(* 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 = {
a[t], b[t], c[t]
};

initialValues = {
a[0] == 0.01, b[0] == 0.01, c[0] == 0.01
};

rates = {
R1, R2, R3, R4, R5, R6, R7, R8
};

rateEquations = {
R1 -> compartment*Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[R1\[LetterSpace]v], R2 -> compartment*linear\[LetterSpace]activation[R2\[LetterSpace]constant, a[t]], R3 -> compartment*Irr\[LetterSpace]Michaelis\[LetterSpace]Menten\[LetterSpace]\[LetterSpace]enzyme\[LetterSpace]\[LetterSpace]userdefined[R3\[LetterSpace]V, b[t], a[t], R3\[LetterSpace]Km], R4 -> compartment*Irr\[LetterSpace]Michaelis\[LetterSpace]Menten\[LetterSpace]\[LetterSpace]enzyme\[LetterSpace]\[LetterSpace]userdefined[R4\[LetterSpace]V, c[t], a[t], R4\[LetterSpace]Km], R5 -> compartment*linear\[LetterSpace]activation[R5\[LetterSpace]constant, a[t]], R6 -> compartment*Henri\[LetterSpace]Michaelis\[LetterSpace]Menten\[LetterSpace]\[LetterSpace]irreversible[b[t], R6\[LetterSpace]Km, R6\[LetterSpace]V], R7 -> compartment*linear\[LetterSpace]activation[R7\[LetterSpace]constant, a[t]], R8 -> compartment*Henri\[LetterSpace]Michaelis\[LetterSpace]Menten\[LetterSpace]\[LetterSpace]irreversible[c[t], R8\[LetterSpace]Km, R8\[LetterSpace]V]
};

parameters = {
R1\[LetterSpace]v -> 0.212, R2\[LetterSpace]constant -> 2.9, R3\[LetterSpace]V -> 1.52, R3\[LetterSpace]Km -> 0.19, R4\[LetterSpace]V -> 4.88, R4\[LetterSpace]Km -> 1.18, R5\[LetterSpace]constant -> 1.24, R6\[LetterSpace]Km -> 29.09, R6\[LetterSpace]V -> 32.24, R7\[LetterSpace]constant -> 13.58, R8\[LetterSpace]Km -> 0.16, R8\[LetterSpace]V -> 153.0, compartment -> 1*^-13
};

assignments = {
Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[v_] -> v, Henri\[LetterSpace]Michaelis\[LetterSpace]Menten\[LetterSpace]\[LetterSpace]irreversible[substrate_,Km_,V_] -> (substrate*V)/(Km + substrate), linear\[LetterSpace]activation[constant_,Activator_] -> Activator*constant, Irr\[LetterSpace]Michaelis\[LetterSpace]Menten\[LetterSpace]\[LetterSpace]enzyme\[LetterSpace]\[LetterSpace]userdefined[V_,E_,S_,Km_] -> (E*S*V)/(Km + S)
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
a'[t] == 1.0*R1 +1.0*R2 -1.0*R3 -1.0*R4, b'[t] == 1.0*R5 -1.0*R6, c'[t] == 1.0*R7 -1.0*R8
};
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]}]