//Created by libAntimony v2.4
model ciliberto_2003__environment(time_)

  // Variable initializations:
  time_ = ;
end

model ciliberto_2003__Clb2(Clb2, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, M, Mcm_a, Cdh1_a, Cdc20_a, Sic1, PClb2, Trim, Cln, time_)

  // Rate Rules:
  Clb2' = ((ks_clb * (epsilon + Mcm_a) * M) / (1 + M / Jm) + kmih * PClb2 + kdiss * Trim + (kd_sic + kd_sic_1 * Cln + kd_sic_2 * Clb2) * Trim) - ((kd_clb_1 + kd_clb_2 * Cdh1_a + kd_clb_3 * Cdc20_a) * Clb2 + kswe * Clb2 + kass * Sic1 * Clb2);

  // Variable initializations:
  Clb2 = 0.184;
  epsilon = 0.5;
  Jm = 10;
  ks_clb = 0.015;
  kd_clb_1 = ;
  kd_clb_2 = ;
  kd_clb_3 = ;
  kswe = ;
  kmih = ;
  kass = ;
  kdiss = ;
  kd_sic = ;
  kd_sic_1 = ;
  kd_sic_2 = ;
  M = ;
  Mcm_a = ;
  Cdh1_a = ;
  Cdc20_a = ;
  Sic1 = ;
  PClb2 = ;
  Trim = ;
  Cln = ;
  time_ = ;
end

model ciliberto_2003__PClb2(PClb2, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a, Cdc20_a, Sic1, Clb2, PTrim, Cln, time_)

  // Rate Rules:
  PClb2' = (kswe * Clb2 + kdiss * PTrim + (kd_sic + kd_sic_1 * Cln + kd_sic_2 * Clb2) * PTrim) - ((kd_clb_1 + kd_clb_2 * Cdh1_a + kd_clb_3 * Cdc20_a) * PClb2 + kmih * PClb2 + kass * Sic1 * PClb2);

  // Variable initializations:
  PClb2 = 0;
  kd_clb_1 = ;
  kd_clb_2 = ;
  kd_clb_3 = ;
  kswe = ;
  kmih = ;
  kass = ;
  kdiss = ;
  kd_sic = ;
  kd_sic_1 = ;
  kd_sic_2 = ;
  Cdh1_a = ;
  Cdc20_a = ;
  Sic1 = ;
  Clb2 = ;
  PTrim = ;
  Cln = ;
  time_ = ;
end

model ciliberto_2003__Trim(Trim, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a, Cdc20_a, Sic1, Clb2, PTrim, Cln, time_)

  // Rate Rules:
  Trim' = (kass * Sic1 * Clb2 + kmih * PTrim) - (kdiss * Trim + (kd_sic + kd_sic_1 * Cln + kd_sic_2 * Clb2) * Trim + (kd_clb_1 + kd_clb_2 * Cdh1_a + kd_clb_3 * Cdc20_a) * Trim + kswe * Trim);

  // Variable initializations:
  Trim = 0.084;
  kd_clb_1 = ;
  kd_clb_2 = ;
  kd_clb_3 = ;
  kswe = ;
  kmih = ;
  kass = ;
  kdiss = ;
  kd_sic = ;
  kd_sic_1 = ;
  kd_sic_2 = ;
  Cdh1_a = ;
  Cdc20_a = ;
  Sic1 = ;
  Clb2 = ;
  PTrim = ;
  Cln = ;
  time_ = ;
end

model ciliberto_2003__PTrim(PTrim, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a, Cdc20_a, Sic1, Clb2, PClb2, Trim, Cln, time_)

  // Rate Rules:
  PTrim' = (kswe * Trim + kass * Sic1 * PClb2) - (kdiss * PTrim + (kd_sic + kd_sic_1 * Cln + kd_sic_2 * Clb2) * PTrim + (kd_clb_1 + kd_clb_2 * Cdh1_a + kd_clb_3 * Cdc20_a) * PTrim + kmih * PTrim);

