// Created by libAntimony v2.8.0
model *Novak2001_FissionYeast_CellCycle()
// Compartments and Species:
compartment cell;
substanceOnly species cdc13T in cell, preMPF in cell, ste9 in cell, slp1T in cell;
substanceOnly species slp1 in cell, IEP in cell, rum1T in cell, SK in cell;
substanceOnly species M in cell, $MPF in cell;
// Assignment Rules:
MPF := ((cdc13T - preMPF)*(cdc13T - Trimer))/cdc13T;
Trimer := (2*cdc13T*rum1T)/(sigma + (sigma^2 - 4*cdc13T*rum1T)^0.5);
sigma := cdc13T + rum1T + Kdiss;
TF := (2*k15*M*J16)/((k16_prime + k16_double_prime*MPF) - k15*M + (k16_prime + k16_double_prime*MPF)*J15 + k15*M*J16 + sqrt(((k16_prime + k16_double_prime*MPF) - k15*M + (k16_prime + k16_double_prime*MPF)*J15 + k15*M*J16)^2 - 4*((k16_prime + k16_double_prime*MPF) - k15*M)*k15*M*J16));
kwee := kwee_prime + (kwee_double_prime - kwee_prime)*((2*Vawee*Jiwee)/(Viwee*MPF - Vawee + Viwee*MPF*Jawee + Vawee*Jiwee + sqrt((Viwee*MPF - Vawee + Viwee*MPF*Jawee + Vawee*Jiwee)^2 - 4*(Viwee*MPF - Vawee)*Vawee*Jiwee)));
k25 := k25_prime + (k25_double_prime - k25_prime)*((2*Va25*MPF*Ji25)/(Vi25 - Va25*MPF + Vi25*Ja25 + Va25*MPF*Ji25 + sqrt((Vi25 - Va25*MPF + Vi25*Ja25 + Va25*MPF*Ji25)^2 - 4*(Vi25 - Va25*MPF)*Va25*MPF*Ji25)));
// Reactions:
R1: => cdc13T; k1*M;
R2: cdc13T => ; (k2_prime + k2_double_prime*ste9 + k2_triple_prime*slp1)*cdc13T;
R3: => preMPF; kwee*(cdc13T - preMPF);
R4: preMPF => ; k25*preMPF;
R5: preMPF => ; (k2_prime + k2_double_prime*ste9 + k2_triple_prime*slp1)*preMPF;
R6: => ste9; ((k3_prime + k3_double_prime*slp1)*(1 - ste9))/((J3 + 1) - ste9);
R7: ste9 => ; ((k4_prime*SK + k4*MPF)*ste9)/(J4 + ste9);
R8: => slp1T; k5_prime + (k5_double_prime*MPF^4)/(J5^4 + MPF^4);
R9: slp1T => ; k6*slp1T;
R10: => slp1; (k7*IEP*(slp1T - slp1))/((J7 + slp1T) - slp1);
R11: slp1 => ; (k8*slp1)/(J8 + slp1);
R12: slp1 => ; k6*slp1;
R13: => IEP; (k9*MPF*(1 - IEP))/((J9 + 1) - IEP);
R14: IEP => ; (k10*IEP)/(J10 + IEP);
R15: => rum1T; k11;
R16: rum1T => ; (k12 + k12_prime*SK + k12_double_prime*MPF)*rum1T;
R17: => SK; k13*TF;
R18: SK => ; k14*SK;
R19: => M; mu*M;
// Events:
event_0000001: at MPF <= 0.1 && flag_MPF == 1: flag_MPF = 0, M = M/2;
event_0000002: at MPF > 0.1: flag_MPF = 1;
// Species initializations:
cdc13T = 0.2/cell;
preMPF = 0;
ste9 = 1/cell;
slp1T = 0;
slp1 = 2.2/cell;
IEP = 0;
rum1T = 0;
SK = 0;
M = 1/cell;
// Compartment initializations:
cell = 1;
Trimer has dimensionless;
// Variable initializations:
flag_MPF = 0;
flag_MPF has dimensionless;
sigma has dimensionless;
Kdiss = 0.001;
Kdiss has dimensionless;
TF has dimensionless;
k15 = 1.5;
k15 has min_inv;
J16 = 0.01;
J16 has dimensionless;
k16_prime = 1;
k16_prime has min_inv;
k16_double_prime = 2;
k16_double_prime has min_inv;
J15 = 0.01;
J15 has dimensionless;
kwee has min_inv;
kwee_prime = 0.15;
kwee_prime has min_inv;
kwee_double_prime = 1.3;
