(* 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 = {
C[t], M[t], X[t], Y[t], Z[t]
};

initialValues = {
C[0] == 0.0, M[0] == 0.0, X[0] == 0.0, Y[0] == 0.0, Z[0] == 0.0
};

rates = {
reaction1, reaction10, reaction11, reaction12, reaction13, reaction2, reaction3, reaction4, reaction5, reaction6, reaction7, reaction8, reaction9
};

rateEquations = {
reaction1 -> reaction1\[LetterSpace]vi, reaction10 -> reaction10\[LetterSpace]alpha*reaction10\[LetterSpace]d1*Z[t], reaction11 -> reaction11\[LetterSpace]alpha*reaction11\[LetterSpace]kd*Z[t], reaction12 -> reaction12\[LetterSpace]vs, reaction13 -> reaction13\[LetterSpace]d1*Y[t], reaction2 -> (reaction2\[LetterSpace]k1*C[t]*X[t])/(reaction2\[LetterSpace]K5 + C[t]), reaction3 -> reaction3\[LetterSpace]kd*C[t], reaction4 -> (V1*(1 - M[t]))/(1 + reaction4\[LetterSpace]K1 - M[t]), reaction5 -> (reaction5\[LetterSpace]V2*M[t])/(reaction5\[LetterSpace]K2 + M[t]), reaction6 -> (V3*(1 - X[t]))/(1 + reaction6\[LetterSpace]K3 - X[t]), reaction7 -> (reaction7\[LetterSpace]V4*X[t])/(reaction7\[LetterSpace]K4 + X[t]), reaction8 -> reaction8\[LetterSpace]a1*C[t]*Y[t], reaction9 -> reaction9\[LetterSpace]a2*Z[t]
};

parameters = {
K6 -> 0.3, V1p -> 0.75, V3p -> 0.3, reaction1\[LetterSpace]vi -> 0.1, reaction2\[LetterSpace]k1 -> 0.5, reaction2\[LetterSpace]K5 -> 0.02, reaction3\[LetterSpace]kd -> 0.02, reaction4\[LetterSpace]K1 -> 0.1, reaction5\[LetterSpace]V2 -> 0.25, reaction5\[LetterSpace]K2 -> 0.1, reaction6\[LetterSpace]K3 -> 0.2, reaction7\[LetterSpace]K4 -> 0.1, reaction7\[LetterSpace]V4 -> 0.1, reaction8\[LetterSpace]a1 -> 0.05, reaction9\[LetterSpace]a2 -> 0.05, reaction10\[LetterSpace]alpha -> 0.1, reaction10\[LetterSpace]d1 -> 0.05, reaction11\[LetterSpace]kd -> 0.02, reaction11\[LetterSpace]alpha -> 0.1, reaction12\[LetterSpace]vs -> 0.2, reaction13\[LetterSpace]d1 -> 0.05, Cell -> 1.0
};

assignments = {
V3 -> V3p*M[t], V1 -> (V1p*C[t])/(K6 + C[t])
};

events = {

};

speciesAnnotations = {
C[t]->"http://identifiers.org/interpro/IPR006670"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
C'[t] == 1.0*reaction1 +1.0*reaction9 +1.0*reaction10 -1.0*reaction2 -1.0*reaction3 -1.0*reaction8, M'[t] == 1.0*reaction4 -1.0*reaction5, X'[t] == 1.0*reaction6 -1.0*reaction7, Y'[t] == 1.0*reaction9 +1.0*reaction11 +1.0*reaction12 -1.0*reaction8 -1.0*reaction13, Z'[t] == 1.0*reaction8 -1.0*reaction9 -1.0*reaction10 -1.0*reaction11
};
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]}]