  // Variable initializations:
  PTrim = 0;
  kd_clb_1 = ;
  kd_clb_2 = ;
  kd_clb_3 = ;
  kswe = ;
  kmih = ;
  kass = ;
  kdiss = ;
  kd_sic = ;
  kd_sic_1 = ;
  kd_sic_2 = ;
  Cdh1_a = ;
  Cdc20_a = ;
  Sic1 = ;
  Clb2 = ;
  PClb2 = ;
  Trim = ;
  Cln = ;
  time_ = ;
end

model ciliberto_2003__Mcm_a(Mcm_a, Mcm, Clb2, time_)

  // Rate Rules:
  Mcm_a' = (- ki_mcm * Mcm_a) / (Ji_mcm + Mcm_a) + (ka_mcm * Mcm * Clb2) / (Ja_mcm + Mcm);

  // Variable initializations:
  Mcm_a = 0.933;
  Ji_mcm = 0.1;
  Ja_mcm = 0.1;
  ki_mcm = 0.15;
  ka_mcm = 1;
  Mcm = ;
  Clb2 = ;
  time_ = ;
end

model ciliberto_2003__Sic1(Sic1, kd_clb_1, kd_clb_2, kd_clb_3, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a, Cdc20_a, Clb2, PClb2, Trim, PTrim, Cln, time_)

  // Rate Rules:
  Sic1' = (ks_sic + kdiss * (PTrim + Trim) + (kd_clb_1 + kd_clb_2 * Cdh1_a + kd_clb_3 * Cdc20_a) * (PTrim + Trim)) - ((kd_sic + kd_sic_1 * Cln + kd_sic_2 * Clb2) * Sic1 + kass * Sic1 * (Clb2 + PClb2));

  // Variable initializations:
  Sic1 = 0.003;
  ks_sic = 0.1;
  kd_clb_1 = ;
  kd_clb_2 = ;
  kd_clb_3 = ;
  kass = ;
  kdiss = ;
  kd_sic = ;
  kd_sic_1 = ;
  kd_sic_2 = ;
  Cdh1_a = ;
  Cdc20_a = ;
  Clb2 = ;
  PClb2 = ;
  Trim = ;
  PTrim = ;
  Cln = ;
  time_ = ;
end

model ciliberto_2003__Mih1_a(Mih1_a, Mih1, Clb2, time_)

  // Rate Rules:
  Mih1_a' = (- Vi_mih * Mih1_a) / (Ji_mih + Mih1_a) + (Va_mih * Clb2 * Mih1) / (Ja_mih + Mih1);

  // Variable initializations:
  Mih1_a = 0.808;
  Ji_mih = 0.1;
  Ja_mih = 0.1;
  Vi_mih = 0.3;
  Va_mih = 1;
  Mih1 = ;
  Clb2 = ;
  time_ = ;
end

model ciliberto_2003__IE_a(IE_a, IE, Clb2, time_)

  // Rate Rules:
  IE_a' = (- ki_ie * IE_a) / (Ji_ie + IE_a) + (ka_ie * Clb2 * IE) / (Ja_ie + IE);

  // Variable initializations:
  IE_a = 0.522;
  Ji_ie = 0.01;
  Ja_ie = 0.01;
  ki_ie = 0.04;
  ka_ie = 0.1;
  IE = ;
  Clb2 = ;
  time_ = ;
end

model ciliberto_2003__Cdc20_a(Cdc20_a, Ji_cdc20, Ja_cdc20, ki_cdc20, kd_cdc20, ka_cdc20, Cdc20, IE_a, time_)

  // Rate Rules:
  Cdc20_a' = (ka_cdc20 * IE_a * Cdc20) / (Ja_cdc20 + Cdc20) - ((ki_cdc20 * Cdc20_a) / (Ji_cdc20 + Cdc20_a) + kd_cdc20 * Cdc20_a);

