//Created by libAntimony v2.4 model csikasz_nagy_2006__environment(time_) // Variable initializations: time_ = ; end model csikasz_nagy_2006__actCycA(actCycA, k_asa, k_sap, k_sapp, k_dia, V_di, V_da, mass, Tri_A, TF_E, freeCKI, time_) // Rate Rules: actCycA' = ((k_sap + k_sapp * TF_E) * mass + (V_di + k_dia) * Tri_A) - (V_da + k_asa * freeCKI) * actCycA; // Variable initializations: actCycA = 0.09450308233499527; k_asa = ; k_sap = ; k_sapp = ; k_dia = ; V_di = ; V_da = ; mass = ; Tri_A = ; TF_E = ; freeCKI = ; time_ = ; end model csikasz_nagy_2006__actCycB(actCycB, k_asb, k_dib, V_sb, V_db, V_25, V_wee, V_di, mass, CycB, freeCKI, Tri_B, preMPF, time_) // Rate Rules: actCycB' = (V_sb * mass + V_25 * (CycB - (Tri_B + actCycB)) + (k_dib + V_di) * (CycB - (preMPF + actCycB))) - (V_db + V_wee + k_asb * freeCKI) * actCycB; // Variable initializations: actCycB = 0.1903585940599442; k_asb = ; k_dib = ; V_sb = ; V_db = ; V_25 = ; V_wee = ; V_di = ; mass = ; CycB = ; freeCKI = ; Tri_B = ; preMPF = ; time_ = ; end model csikasz_nagy_2006__actCycE(actCycE, k_die, k_ase, k_sep, k_sepp, V_di, V_de, Tri_E, TF_E, freeCKI, mass, time_) // Rate Rules: actCycE' = ((k_sep + k_sepp * TF_E) * mass + (V_di + k_die) * Tri_E) - (V_de + k_ase * freeCKI) * actCycE; // Variable initializations: actCycE = 0.2092024385929108; k_die = ; k_ase = ; k_sep = ; k_sepp = ; V_di = ; V_de = ; Tri_E = ; TF_E = ; freeCKI = ; mass = ; time_ = ; end model csikasz_nagy_2006__CycA(CycA, k_sap, k_sapp, V_da, mass, TF_E, time_) // Rate Rules: CycA' = (k_sap + k_sapp * TF_E) * mass - V_da * CycA; // Variable initializations: CycA = 0.09450308233499527; k_sap = ; k_sapp = ; V_da = ; mass = ; TF_E = ; time_ = ; end model csikasz_nagy_2006__CycB(CycB, V_sb, V_db, mass, time_) // Rate Rules: CycB' = V_sb * mass - V_db * CycB; // Variable initializations: CycB = 0.09450308233499527; V_sb = ; V_db = ; mass = ; time_ = ; end model csikasz_nagy_2006__CycE(CycE, k_sep, k_sepp, V_de, mass, TF_E, time_) // Rate Rules: CycE' = (k_sep + k_sepp * TF_E) * mass - V_de * CycE; // Variable initializations: CycE = 0.09450308233499527; k_sep = ; k_sepp = ; V_de = ; mass = ; TF_E = ; time_ = ; end model csikasz_nagy_2006__CycD(CycD, mass) // Assignment Rules: CycD := CycD_0 * mass; // Variable initializations: CycD_0 = 0.108; mass = ; end model csikasz_nagy_2006__Cdc20_A(Cdc20_A, k_a20, k_i20, k_d20, APCP, Cdc20_T, time_) // Rate Rules: Cdc20_A' = (k_a20 * APCP * (Cdc20_T - Cdc20_A)) / ((J_a20 + Cdc20_T) - Cdc20_A) - (k_i20 / (J_i20 + Cdc20_A) + k_d20) * Cdc20_A; // Variable initializations: Cdc20_A = 0.3572723865509033; k_a20 = ; k_i20 = ; k_d20 = ; APCP = ; Cdc20_T = ; J_a20 = 1; J_i20 = 1; time_ = ; end model csikasz_nagy_2006__Cdc20_T(Cdc20_T, k_d20, k_s20p, k_s20pp, actCycB, time_) // Rate Rules: Cdc20_T' = (k_s20p + k_s20pp * power(actCycB, n)) / (power(J_20, n) + power(actCycB, n)) - k_d20 * Cdc20_T; // Variable initializations: Cdc20_T = 0.7702387571334839; k_d20 = ; k_s20p = ; k_s20pp = ; actCycB = ; n = 1; J_20 = 10; time_ = ; end model csikasz_nagy_2006__APCP(APCP, k_aAPC, k_iAPC, actCycB, time_) // Rate Rules: APCP' = (k_aAPC * actCycB * (1 - APCP)) / ((J_aAPC + 1) - APCP) - (k_iAPC * APCP) / (J_iAPC + APCP); // Variable initializations: APCP = 0.07591402530670166; k_aAPC = ; k_iAPC = ; actCycB = ; J_aAPC = 0.1; J_iAPC = 0.1; time_ = ; end model csikasz_nagy_2006__Tri_A(Tri_A, actCycA, CycA) // Assignment Rules: Tri_A := CycA - actCycA; // Variable initializations: actCycA = ; CycA = ; end model csikasz_nagy_2006__Tri_E(Tri_E, actCycE, CycE) // Assignment Rules: Tri_E := CycE - actCycE; // Variable initializations: actCycE = ; CycE = ; end model csikasz_nagy_2006__freeCKI(freeCKI, CKI, Tri_B, Tri_E, Tri_A) // Assignment Rules: freeCKI := CKI - (Tri_B + Tri_A + Tri_E); // Variable initializations: CKI = ; Tri_B = ; Tri_E = ; Tri_A = ; end model csikasz_nagy_2006__Cdh1(Cdh1, k_ah1p, k_ah1pp, k_ih1p, k_ih1pp, k_ih1ppp, k_ih1pppp, k_ih1ppppp, Cdc14, actCycA, actCycE, actCycB, CycD, time_) // Rate Rules: Cdh1' = ((k_ah1p + k_ah1pp * Cdc14) * (1 - Cdh1)) / ((J_ah1 + 1) - Cdh1) - ((k_ih1p + k_ih1pp * actCycA + k_ih1ppp * actCycB + k_ih1pppp * actCycE + k_ih1ppppp * CycD) * Cdh1) / (J_ih1 + Cdh1); // Variable initializations: Cdh1 = 0.7189393639564514; k_ah1p = ; k_ah1pp = ; k_ih1p = ; k_ih1pp = ; k_ih1ppp = ; k_ih1pppp = ; k_ih1ppppp = ; Cdc14 = ; actCycA = ; actCycE = ; actCycB = ; CycD = ; J_ah1 = 0.03; J_ih1 = 0.03; time_ = ; end model csikasz_nagy_2006__mass(mass, time_) // Rate Rules: mass' = mu * mass * (1 - mass / maxmass); // Variable initializations: mass = 1.338267803192139; mu = 0.005776; maxmass = 10000; time_ = ; end model csikasz_nagy_2006__V_atf(V_atf, k_atfp, k_atfpp, k_atfppp, k_atfpppp, actCycA, actCycE, CycD) // Assignment Rules: V_atf := k_atfp + k_atfpp * actCycA + k_atfppp * actCycE + k_atfpppp * CycD; // Variable initializations: k_atfp = ; k_atfpp = ; k_atfppp = ; k_atfpppp = ; actCycA = ; actCycE = ; CycD = ; end model csikasz_nagy_2006__TF_E(TF_E, V_atf, k_itfp, k_itfpp, k_itfppp, actCycA, actCycB) // Assignment Rules: TF_E := (2 * A4 * A1) / ((A2 + - A1 + A3 * A2 + A4 * A1) + root(power(A2 + - A1 + A3 * A2 + A4 * A1, 2) - 4 * (A2 - A1) * A4 * A1)); A1 := V_atf; A2 := k_itfp + k_itfpp * actCycB + k_itfppp * actCycA; A3 := J_atf; A4 := J_itf; // Variable initializations: V_atf = ; k_itfp = ; k_itfpp = ; k_itfppp = ; actCycA = ; actCycB = ; J_itf = 0.01; J_atf = 0.01; end model csikasz_nagy_2006__V_de(V_de, k_dep, k_depp, k_deppp, k_depppp, actCycA, actCycE, actCycB) // Assignment Rules: V_de := k_dep + k_depp * actCycE + k_deppp * actCycA + k_depppp * actCycB; // Variable initializations: k_dep = ; k_depp = ; k_deppp = ; k_depppp = ; actCycA = ; actCycE = ; actCycB = ; end model csikasz_nagy_2006__V_da(V_da, k_dap, k_dapp, k_dappp, Cdc20_A, Cdc20_T) // Assignment Rules: V_da := k_dap + k_dapp * Cdc20_A + k_dappp * Cdc20_T; // Variable initializations: k_dap = ; k_dapp = ; k_dappp = ; Cdc20_A = ; Cdc20_T = ; end model csikasz_nagy_2006__TF_I(TF_I, Cdc14, actCycB, Cdc20_A, k_afi, k_ifip, k_ifipp) // Assignment Rules: TF_I := (2 * A4 * A1) / ((A2 + - A1 + A3 * A2 + A4 * A1) + root(power(A2 + - A1 + A3 * A2 + A4 * A1, 2) - 4 * (A2 - A1) * A4 * A1)); Cdc14 := Cdc20_A; A1 := k_afi * Cdc14; A2 := k_ifip + k_ifipp * actCycB; A3 := J_afi; A4 := J_ifi; // Variable initializations: actCycB = ; Cdc20_A = ; k_afi = ; k_ifip = ; k_ifipp = ; J_ifi = 2; J_afi = 1; end model csikasz_nagy_2006__V_si(V_si, k_sip, k_sipp, TF_I) // Assignment Rules: V_si := k_sip + k_sipp * TF_I; // Variable initializations: k_sip = ; k_sipp = ; TF_I = ; end model csikasz_nagy_2006__V_di(V_di, k_dip, k_dipp, k_dippp, k_dipppp, k_dippppp, J_14di, actCycA, actCycB, actCycE, CycD, Cdc14) // Assignment Rules: V_di := (k_dip + k_dipp * actCycA + k_dippp * actCycB + k_dipppp * actCycE + k_dippppp * CycD) / (1 + Cdc14 / J_14di); // Variable initializations: k_dip = ; k_dipp = ; k_dippp = ; k_dipppp = ; k_dippppp = ; J_14di = ; actCycA = ; actCycB = ; actCycE = ; CycD = ; Cdc14 = ; end model csikasz_nagy_2006__preMPF(preMPF, V_wee, V_25, V_db, CycB, time_) // Rate Rules: preMPF' = V_wee * (CycB - preMPF) - (V_25 + V_db) * preMPF; // Variable initializations: preMPF = 0.01; V_wee = ; V_25 = ; V_db = ; CycB = ; time_ = ; end model csikasz_nagy_2006__Tri_B(Tri_B, k_asb, k_dib, V_di, V_db, CycB, freeCKI, time_) // Rate