kwee_double_prime has min_inv;
Vawee = 0.25;
Vawee has min_inv;
Jiwee = 0.01;
Jiwee has dimensionless;
Viwee = 1;
Viwee has min_inv;
Jawee = 0.01;
Jawee has dimensionless;
k25 has min_inv;
k25_prime = 0.05;
k25_prime has min_inv;
k25_double_prime = 5;
k25_double_prime has min_inv;
Va25 = 1;
Va25 has min_inv;
Ji25 = 0.01;
Ji25 has dimensionless;
Vi25 = 0.25;
Vi25 has min_inv;
Ja25 = 0.01;
Ja25 has dimensionless;
k1 = 0.03;
k1 has min_inv;
k2_prime = 0.03;
k2_prime has min_inv;
k2_double_prime = 1;
k2_double_prime has min_inv;
k2_triple_prime = 0.1;
k2_triple_prime has min_inv;
k3_prime = 1;
k3_prime has min_inv;
k3_double_prime = 10;
k3_double_prime has min_inv;
J3 = 0.01;
J3 has dimensionless;
k4_prime = 2;
k4_prime has min_inv;
k4 = 35;
k4 has min_inv;
J4 = 0.01;
J4 has dimensionless;
k5_prime = 0.005;
k5_prime has min_inv;
k5_double_prime = 0.3;
k5_double_prime has min_inv;
J5 = 0.3;
J5 has dimensionless;
k6 = 0.1;
k6 has min_inv;
k7 = 1;
k7 has min_inv;
J7 = 0.001;
J7 has dimensionless;
k8 = 0.25;
k8 has min_inv;
J8 = 0.001;
J8 has dimensionless;
k9 = 0.1;
k9 has min_inv;
J9 = 0.01;
J9 has dimensionless;
k10 = 0.04;
k10 has min_inv;
J10 = 0.01;
J10 has dimensionless;
k11 = 0.1;
k11 has min_inv;
k12 = 0.01;
k12 has min_inv;
k12_prime = 1;
k12_prime has min_inv;
k12_double_prime = 3;
k12_double_prime has min_inv;
k13 = 0.1;
k13 has min_inv;
k14 = 0.1;
k14 has min_inv;
mu = 0.005;
mu has min_inv;
// Other declarations:
var Trimer, flag_MPF, sigma, TF, kwee, k25;
const cell, Kdiss, k15, J16, k16_prime, k16_double_prime, J15, kwee_prime;
const kwee_double_prime, Vawee, Jiwee, Viwee, Jawee, k25_prime, k25_double_prime;
const Va25, Ji25, Vi25, Ja25, k1, k2_prime, k2_double_prime, k2_triple_prime;
const k3_prime, k3_double_prime, J3, k4_prime, k4, J4, k5_prime, k5_double_prime;
const J5, k6, k7, J7, k8, J8, k9, J9, k10, J10, k11, k12, k12_prime, k12_double_prime;
const k13, k14, mu;
// Unit definitions:
unit time_unit = 60 second;
unit min_inv = 1 / 60 second;
unit substance = dimensionless;
// Display Names:
time_unit is "minutes";
substance is "norm. substance";
cdc13T is "Total cdc13";
M is "Cell Mass";
MPF is "M-phase promoting factor";
R1 is "cdc13T synthesis";
R2 is "Targeting cdc13T to APC core";
R3 is "wee1 dependent MPF inactivation";
R4 is "cdc25 dependent preMPF phosphorylation";
R5 is "preMPF inactivation";
R6 is "slp1 dependent ste9 activation";
R7 is "ste9 phosphorylation (inactivation) by starter kinase";
R8 is "slp1T activation by MPF";
R9 is "slp1T inactivation";
R10 is "slp1 activation by intermediary enzyme";
R11 is "slp1 inactivation";
R12 is "slp1 inactivation";
R13 is "Intermediary enzyme activation";
R14 is "IEP inactivation";
R15 is "rum1T activation";
R16 is "SK dependent rum1T inactivation";
R17 is "SK synthesis";
R18 is "SK degradation";
R19 is "Cell growth";
end