//Created by libAntimony v2.4 model chen_2000__environment(time_) // Variable initializations: time_ = ; end model chen_2000__Cln2(Cln2, mass, SBF, time_) // Rate Rules: Cln2' = mass * (ks_n2 + ks_n2_ * SBF) - kd_n2 * Cln2; // Variable initializations: Cln2 = 0.0078; ks_n2 = 0; ks_n2_ = 0.05; kd_n2 = 0.1; mass = ; SBF = ; time_ = ; end model chen_2000__Clb2_T(Clb2_T, Hct1_T, Vd_b2, mass, Mcm1, Hct1, Cdc20, time_) // Assignment Rules: Vd_b2 := kd_b2 * (Hct1_T - Hct1) + kd_b2_ * Hct1 + kd_b2__ * Cdc20; // Rate Rules: Clb2_T' = mass * (ks_b2 + ks_b2_ * Mcm1) - Vd_b2 * Clb2_T; // Variable initializations: Clb2_T = 0.2342; Hct1_T = 1; ks_b2 = 0.002; ks_b2_ = 0.05; kd_b2 = 0.01; kd_b2_ = 2; kd_b2__ = 0.05; mass = ; Mcm1 = ; Hct1 = ; Cdc20 = ; time_ = ; end model chen_2000__Clb2(Clb2, Clb2_Sic1, Clb2_T) // Assignment Rules: Clb2 := Clb2_T - Clb2_Sic1; // Variable initializations: Clb2_Sic1 = ; Clb2_T = ; end model chen_2000__Clb5(Clb5, Clb5_Sic1, Clb5_T) // Assignment Rules: Clb5 := Clb5_T - Clb5_Sic1; // Variable initializations: Clb5_Sic1 = ; Clb5_T = ; end model chen_2000__Sic1(Sic1, Clb2_Sic1, Clb5_Sic1, Sic1_T) // Assignment Rules: Sic1 := Sic1_T - (Clb2_Sic1 + Clb5_Sic1); // Variable initializations: Clb2_Sic1 = ; Clb5_Sic1 = ; Sic1_T = ; end model chen_2000__Clb5_T(Clb5_T, Vd_b5, mass, MBF, Cdc20, time_) // Assignment Rules: Vd_b5 := kd_b5 + kd_b5_ * Cdc20; // Rate Rules: Clb5_T' = mass * (ks_b5 + ks_b5_ * MBF) - Vd_b5 * Clb5_T; // Variable initializations: Clb5_T = 0.0614; ks_b5 = 0.006; ks_b5_ = 0.02; kd_b5 = 0.1; kd_b5_ = 0.25; mass = ; MBF = ; Cdc20 = ; time_ = ; end model chen_2000__Bck2(Bck2, mass) // Assignment Rules: Bck2 := Bck2_0 * mass; // Variable initializations: Bck2_0 = 0.0027; mass = ; end model chen_2000__Cln3(Cln3, mass) // Assignment Rules: Cln3 := (Cln3_max * Dn3 * mass) / (Jn3 + Dn3 * mass); // Variable initializations: Jn3 = 6; Dn3 = 1; Cln3_max = 0.02; mass = ; end model chen_2000__Sic1_T(Sic1_T, kd1_c1, Jd2_c1, Vd2_c1, Swi5, time_) // Rate Rules: Sic1_T' = (ks_c1 + ks_c1_ * Swi5) - Sic1_T * (kd1_c1 + Vd2_c1 / (Jd2_c1 + Sic1_T)); // Variable initializations: Sic1_T = 0.1231; ks_c1 = 0.02; ks_c1_ = 0.1; kd1_c1 = ; Jd2_c1 = ; Vd2_c1 = ; Swi5 = ; time_ = ; end model chen_2000__Clb2_Sic1(Clb2_Sic1, Vd_b2, kd1_c1, Jd2_c1, Vd2_c1, Sic1_T, Sic1, Clb2, time_) // Rate Rules: Clb2_Sic1' = kas_b2 * Clb2 * Sic1 - Clb2_Sic1 * (kdi_b2 + Vd_b2 + kd1_c1 + Vd2_c1 / (Jd2_c1 + Sic1_T)); // Variable initializations: Clb2_Sic1 = 0.079; kas_b2 = 50; kdi_b2 = 0.05; Vd_b2 = ; kd1_c1 = ; Jd2_c1 = ; Vd2_c1 = ; Sic1_T = ; Sic1 = ; Clb2 = ; time_ = ; end model chen_2000__Clb5_Sic1(Clb5_Sic1, Vd_b5, kd1_c1, Jd2_c1, Vd2_c1, Sic1_T, Sic1, Clb5, time_) // Rate Rules: Clb5_Sic1' = kas_b5 * Clb5 * Sic1 - Clb5_Sic1 * (kdi_b5 + Vd_b5 + kd1_c1 + Vd2_c1 / (Jd2_c1 + Sic1_T)); // Variable initializations: Clb5_Sic1 = 0.0207; kas_b5 = 50; kdi_b5 = 0.05; Vd_b5 = ; kd1_c1 = ; Jd2_c1 = ; Vd2_c1 = ; Sic1_T = ; Sic1 = ; Clb5 = ; time_ = ; end model chen_2000__Vd2_c1(Vd2_c1, Cln3, Bck2, Cln2, Clb5, Clb2) // Assignment Rules: Vd2_c1 := kd2_c1 * (epsilonc1_n3 * Cln3 + epsilonc1_k2 * Bck2 + Cln2 + epsilonc1_b5 * Clb5 + epsilonc1_b2 * Clb2); // Variable initializations: kd2_c1 = 0.3; epsilonc1_n3 = 20; epsilonc1_k2 = 2; epsilonc1_b5 = 1; epsilonc1_b2 = 0.067; Cln3 = ; Bck2 = ; Cln2 = ; Clb5 = ; Clb2 = ; end model chen_2000__Cdc20_T(Cdc20_T, kd_20, Clb2, time_) // Rate Rules: Cdc20_T' = (ks_20 + ks_20_ * Clb2) - kd_20 * Cdc20_T; // Variable initializations: Cdc20_T = 0.8332; ks_20 = 0.005; ks_20_ = 0.06; kd_20 = ; Clb2 = ; time_ = ; end model chen_2000__Cdc20(Cdc20, Vi_20, kd_20, Cdc20_T, time_, ORI, SPN) // Assignment Rules: Vi_20 := piecewise( ki_20_ , geq(ORI, 1) , ki_20 , geq(SPN, 1) , 0.1 ); // Rate Rules: Cdc20' = ka_20 * (Cdc20_T - Cdc20) - Cdc20 * (Vi_20 + kd_20); // Variable initializations: Cdc20 = 0.6848; ka_20 = 1; ki_20 = 0.1; ki_20_ = 10; kd_20 = ; Cdc20_T = ; time_ = ; ORI = ; SPN = ; end model chen_2000__Hct1(Hct1, Cdc20, Hct1_T, Cln3, Clb5, Cln2, Clb2, time_) // Assignment Rules: Vi_t1 := ki_t1 + ki_t1_ * (Cln3 + epsiloni_t1_n2 * Cln2 + epsiloni_t1_b5 * Clb5 + epsiloni_t1_b2 * Clb2); // Rate Rules: Hct1' = ((ka_t1 + ka_t1_ * Cdc20) * (Hct1_T - Hct1)) / ((Ja_t1 + Hct1_T) - Hct1) - (Vi_t1 * Hct1) / (Ji_t1 + Hct1); // Variable initializations: Hct1 = 0.9946; ka_t1 = 0.04; ka_t1_ = 2; ki_t1 = 0; ki_t1_ = 0.64; Ji_t1 = 0.05; Ja_t1 = 