(* Generated by JWS Online *)

(* This is an experimental feature of JWS Online. Please report any mistakes.*)

(* Note that the following notable SBML entities or features are not supported in notebook outputyet: *)
    (* Events *)
    (* Constraints *)
    (* Units and UnitDefinitions *)
    (* AlgebraicRules *)
    (* conversionFactors *)

variables = {
CKIt[t], Cdc20a[t], Cdc20t[t], Cdh1[t], CycBt[t], IEP[t], SK[t], m[t]
};

initialValues = {
CKIt[0] == 0.001, Cdc20a[0] == 0.001, Cdc20t[0] == 0.001, Cdh1[0] == 0.001, CycBt[0] == 0.001, IEP[0] == 0.001, SK[0] == 0.001, m[0] == 0.5
};

rates = {
CKIdegradation, CKItphosphorilationviaSK, CKItsynthesis, Cdc20activation, Cdc20adegradation, Cdc20ainhibition, Cdc20t\[LetterSpace]deg, Cdc20tsynthesis, Cdh1degradation, Cdh1synthesis, CycBdegradation, CycBdegradationviaCdh1, CycBt\[LetterSpace]synthesis, CycBtdegradationviaCdc20a, IEPdegradation, IEPsynthesis, SKdegradation, SKsynthesis, eq\[LetterSpace]7, growth
};

rateEquations = {
CKIdegradation -> k12p*CKIt[t], CKItphosphorilationviaSK -> k12pp*CKIt[t]*SK[t], CKItsynthesis -> k11, Cdc20activation -> (k7*(-Cdc20a[t] + Cdc20t[t])*IEP[t])/(J7 - Cdc20a[t] + Cdc20t[t]), Cdc20adegradation -> k6*Cdc20a[t], Cdc20ainhibition -> (k8*Mad*Cdc20a[t])/(J8 + Cdc20a[t]), Cdc20t\[LetterSpace]deg -> k6*Cdc20t[t], Cdc20tsynthesis -> k5p + (k5pp*((CycB*m[t])/J5)^n)/(1 + ((CycB*m[t])/J5)^n), Cdh1degradation -> (CycB*k4*Cdh1[t]*m[t] + k4p*Cdh1[t]*SK[t])/(J4 + Cdh1[t]), Cdh1synthesis -> ((k3p + k3pp*Cdc20a[t])*(1 - Cdh1[t]))/(1 + J3 - Cdh1[t]), CycBdegradation -> k2p*CycBt[t], CycBdegradationviaCdh1 -> k2pp*Cdh1[t]*CycBt[t], CycBt\[LetterSpace]synthesis -> k1, CycBtdegradationviaCdc20a -> k2ppp*Cdc20a[t]*CycBt[t], IEPdegradation -> k10*IEP[t], IEPsynthesis -> CycB*k9*(1 - IEP[t])*m[t], SKdegradation -> k14*SK[t], SKsynthesis -> k13*TF, eq\[LetterSpace]7 -> CycB*k12ppp*CKIt[t]*m[t], growth -> mu*m[t]*(1 - m[t]/mmax)
};

parameters = {
J15 -> 0.01, J16 -> 0.01, J3 -> 0.04, J4 -> 0.04, J5 -> 0.3, J7 -> 0.001, J8 -> 0.001, Keq -> 1000.0, k1 -> 0.04, k10 -> 0.02, k11 -> 1.0, k12p -> 0.2, k12pp -> 50.0, k12ppp -> 100.0, k13 -> 1.0, k14 -> 1.0, k15p -> 1.5, k15pp -> 0.05, k16p -> 1.0, k16pp -> 3.0, k2p -> 0.04, k2pp -> 1.0, k2ppp -> 1.0, k3p -> 1.0, k3pp -> 10.0, k4 -> 35.0, k4p -> 2.0, k5p -> 0.005, k5pp -> 0.2, k6 -> 0.1, k7 -> 1.0, k8 -> 0.5, k9 -> 0.1, mmax -> 10.0, mu -> 0.005, n -> 4.0, cell -> 1.0
};

assignments = {
GK[A1_,A2_,A3_,A4_] -> (2*A1*A4)/(-A1 + A2 + A2*A3 + A1*A4 + Sqrt[-4*A1*(-A1 + A2)*A4 + (-A1 + A2 + A2*A3 + A1*A4)^2]), CycB -> CycBt[t] - (2*CKIt[t]*CycBt[t])/(Keq^(-1) + CKIt[t] + CycBt[t] + Sqrt[-4*CKIt[t]*CycBt[t] + (Keq^(-1) + CKIt[t] + CycBt[t])^2]), Mad -> 1, TF -> GK[k15p*m[t] + k15pp*SK[t], k16p + CycB*k16pp*m[t], J15, J16], Trimer -> (2*CKIt[t]*CycBt[t])/(Keq^(-1) + CKIt[t] + CycBt[t] + Sqrt[-4*CKIt[t]*CycBt[t] + (Keq^(-1) + CKIt[t] + CycBt[t])^2])
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

units = {
{"time" -> "", "metabolite" -> "", "extent" -> ""}
};

(* Time evolution *)
odes = {
CKIt'[t] == 1.0*CKItsynthesis -1.0*CKIdegradation -1.0*CKItphosphorilationviaSK -1.0*eq\[LetterSpace]7, Cdc20a'[t] == 1.0*Cdc20activation -1.0*Cdc20ainhibition -1.0*Cdc20adegradation, Cdc20t'[t] == 1.0*Cdc20tsynthesis -1.0*Cdc20t\[LetterSpace]deg, Cdh1'[t] == 1.0*Cdh1synthesis -1.0*Cdh1degradation, CycBt'[t] == 1.0*CycBt\[LetterSpace]synthesis -1.0*CycBdegradation -1.0*CycBdegradationviaCdh1 -1.0*CycBtdegradationviaCdc20a, IEP'[t] == 1.0*IEPsynthesis -1.0*IEPdegradation, SK'[t] == 1.0*SKsynthesis -1.0*SKdegradation, m'[t] == 1.0*growth 
};
timeCourse = NDSolve[Join[odes, initialValues]//.rateEquations//.assignments//.parameters, variables, {t, 0, 100}];

(* Steady-state solution initialized with result of time evolution *)
findRootEquations = odes /.D[_[t],t]->0;
findRootVariables = Partition[Flatten[{#, #/.timeCourse/.t->100} &/@variables],2];
steadyStateVariables = FindRoot[findRootEquations//.rateEquations//.assignments//.parameters, findRootVariables, MaxIterations->100]
fluxes = #//.assignments//.parameters/.steadyStateVariables&/@rateEquations

(* Plot the time evolution of the variables *)
plotTable=Table[Plot[variables[[i]]/.parameters/.timeCourse,{t,0,100},PlotLegends->variables[[i]],PlotRange->Full],{i,Length[variables]}]