Rules: Tri_B' = k_asb * (CycB - Tri_B) * freeCKI - (k_dib + V_db + V_di) * Tri_B; // Variable initializations: Tri_B = 0.01; k_asb = ; k_dib = ; V_di = ; V_db = ; CycB = ; freeCKI = ; time_ = ; end model csikasz_nagy_2006__CKI(CKI, V_di, V_si, time_) // Rate Rules: CKI' = V_si - V_di * CKI; // Variable initializations: CKI = 0.01; V_di = ; V_si = ; time_ = ; end model csikasz_nagy_2006__TF_B(TF_B, k_afb, k_ifb, actCycB) // Assignment Rules: TF_B := (2 * A4 * A1) / ((A2 + - A1 + A3 * A2 + A4 * A1) + root(power(A2 + - A1 + A3 * A2 + A4 * A1, 2) - 4 * (A2 - A1) * A4 * A1)); A1 := k_afb * actCycB; A2 := k_ifb; A3 := J_afb; A4 := J_ifb; // Variable initializations: k_afb = ; k_ifb = ; J_ifb = 0.1; J_afb = 0.1; actCycB = ; end model csikasz_nagy_2006__V_sb(V_sb, k_sbp, k_sbpp, TF_B) // Assignment Rules: V_sb := k_sbp + k_sbpp * TF_B; // Variable initializations: k_sbp = ; k_sbpp = ; TF_B = ; end model csikasz_nagy_2006__V_db(V_db, k_dbp, k_dbpp, k_dbppp, Cdc20_A, Cdh1) // Assignment Rules: V_db := k_dbp + k_dbpp * Cdh1 + k_dbppp * Cdc20_A; // Variable initializations: k_dbp = ; k_dbpp = ; k_dbppp = ; Cdc20_A = ; Cdh1 = ; end model csikasz_nagy_2006__Wee1(Wee1, k_aweep, k_aweepp, k_iwee, Cdc14, actCycB) // Assignment Rules: Wee1 := (2 * A4 * A1) / ((A2 + - A1 + A3 * A2 + A4 * A1) + root(power(A2 + - A1 + A3 * A2 + A4 * A1, 2) - 4 * (A2 - A1) * A4 * A1)); A1 := k_aweep + k_aweepp * Cdc14; A2 := k_iwee * actCycB; A3 := J_awee; A4 := J_iwee; // Variable initializations: k_aweep = ; k_aweepp = ; k_iwee = ; J_iwee = 0.05; J_awee = 0.05; Cdc14 = ; actCycB = ; end model csikasz_nagy_2006__V_wee(V_wee, k_weep, k_weepp, Wee1) // Assignment Rules: V_wee := k_weep + k_weepp * Wee1; // Variable initializations: k_weep = ; k_weepp = ; Wee1 = ; end model csikasz_nagy_2006__Cdc25(Cdc25, k_a25, k_i25p, k_i25pp, Cdc14, actCycB) // Assignment Rules: Cdc25 := (2 * A4 * A1) / ((A2 + - A1 + A3 * A2 + A4 * A1) + root(power(A2 + - A1 + A3 * A2 + A4 * A1, 2) - 4 * (A2 - A1) * A4 * A1)); A1 := k_a25 * actCycB; A2 := k_i25p + k_i25pp * Cdc14; A3 := J_a25; A4 := J_i25; // Variable initializations: k_a25 = ; k_i25p = ; k_i25pp = ; J_i25 = 0.1; J_a25 = 0.1; Cdc14 = ; actCycB = ; end model csikasz_nagy_2006__V_25(V_25, k_25p, k_25pp, Cdc25) // Assignment Rules: V_25 := k_25p + k_25pp * Cdc25; // Variable initializations: k_25p = ; k_25pp = ; Cdc25 = ; end model