(* 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 = {
W\[LetterSpace]star[t], Wt[t], Y[t], Z[t]
};

initialValues = {
W\[LetterSpace]star[0] == 0.0, Wt[0] == 1.0, Y[0] == 1.6, Z[0] == 0.15
};

rates = {
Protein\[LetterSpace]Phosphorylation, R0, R1, R2, R3, R\[LetterSpace]eff, Rf
};

rateEquations = {
Protein\[LetterSpace]Phosphorylation -> (cytosol*vp*((vk*(1 - W\[LetterSpace]star[t]))/(vp*(1 + K1 - W\[LetterSpace]star[t])) - W\[LetterSpace]star[t]/(K2 + W\[LetterSpace]star[t])))/Wt[t], R0 -> cytosol*v0, R1 -> cytosol*v1\[LetterSpace]beta, R2 -> (cytosol*Vm2*Z[t]^n)/(Kp^n + Z[t]^n), R3 -> (store*Vm3*Y[t]^m*Z[t]^p)/((Kr^m + Y[t]^m)*(K\[LetterSpace]A^p + Z[t]^p)), R\[LetterSpace]eff -> cytosol*k*Z[t], Rf -> kf*store*Y[t]
};

parameters = {
K1 -> 0.01, K2 -> 0.01, K\[LetterSpace]A -> 0.9, Ka -> 2.5, Kp -> 1.0, Kr -> 2.0, Vm2 -> 65.0, Vm3 -> 500.0, k -> 10.0, kf -> 1.0, m -> 2.0, n -> 2.0, p -> 4.0, q -> 1.0, v0 -> 1.0, v1\[LetterSpace]beta -> 2.7, vMK -> 20.0, vp -> 2.5, cytosol -> 1.0, store -> 1.0
};

assignments = {
vk -> (vMK*Z[t]^q)/(Ka^q + Z[t]^q)
};

events = {

};

speciesAnnotations = {
Y[t]->"http://identifiers.org/chebi/CHEBI:29108", Y[t]->"http://identifiers.org/kegg.compound/C00076", Z[t]->"http://identifiers.org/chebi/CHEBI:29108", Z[t]->"http://identifiers.org/kegg.compound/C00076"
};

reactionAnnotations = {
Protein\[LetterSpace]Phosphorylation->"http://identifiers.org/go/GO:0042327", R0->"http://identifiers.org/go/GO:0006816", R1->"http://identifiers.org/go/GO:0005220", R2->"http://identifiers.org/go/GO:0032470", R3->"http://identifiers.org/go/GO:0048763", R3->"http://identifiers.org/go/GO:0007204", R\[LetterSpace]eff->"http://identifiers.org/go/GO:0006816", Rf->"http://identifiers.org/go/GO:0006816"
};

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

(* Time evolution *)
odes = {
W\[LetterSpace]star'[t] == 1.0*Protein\[LetterSpace]Phosphorylation , Wt'[t] == 0.0 , Y'[t] == 1.0*R2 -1.0*R3 -1.0*Rf, Z'[t] == 1.0*R0 +1.0*R1 +1.0*R3 +1.0*Rf -1.0*R2 -1.0*R\[LetterSpace]eff
};
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]}]