(* 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 = {
AprE[t], DegU[t], DegUP[t], Dim[t], mAprE[t], mDegU[t]
};

initialValues = {
AprE[0] == 0.0, DegU[0] == 0.0, DegUP[0] == 0.0, Dim[0] == 0.0, mAprE[0] == 0.0, mDegU[0] == 0.0
};

rates = {
AprEdeg, AprEsyn, DimerAss, DimerDis, degradation1, degradation2, degradation3, degradationmRNA, dephosphorylation, mRNAAprEdeg, mRNAAprEsyn, phosphorylation, synthesisDegU, synthesismRNA
};

rateEquations = {
AprEdeg -> kdeg*AprE[t], AprEsyn -> ksyn*univ*mAprE[t], DimerAss -> ka*DegUP[t]^2, DimerDis -> kd*Dim[t], degradation1 -> kdeg*univ*DegU[t], degradation2 -> kdeg*univ*DegUP[t], degradation3 -> kdeg*univ*Dim[t], degradationmRNA -> kdegm*mDegU[t], dephosphorylation -> kdephos*DegUP[t], mRNAAprEdeg -> kdegm*mAprE[t], mRNAAprEsyn -> (Kr1*((Irmax*univ^2*Dim[t]^2)/(Kdim^2*(1 + R/Kr + (univ*Dim[t])/Kdim + (univ^2*Dim[t]^2)/Kdim^2)) + (Iro*(1 + (univ*Dim[t])/Kdim))/(1 + R/Kr + (univ*Dim[t])/Kdim + (univ^2*Dim[t]^2)/Kdim^2)))/(Kr1 + R), phosphorylation -> kphos*DegU[t], synthesisDegU -> ksyn1*univ*mDegU[t], synthesismRNA -> (Io*K)/(K + univ*Dim[t]) + (Imax*univ*Dim[t])/(K + univ*Dim[t])
};

parameters = {
Imax -> 0.048, Io -> 0.004, Irmax -> 0.4, Iro -> 0.02, K -> 7.0, Kdim -> 12.0, Kr -> 7.0, Kr1 -> 7.0, R -> 7.0, V -> 1.0, ka -> 0.025, kd -> 0.1, kdeg -> 0.0004, kdegA -> 0.0001, kdegm -> 0.01, ksyn -> 0.04, ksyn1 -> 0.04, p -> 0.15, q -> 0.004, ratio -> 0.026666667, univ -> 1.0
};

assignments = {
DegU\[LetterSpace]Total -> DegU[t] + DegUP[t] + 2*Dim[t], kdephos -> q/ratio, kphos -> p*ratio
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
AprE'[t] == 1.0*AprEsyn -1.0*AprEdeg, DegU'[t] == 1.0*dephosphorylation +1.0*synthesisDegU -1.0*degradation1 -1.0*phosphorylation, DegUP'[t] == 2.0*DimerDis +1.0*phosphorylation -2.0*DimerAss -1.0*degradation2 -1.0*dephosphorylation, Dim'[t] == 1.0*DimerAss -1.0*DimerDis -1.0*degradation3, mAprE'[t] == 1.0*mRNAAprEsyn -1.0*mRNAAprEdeg, mDegU'[t] == 1.0*synthesismRNA -1.0*degradationmRNA
};
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]}]