  // Variable initializations:
  Cdc20_a = 1.438;
  Ji_cdc20 = ;
  Ja_cdc20 = ;
  ki_cdc20 = ;
  kd_cdc20 = ;
  ka_cdc20 = ;
  Cdc20 = ;
  IE_a = ;
  time_ = ;
end

model ciliberto_2003__Cdc20(Cdc20, Ji_cdc20, Ja_cdc20, ki_cdc20, kd_cdc20, ka_cdc20, Cdc20_a, Clb2, IE_a, time_)

  // Rate Rules:
  Cdc20' = (ks_cdc20_1 + (ks_cdc20_2 * power(Clb2, 4)) / (power(Js_cdc20, 4) + power(Clb2, 4)) + (ki_cdc20 * Cdc20_a) / (Ji_cdc20 + Cdc20_a)) - ((ka_cdc20 * IE_a * Cdc20) / (Ja_cdc20 + Cdc20) + kd_cdc20 * Cdc20);

  // Variable initializations:
  Cdc20 = 1.172;
  ks_cdc20_1 = 0.005;
  ks_cdc20_2 = 0.3;
  Js_cdc20 = 0.3;
  Ji_cdc20 = ;
  Ja_cdc20 = ;
  ki_cdc20 = ;
  kd_cdc20 = ;
  ka_cdc20 = ;
  Cdc20_a = ;
  Clb2 = ;
  IE_a = ;
  time_ = ;
end

model ciliberto_2003__Cdh1_a(Cdh1_a, Cln, Clb2, Cdh1, Cdc20_a, time_)

  // Rate Rules:
  Cdh1_a' = (-(ki_cdh * Clb2 + ki_cdh_1 * Cln) * Cdh1_a) / (Ji_cdh + Cdh1_a) + ((ka_cdh_1 + ka_cdh_2 * Cdc20_a) * Cdh1) / (Ja_cdh + Cdh1);

  // Variable initializations:
  Cdh1_a = 0.993;
  Ji_cdh = 0.01;
  Ja_cdh = 0.01;
  ki_cdh = 35;
  ka_cdh_1 = 1;
  ki_cdh_1 = 2;
  ka_cdh_2 = 10;
  Cln = ;
  Clb2 = ;
  Cdh1 = ;
  Cdc20_a = ;
  time_ = ;
end

model ciliberto_2003__Cln(Cln, SBF_a, time_)

  // Rate Rules:
  Cln' = ks_cln * SBF_a - kd_cln * Cln;

  // Variable initializations:
  Cln = 0.054;
  ks_cln = 0.1;
  kd_cln = 0.1;
  SBF_a = ;
  time_ = ;
end

model ciliberto_2003__SBF_a(SBF_a, Cln, M, Clb2, SBF, time_)

  // Rate Rules:
  SBF_a' = (-(ki_sbf_1 + ki_sbf_2 * Clb2) * SBF_a) / (Ji_sbf + SBF_a) + ((ka_sbf_1 * M + ka_sbf_2 * Cln) * SBF) / (Ja_sbf + SBF);

  // Variable initializations:
  SBF_a = 0.124;
  Ji_sbf = 0.01;
  Ja_sbf = 0.01;
  ki_sbf_1 = 1;
  ka_sbf_1 = 1;
  ki_sbf_2 = 2;
  ka_sbf_2 = 0;
  Cln = ;
  M = ;
  Clb2 = ;
  SBF = ;
  time_ = ;
end

model ciliberto_2003__Swe1(Swe1, khsl1, khsl1r, kd_swe_1, Ji_wee, Ja_wee, Vi_wee, Va_wee, SBF_a, Clb2, BUD, PSwe1, Swe1M, time_)

  // Rate Rules:
  Swe1' = (ks_swe * SBF_a + ks_sweC + khsl1r * Swe1M + (Va_wee * PSwe1) / (Ja_wee + PSwe1)) - (khsl1 * BUD * Swe1 + (Vi_wee * Clb2 * Swe1) / (Ji_wee + Swe1) + kd_swe_1 * Swe1);