0.05; epsiloni_t1_n2 = 1; epsiloni_t1_b5 = 0.5; epsiloni_t1_b2 = 1; Cdc20 = ; Hct1_T = ; Cln3 = ; Clb5 = ; Cln2 = ; Clb2 = ; time_ = ; end model chen_2000__mass(mass, Clb2, time_) // Rate Rules: mass' = mu * mass; // Variable initializations: mass = 0.6608; mu = 0.005776; Clb2 = ; time_ = ; end model chen_2000__ORI(ORI, Clb5, Clb2, time_) // Rate Rules: ORI' = ks_ori * (Clb5 + epsilonori_b2 * Clb2) - kd_ori * ORI; // Variable initializations: ORI = 0; ks_ori = 2; kd_ori = 0.06; epsilonori_b2 = 0.4; Clb5 = ; Clb2 = ; time_ = ; end model chen_2000__BUD(Clb5, Cln2, Clb2, Cln3, time_) // Rate Rules: BUD' = ks_bud * (Cln2 + Cln3 + epsilonbud_b5 * Clb5) - kd_bud * BUD; // Variable initializations: BUD = 0; ks_bud = 0.3; kd_bud = 0.06; epsilonbud_b5 = 1; Clb5 = ; Cln2 = ; Clb2 = ; Cln3 = ; time_ = ; end model chen_2000__SPN(SPN, Clb2, time_) // Rate Rules: SPN' = (ks_spn * Clb2) / (J_spn + Clb2) - kd_spn * SPN; // Variable initializations: SPN = 0; ks_spn = 0.08; kd_spn = 0.06; J_spn = 0.2; Clb2 = ; time_ = ; end model chen_2000__SBF(SBF, Bck2, Cln3, Clb5, Cln2, Clb2) // Assignment Rules: SBF := (2 * Va_sbf * Ji_sbf) / (((ki_sbf + ki_sbf_ * Clb2 + Va_sbf * Ji_sbf + (ki_sbf + ki_sbf_ * Clb2) * Ja_sbf) - Va_sbf) + root(power((ki_sbf + ki_sbf_ * Clb2 + Va_sbf * Ji_sbf + (ki_sbf + ki_sbf_ * Clb2) * Ja_sbf) - Va_sbf, 2) - 4 * Va_sbf * Ji_sbf * ((ki_sbf + ki_sbf_ * Clb2) - Va_sbf))); Va_sbf := ka_sbf * (Cln2 + epsilonsbf_n3 * (Cln3 + Bck2) + epsilonsbf_b5 * Clb5); // Variable initializations: ka_sbf = 1; ki_sbf = 0.5; ki_sbf_ = 6; Ji_sbf = 0.01; Ja_sbf = 0.01; epsilonsbf_n3 = 75; epsilonsbf_b5 = 0.5; Bck2 = ; Cln3 = ; Clb5 = ; Cln2 = ; Clb2 = ; end model chen_2000__MBF(MBF, SBF) // Assignment Rules: MBF := SBF; // Variable initializations: SBF = ; end model chen_2000__Mcm1(Mcm1, Clb2) // Assignment Rules: Mcm1 := (2 * ka_mcm * Clb2 * Ji_mcm) / (((ki_mcm + ka_mcm * Clb2 * Ji_mcm + ki_mcm * Ja_mcm) - ka_mcm * Clb2) + root(power((ki_mcm + ka_mcm * Clb2 * Ji_mcm + ki_mcm * Ja_mcm) - ka_mcm * Clb2, 2) - 4 * (ki_mcm - ka_mcm * Clb2) * ka_mcm * Clb2 * Ji_mcm)); // Variable initializations: ka_mcm = 1; ki_mcm = 0.15; Ji_mcm = 1; Ja_mcm = 1; Clb2 = ; end model chen_2000__Swi5(Swi5, Cdc20, Clb2) // Assignment