6) - k1_pAkt_S6 * pAkt * S6; // Variable initializations: S6 = 3.55234e0; pAkt_S6 = ; pS6 = ; pAkt = ; k1_pAkt_S6 = ; k2_pAkt_S6 = ; k1_pS6_dephosphorylation = ; time_ = ; end model fujita_2010__pS6(pS6, pAkt_S6, k1_S6_phosphorylation, k1_pS6_dephosphorylation, time_) // Rate Rules: pS6' = k1_S6_phosphorylation * pAkt_S6 - k1_pS6_dephosphorylation * pS6; // Variable initializations: pS6 = 0.0; pAkt_S6 = ; k1_S6_phosphorylation = ; k1_pS6_dephosphorylation = ; time_ = ; end model fujita_2010__pTrkA_total(pTrkA, pTrkA_Akt) // Assignment Rules: pTrkA_total := (pTrkA + pTrkA_Akt) * pTrkA_scalefactor; // Variable initializations: pTrkA_scalefactor = 8.48783e-1; pTrkA = ; pTrkA_Akt = ; end model fujita_2010__pAkt_total(pAkt, pAkt_S6) // Assignment Rules: pAkt_total := (pAkt + pAkt_S6) * pAkt_scalefactor; // Variable initializations: pAkt_scalefactor = 2.42381e0; pAkt = ; pAkt_S6 = ; end model fujita_2010__pS6_total(pS6) // Assignment Rules: pS6_total := pS6 * pS6_scalefactor; // Variable initializations: pS6_scalefactor = 5.25843e-1; pS6 = ; end model fujita_2010__model_parameters(k2_NGF_TrkA, k1_NGF_TrkA, TrkA_turnover, k1_S6_phosphorylation, k1_pS6_dephosphorylation, k1_pAkt_S6, k2_pAkt_S6, k1_Akt_phosphorylation, k1_pAkt_dephosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, k1_pTrkA_degradation, k1_TrkA_phosphorylation) // Variable initializations: k2_NGF_TrkA = 1.33747e-2; k1_NGF_TrkA = 2.69408e-3; TrkA_turnover = 0.0011032440769796; k1_S6_phosphorylation = 5.65150e-3; k1_pS6_dephosphorylation = 2.93167e-4; k1_pAkt_S6 = 6.83666e1; k2_pAkt_S6 = 5.23519e-00; k1_Akt_phosphorylation = 2.02517e-2; k1_pAkt_dephosphorylation = 1.28135e0; k1_pTrkA_Akt = 8.82701e-2; k2_pTrkA_Akt = 1.47518e-10; k1_pTrkA_degradation = 6.8084e-2; k1_TrkA_phosphorylation = 8.33178e-3; end model *fujita_2010____main() // Sub-modules, and any changes to those submodules: environment: fujita_2010__environment(time_); NGF: fujita_2010__NGF(NGF0); pro_TrkA: fujita_2010__pro_TrkA(pro_TrkA0); TrkA: fujita_2010__TrkA(TrkA0, NGF_TrkA0, NGF0, pro_TrkA0, k2_NGF_TrkA, k1_NGF_TrkA, TrkA_turnover, time_); NGF_TrkA: fujita_2010__NGF_TrkA(NGF_TrkA0, TrkA0, NGF0, k2_NGF_TrkA, k1_NGF_TrkA, k1_TrkA_phosphorylation, time_); pTrkA: fujita_2010__pTrkA(pTrkA0, NGF_TrkA0, pTrkA_Akt0, Akt0, k1_pTrkA_degradation, k1_Akt_phosphorylation, k1_TrkA_phosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, time_); pTrkA_Akt: fujita_2010__pTrkA_Akt(pTrkA_Akt0, pTrkA0, Akt0, k1_Akt_phosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, time_); Akt: fujita_2010__Akt(Akt0, pTrkA0, pTrkA_Akt0, pAkt0, k1_pAkt_dephosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, time_); pAkt: fujita_2010__pAkt(pAkt0, S60, pTrkA_Akt0, pAkt_S60, k1_Akt_phosphorylation, k1_pAkt_S6, k2_pAkt_S6, k1_S6_phosphorylation, k1_pAkt_dephosphorylation, time_); pAkt_S6: fujita_2010__pAkt_S6(pAkt_S60, S60, pAkt0, k1_pAkt_S6, k2_pAkt_S6, k1_S6_phosphorylation, time_); S6: fujita_2010__S6(S60, pAkt_S60, pS60, pAkt0, k1_pAkt_S6, k2_pAkt_S6, k1_pS6_dephosphorylation, time_); pS6: fujita_2010__pS6(pS60, pAkt_S60, k1_S6_phosphorylation, k1_pS6_dephosphorylation, time_); pTrkA_total: fujita_2010__pTrkA_total(pTrkA0, pTrkA_Akt0); pAkt_total: fujita_2010__pAkt_total(pAkt0, pAkt_S60); pS6_total: fujita_2010__pS6_total(pS60); model_parameters: fujita_2010__model_parameters(k2_NGF_TrkA, k1_NGF_TrkA, TrkA_turnover, k1_S6_phosphorylation, k1_pS6_dephosphorylation, k1_pAkt_S6, k2_pAkt_S6, k1_Akt_phosphorylation, k1_pAkt_dephosphorylation, k1_pTrkA_Akt, k2_pTrkA_Akt, k1_pTrkA_degradation, k1_TrkA_phosphorylation); end