  // Variable initializations:
  Swe1 = 0;
  ks_swe = 0.0025;
  ks_sweC = 0;
  khsl1 = ;
  khsl1r = ;
  kd_swe_1 = ;
  Ji_wee = ;
  Ja_wee = ;
  Vi_wee = ;
  Va_wee = ;
  SBF_a = ;
  Clb2 = ;
  BUD = ;
  PSwe1 = ;
  Swe1M = ;
  time_ = ;
end

model ciliberto_2003__PSwe1(PSwe1, khsl1, khsl1r, kd_swe_1, Ja_wee, Va_wee, BUD, PSwe1M, Clb2, Ji_wee, Swe1, Vi_wee, time_)

  // Rate Rules:
  PSwe1' = (khsl1r * PSwe1M + (Vi_wee * Swe1 * Clb2) / (Ji_wee + Swe1)) - (khsl1 * BUD * PSwe1 + (Va_wee * PSwe1) / (Ja_wee + PSwe1) + kd_swe_1 * PSwe1);

  // Variable initializations:
  PSwe1 = 0;
  khsl1 = ;
  khsl1r = ;
  kd_swe_1 = ;
  Ja_wee = ;
  Va_wee = ;
  BUD = ;
  PSwe1M = ;
  Clb2 = ;
  Ji_wee = ;
  Swe1 = ;
  Vi_wee = ;
  time_ = ;
end

model ciliberto_2003__Swe1M(Swe1M, khsl1, khsl1r, kd_swe_1, Ji_wee, Ja_wee, Vi_wee, Va_wee, Swe1, Clb2, BUD, PSwe1M, time_)

  // Rate Rules:
  Swe1M' = (khsl1 * BUD * Swe1 + (Va_wee * PSwe1M) / (Ja_wee + PSwe1M)) - (khsl1r * Swe1M + (Vi_wee * Clb2 * Swe1M) / (Ji_wee + Swe1M) + kd_swe_1 * Swe1M);

  // Variable initializations:
  Swe1M = 0.018;
  khsl1 = ;
  khsl1r = ;
  kd_swe_1 = ;
  Ji_wee = ;
  Ja_wee = ;
  Vi_wee = ;
  Va_wee = ;
  Swe1 = ;
  Clb2 = ;
  BUD = ;
  PSwe1M = ;
  time_ = ;
end

model ciliberto_2003__PSwe1M(PSwe1M, kd_swe_1, khsl1, khsl1r, Ji_wee, Ja_wee, Vi_wee, Va_wee, Swe1M, Clb2, BUD, PSwe1, time_)

  // Rate Rules:
  PSwe1M' = (khsl1 * BUD * PSwe1 + (Vi_wee * Clb2 * Swe1M) / (Ji_wee + Swe1M)) - (khsl1r * PSwe1M + (Va_wee * PSwe1M) / (Ja_wee + PSwe1M) + kd_swe_2 * PSwe1M);

  // Variable initializations:
  PSwe1M = 0.013;
  kd_swe_2 = 0.05;
  kd_swe_1 = ;
  khsl1 = ;
  khsl1r = ;
  Ji_wee = ;
  Ja_wee = ;
  Vi_wee = ;
  Va_wee = ;
  Swe1M = ;
  Clb2 = ;
  BUD = ;
  PSwe1 = ;
  time_ = ;
end

model ciliberto_2003__BE(BE, Cln, time_)

  // Rate Rules:
  BE' = ks_bud * Cln - kd_bud * BE;

  // Variable initializations:
  BE = 0;
  ks_bud = 0.1;
  kd_bud = 0.1;
  Cln = ;
  time_ = ;
end

model ciliberto_2003__M(M, time_)

  // Rate Rules:
  M' = mu * M;

  // Variable initializations:
  M = 0.802;
  mu = 0.005;
  time_ = ;
end

model ciliberto_2003__IE(IE, IE_a)

  // Assignment Rules:
  IE := IE_total - IE_a;