Rules: Swi5 := (2 * ka_swi * Cdc20 * Ji_swi) / (((ki_swi + ki_swi_ * Clb2 + ka_swi * Cdc20 * Ji_swi + (ki_swi + ki_swi_ * Clb2) * Ja_swi) - ka_swi * Cdc20) + root(power((ki_swi + ki_swi_ * Clb2 + ka_swi * Cdc20 * Ji_swi + (ki_swi + ki_swi_ * Clb2) * Ja_swi) - ka_swi * Cdc20, 2) - 4 * ((ki_swi + ki_swi_ * Clb2) - ka_swi * Cdc20) * ka_swi * Cdc20 * Ji_swi)); // Variable initializations: ka_swi = 1; ki_swi = 0.3; ki_swi_ = 0.2; Ji_swi = 0.1; Ja_swi = 0.1; Cdc20 = ; Clb2 = ; end model chen_2000__parameters(kd1_c1, kd_20, Jd2_c1) // Variable initializations: kd1_c1 = 0.01; kd_20 = 0.08; Jd2_c1 = 0.05; end model *chen_2000____main() // Sub-modules, and any changes to those submodules: environment: chen_2000__environment(time_); Cln2: chen_2000__Cln2(Cln20, mass0, SBF0, time_); Clb2_T: chen_2000__Clb2_T(Clb2_T0, Hct1_T, Vd_b2, mass0, Mcm10, Hct10, Cdc200, time_); Clb2: chen_2000__Clb2(Clb20, Clb2_Sic10, Clb2_T0); Clb5: chen_2000__Clb5(Clb50, Clb5_Sic10, Clb5_T0); Sic1: chen_2000__Sic1(Sic10, Clb2_Sic10, Clb5_Sic10, Sic1_T0); Clb5_T: chen_2000__Clb5_T(Clb5_T0, Vd_b5, mass0, MBF0, Cdc200, time_); Bck2: chen_2000__Bck2(Bck20, mass0); Cln3: chen_2000__Cln3(Cln30, mass0); Sic1_T: chen_2000__Sic1_T(Sic1_T0, kd1_c1, Jd2_c1, Vd2_c10, Swi50, time_); Clb2_Sic1: chen_2000__Clb2_Sic1(Clb2_Sic10, Vd_b2, kd1_c1, Jd2_c1, Vd2_c10, Sic1_T0, Sic10, Clb20, time_); Clb5_Sic1: chen_2000__Clb5_Sic1(Clb5_Sic10, Vd_b5, kd1_c1, Jd2_c1, Vd2_c10, Sic1_T0, Sic10, Clb50, time_); Vd2_c1: chen_2000__Vd2_c1(Vd2_c10, Cln30, Bck20, Cln20, Clb50, Clb20); Cdc20_T: chen_2000__Cdc20_T(Cdc20_T0, kd_20, Clb20, time_); Cdc20: chen_2000__Cdc20(Cdc200, Vi_20, kd_20, Cdc20_T0, time_, ORI0, SPN0); Hct1: chen_2000__Hct1(Hct10, Cdc200, Hct1_T, Cln30, Clb50, Cln20, Clb20, time_); mass: chen_2000__mass(mass0, Clb20, time_); ORI: chen_2000__ORI(ORI0, Clb50, Clb20, time_); BUD: chen_2000__BUD(Clb50, Cln20, Clb20, Cln30, time_); SPN: chen_2000__SPN(SPN0, Clb20, time_); SBF: chen_2000__SBF(SBF0, Bck20, Cln30, Clb50, Cln20, Clb20); MBF: chen_2000__MBF(MBF0, SBF0); Mcm1: chen_2000__Mcm1(Mcm10, Clb20); Swi5: chen_2000__Swi5(Swi50, Cdc200, Clb20); parameters: chen_2000__parameters(kd1_c1, kd_20, Jd2_c1); end