csikasz_nagy_2006__kinetic_parameters(k_25p, k_25pp, J_14di, k_a20, k_a25, k_afb, k_afi, k_ah1p, k_ah1pp, k_aAPC, k_asa, k_asb, k_ase, k_atfp, k_atfpp, k_atfpppp, k_atfppp, k_aweep, k_aweepp, k_d20, k_dap, k_dapp, k_dappp, k_dbp, k_dbpp, k_dbppp, k_dep, k_deppp, k_depppp, k_depp, k_dip, k_dipp, k_dippp, k_dippppp, k_dipppp, k_die, k_dib, k_dia, k_i20, k_i25p, k_i25pp, k_itfp, k_itfppp, k_itfpp, k_ifb, k_ifip, k_ifipp, k_ih1p, k_ih1pp, k_ih1ppp, k_ih1ppppp, k_ih1pppp, k_iAPC, k_s20p, k_s20pp, k_sbp, k_sbpp, k_sip, k_sipp, k_iwee, k_weep, k_weepp, k_sap, k_sapp, k_sep, k_sepp) // Variable initializations: k_25p = 0.01; k_25pp = 5; J_14di = 12; k_a20 = 1; k_a25 = 0; k_afb = 1; k_afi = 6; k_ah1p = 0.02; k_ah1pp = 0.8; k_aAPC = 0.1; k_asa = 50; k_asb = 60; k_ase = 0; k_atfp = 0; k_atfpp = 1.5; k_atfpppp = 3; k_atfppp = 0.38; k_aweep = 0.3; k_aweepp = 0; k_d20 = 0.05; k_dap = 0.01; k_dapp = 0.16; k_dappp = 0; k_dbp = 0.003; k_dbpp = 0.4; k_dbppp = 0.15; k_dep = 0.12; k_deppp = 0; k_depppp = 0; k_depp = 0; k_dip = 0.02; k_dipp = 0.1; k_dippp = 0.8; k_dippppp = 0.1; k_dipppp = 0.12; k_die = 0; k_dib = 0.05; k_dia = 0.06; k_i20 = 0.16; k_i25p = 0.3; k_i25pp = 0; k_itfp = 0.75; k_itfppp = 0; k_itfpp = 8; k_ifb = 0.15; k_ifip = 0.008; k_ifipp = 0.05; k_ih1p = 0.001; k_ih1pp = 0.35; k_ih1ppp = 0.1; k_ih1ppppp = 0.005; k_ih1pppp = 0.06; k_iAPC = 0.15; k_s20p = 0.001; k_s20pp = 1; k_sbp = 0.004; k_sbpp = 0.04; k_sip = 0.018; k_sipp = 0.18; k_iwee = 1; k_weep = 0.02; k_weepp = 0.2; k_sap = 0.0015; k_sapp = 0.01; k_sep = 0; k_sepp = 0.15; end model *csikasz_nagy_2006____main() // Sub-modules, and any changes to those submodules: environment: csikasz_nagy_2006__environment(time_); actCycA: csikasz_nagy_2006__actCycA(actCycA0, k_asa, k_sap, k_sapp, k_dia, V_di0, V_da0, mass0, Tri_A0, TF_E0, freeCKI0, time_); actCycB: csikasz_nagy_2006__actCycB(actCycB0, k_asb, k_dib, V_sb0, V_db0, V_250, V_wee0, V_di0, mass0, CycB0, freeCKI0, Tri_B0, preMPF0, time_); actCycE: csikasz_nagy_2006__actCycE(actCycE0, k_die, k_ase, k_sep, k_sepp, V_di0, V_de0, Tri_E0, TF_E0, freeCKI0, mass0, time_); CycA: csikasz_nagy_2006__CycA(CycA0, k_sap, k_sapp, V_da0, mass0, TF_E0, time_); CycB: csikasz_nagy_2006__CycB(CycB0, V_sb0, V_db0, mass0, time_); CycE: csikasz_nagy_2006__CycE(CycE0, k_sep, k_sepp, V_de0, mass0, TF_E0, time_); CycD: csikasz_nagy_2006__CycD(CycD0, mass0); Cdc20_A: csikasz_nagy_2006__Cdc20_A(Cdc20_A0, k_a20, k_i20, k_d20, APCP0, Cdc20_T0, time_); Cdc20_T: csikasz_nagy_2006__Cdc20_T(Cdc20_T0, k_d20, k_s20p, k_s20pp, actCycB0, time_); APCP: csikasz_nagy_2006__APCP(APCP0, k_aAPC, k_iAPC, actCycB0, time_); Tri_A: csikasz_nagy_2006__Tri_A(Tri_A0, actCycA0, CycA0); Tri_E: csikasz_nagy_2006__Tri_E(Tri_E0, actCycE0, CycE0); freeCKI: csikasz_nagy_2006__freeCKI(freeCKI0, CKI0, Tri_B0, Tri_E0, Tri_A0); Cdh1: csikasz_nagy_2006__Cdh1(Cdh10, k_ah1p, k_ah1pp, k_ih1p, k_ih1pp, k_ih1ppp, k_ih1pppp, k_ih1ppppp, Cdc14, actCycA0, actCycE0, actCycB0, CycD0, time_); mass: csikasz_nagy_2006__mass(mass0, time_); V_atf: csikasz_nagy_2006__V_atf(V_atf0, k_atfp, k_atfpp, k_atfppp, k_atfpppp, actCycA0, actCycE0, CycD0); TF_E: csikasz_nagy_2006__TF_E(TF_E0, V_atf0, k_itfp, k_itfpp, k_itfppp, actCycA0, actCycB0); V_de: csikasz_nagy_2006__V_de(V_de0, k_dep, k_depp, k_deppp, k_depppp, actCycA0, actCycE0, actCycB0); V_da: csikasz_nagy_2006__V_da(V_da0, k_dap, k_dapp, k_dappp, Cdc20_A0, Cdc20_T0); TF_I: csikasz_nagy_2006__TF_I(TF_I0, Cdc14, actCycB0, Cdc20_A0, k_afi, k_ifip, k_ifipp); V_si: csikasz_nagy_2006__V_si(V_si0, k_sip, k_sipp, TF_I0); V_di: csikasz_nagy_2006__V_di(V_di0, k_dip, k_dipp, k_dippp, k_dipppp, k_dippppp, J_14di, actCycA0, actCycB0, actCycE0, CycD0, Cdc14); preMPF: csikasz_nagy_2006__preMPF(preMPF0, V_wee0, V_250, V_db0, CycB0, time_); Tri_B: csikasz_nagy_2006__Tri_B(Tri_B0, k_asb, k_dib, V_di0, V_db0, CycB0, freeCKI0, time_); CKI: csikasz_nagy_2006__CKI(CKI0, V_di0, V_si0, time_); TF_B: csikasz_nagy_2006__TF_B(TF_B0, k_afb, k_ifb, actCycB0); V_sb: csikasz_nagy_2006__V_sb(V_sb0, k_sbp, k_sbpp, TF_B0); V_db: csikasz_nagy_2006__V_db(V_db0, k_dbp, k_dbpp, k_dbppp, Cdc20_A0, Cdh10); Wee1: csikasz_nagy_2006__Wee1(Wee10, k_aweep, k_aweepp, k_iwee, Cdc14, actCycB0); V_wee: csikasz_nagy_2006__V_wee(V_wee0, k_weep, k_weepp, Wee10); Cdc25: csikasz_nagy_2006__Cdc25(Cdc250, k_a25, k_i25p, k_i25pp, Cdc14, actCycB0); V_25: csikasz_nagy_2006__V_25(V_250, k_25p, k_25pp, Cdc250); kinetic_parameters: csikasz_nagy_2006__kinetic_parameters(k_25p, k_25pp, J_14di, k_a20, k_a25, k_afb, k_afi, k_ah1p, k_ah1pp, k_aAPC, k_asa, k_asb, k_ase, k_atfp, k_atfpp, k_atfpppp, k_atfppp, k_aweep, k_aweepp, k_d20, k_dap, k_dapp, k_dappp, k_dbp, k_dbpp, k_dbppp, k_dep, k_deppp, k_depppp, k_depp, k_dip, k_dipp, k_dippp, k_dippppp, k_dipppp, k_die, k_dib, k_dia, k_i20, k_i25p, k_i25pp, k_itfp, k_itfppp, k_itfpp, k_ifb, k_ifip, k_ifipp, k_ih1p, k_ih1pp, k_ih1ppp, k_ih1ppppp, k_ih1pppp, k_iAPC, k_s20p, k_s20pp, k_sbp, k_sbpp, k_sip, k_sipp, k_iwee, k_weep, k_weepp, k_sap, k_sapp, k_sep, k_sepp); end