  // Variable initializations:
  IE_total = 1;
  IE_a = ;
end

model ciliberto_2003__Cdh1(Cdh1, Cdh1_a)

  // Assignment Rules:
  Cdh1 := Cdh1_total - Cdh1_a;

  // Variable initializations:
  Cdh1_total = 1;
  Cdh1_a = ;
end

model ciliberto_2003__Mih1(Mih1, Mih1_a)

  // Assignment Rules:
  Mih1 := Mih1_total - Mih1_a;

  // Variable initializations:
  Mih1_total = 1;
  Mih1_a = ;
end

model ciliberto_2003__Mcm(Mcm, Mcm_a)

  // Assignment Rules:
  Mcm := Mcm_total - Mcm_a;

  // Variable initializations:
  Mcm_total = 1;
  Mcm_a = ;
end

model ciliberto_2003__SBF(SBF, SBF_a)

  // Assignment Rules:
  SBF := SBF_total - SBF_a;

  // Variable initializations:
  SBF_total = 1;
  SBF_a = ;
end

model ciliberto_2003__Swe1_total(Swe1_total, Swe1, PSwe1, Swe1M, PSwe1M)

  // Assignment Rules:
  Swe1_total := Swe1 + PSwe1 + Swe1M + PSwe1M;

  // Variable initializations:
  Swe1 = ;
  PSwe1 = ;
  Swe1M = ;
  PSwe1M = ;
end

model ciliberto_2003__BUD(BUD, BE, Clb2)

  // Assignment Rules:
  BUD := piecewise( 0 , ( BE <= 0.6) && (Clb2 < 0.2 ), 1 );

  // Variable initializations:
  BE = ;
  Clb2 = ;
end

model ciliberto_2003__kinetic_parameters(Ji_cdc20, Ja_cdc20, ki_cdc20, kd_cdc20, ka_cdc20, khsl1, khsl1r, kd_swe_1, Ji_wee, Ja_wee, Vi_wee, Va_wee, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Mih1_a, Mih1, Swe1, Swe1M, PSwe1, PSwe1M)

  // Assignment Rules:
  kswe := kswe_1 * Swe1 + kswe_2 * Swe1M + kswe_3 * PSwe1;
  kmih := kmih_1 * Mih1_a + kmih_2 * Mih1;

  // Variable initializations:
  Ji_cdc20 = 0.001;
  Ja_cdc20 = 0.001;
  ki_cdc20 = 0.25;
  kd_cdc20 = 0.1;
  ka_cdc20 = 1;
  khsl1 = 1;
  khsl1r = 0.01;
  kd_swe_1 = 0.007;
  Ji_wee = 0.05;
  Ja_wee = 0.05;
  Vi_wee = 1;
  Va_wee = 0.3;
  kd_clb_1 = 0.015;
  kd_clb_2 = 1;
  kd_clb_3 = 0.1;
  kass = 300;
  kdiss = 0.1;
  kd_sic = 0.01;
  kd_sic_1 = 1;
  kd_sic_2 = 3;
  kswe_1 = 2;
  kswe_2 = 0.01;
  kswe_3 = 0.2;
  kmih_1 = 5;
  kmih_2 = 0.5;
  Mih1_a = ;
  Mih1 = ;
  Swe1 = ;
  Swe1M = ;
  PSwe1 = ;
  PSwe1M = ;
end

model *ciliberto_2003____main()

  // Sub-modules, and any changes to those submodules:
  environment: ciliberto_2003__environment(time_);
  Clb2: ciliberto_2003__Clb2(Clb20, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, M0, Mcm_a0, Cdh1_a0, Cdc20_a0, Sic10, PClb20, Trim0, Cln0, time_);
  PClb2: ciliberto_2003__PClb2(PClb20, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a0, Cdc20_a0, Sic10, Clb20, PTrim0, Cln0, time_);
  Trim: ciliberto_2003__Trim(Trim0, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a0, Cdc20_a0, Sic10, Clb20, PTrim0, Cln0, time_);
  PTrim: ciliberto_2003__PTrim(PTrim0, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a0, Cdc20_a0, Sic10, Clb20, PClb20, Trim0, Cln0, time_);
  Mcm_a: ciliberto_2003__Mcm_a(Mcm_a0, Mcm0, Clb20, time_);
  Sic1: ciliberto_2003__Sic1(Sic10, kd_clb_1, kd_clb_2, kd_clb_3, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Cdh1_a0, Cdc20_a0, Clb20, PClb20, Trim0, PTrim0, Cln0, time_);
  Mih1_a: ciliberto_2003__Mih1_a(Mih1_a0, Mih10, Clb20, time_);
  IE_a: ciliberto_2003__IE_a(IE_a0, IE0, Clb20, time_);
  Cdc20_a: ciliberto_2003__Cdc20_a(Cdc20_a0, Ji_cdc20, Ja_cdc20, ki_cdc20, kd_cdc20, ka_cdc20, Cdc200, IE_a0, time_);
  Cdc20: ciliberto_2003__Cdc20(Cdc200, Ji_cdc20, Ja_cdc20, ki_cdc20, kd_cdc20, ka_cdc20, Cdc20_a0, Clb20, IE_a0, time_);
  Cdh1_a: ciliberto_2003__Cdh1_a(Cdh1_a0, Cln0, Clb20, Cdh10, Cdc20_a0, time_);
  Cln: ciliberto_2003__Cln(Cln0, SBF_a0, time_);
  SBF_a: ciliberto_2003__SBF_a(SBF_a0, Cln0, M0, Clb20, SBF0, time_);
  Swe1: ciliberto_2003__Swe1(Swe10, khsl1, khsl1r, kd_swe_1, Ji_wee, Ja_wee, Vi_wee, Va_wee, SBF_a0, Clb20, BUD0, PSwe10, Swe1M0, time_);
  PSwe1: ciliberto_2003__PSwe1(PSwe10, khsl1, khsl1r, kd_swe_1, Ja_wee, Va_wee, BUD0, PSwe1M0, Clb20, Ji_wee, Swe10, Vi_wee, time_);
  Swe1M: ciliberto_2003__Swe1M(Swe1M0, khsl1, khsl1r, kd_swe_1, Ji_wee, Ja_wee, Vi_wee, Va_wee, Swe10, Clb20, BUD0, PSwe1M0, time_);
  PSwe1M: ciliberto_2003__PSwe1M(PSwe1M0, kd_swe_1, khsl1, khsl1r, Ji_wee, Ja_wee, Vi_wee, Va_wee, Swe1M0, Clb20, BUD0, PSwe10, time_);
  BE: ciliberto_2003__BE(BE0, Cln0, time_);
  M: ciliberto_2003__M(M0, time_);
  IE: ciliberto_2003__IE(IE0, IE_a0);
  Cdh1: ciliberto_2003__Cdh1(Cdh10, Cdh1_a0);
  Mih1: ciliberto_2003__Mih1(Mih10, Mih1_a0);
  Mcm: ciliberto_2003__Mcm(Mcm0, Mcm_a0);
  SBF: ciliberto_2003__SBF(SBF0, SBF_a0);
  Swe1_total: ciliberto_2003__Swe1_total(Swe1_total0, Swe10, PSwe10, Swe1M0, PSwe1M0);
  BUD: ciliberto_2003__BUD(BUD0, BE0, Clb20);
  kinetic_parameters: ciliberto_2003__kinetic_parameters(Ji_cdc20, Ja_cdc20, ki_cdc20, kd_cdc20, ka_cdc20, khsl1, khsl1r, kd_swe_1, Ji_wee, Ja_wee, Vi_wee, Va_wee, kd_clb_1, kd_clb_2, kd_clb_3, kswe, kmih, kass, kdiss, kd_sic, kd_sic_1, kd_sic_2, Mih1_a0, Mih10, Swe10, Swe1M0, PSwe10, PSwe1M0);
end