(* 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 = {
II[t], IIa[t], IIa\[LetterSpace]ATIII[t], IIa\[LetterSpace]alpha2M[t], PL[t], PT[t], RVV[t], V[t], Va[t], X[t], Xa[t], Xa\[LetterSpace]ATIII[t]
};

initialValues = {
II[0] == 1.4, IIa[0] == 0.0, IIa\[LetterSpace]ATIII[0] == 0.0, IIa\[LetterSpace]alpha2M[0] == 0.0, PL[0] == 0.04999999, PT[0] == 0.0, RVV[0] == 0.03, V[0] == 0.02999999, Va[0] == 0.0, X[0] == 0.1999999, Xa[0] == 0.0, Xa\[LetterSpace]ATIII[0] == 0.0
};

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

rateEquations = {
R1 -> compartment\[LetterSpace]1*HenriMichaelisMenten\[LetterSpace]irreversible\[LetterSpace]kcat[kcat\[LetterSpace]X, RVV[t], X[t], km\[LetterSpace]X], R2 -> compartment\[LetterSpace]1*ki\[LetterSpace]Xa*Xa[t], R3 -> compartment\[LetterSpace]1*(-(k\[LetterSpace]PL*PT[t]) + k\[LetterSpace]PT*PL[t]*Va[t]*Xa[t]), R4 -> compartment\[LetterSpace]1*HenriMichaelisMenten\[LetterSpace]irreversible\[LetterSpace]kcat[kcat\[LetterSpace]V, IIa[t], V[t], km\[LetterSpace]V], R5 -> compartment\[LetterSpace]1*HenriMichaelisMenten\[LetterSpace]irreversible\[LetterSpace]kcat[kcat\[LetterSpace]II, PT[t], II[t], km\[LetterSpace]II], R6 -> compartment\[LetterSpace]1*HenriMichaelisMenten\[LetterSpace]irreversible\[LetterSpace]kcat[kcat\[LetterSpace]2, Xa[t], II[t], km\[LetterSpace]2], R7 -> compartment\[LetterSpace]1*ki\[LetterSpace]IIaAlpha2M*IIa[t], R8 -> compartment\[LetterSpace]1*ki\[LetterSpace]IIaATIII*IIa[t]
};

parameters = {
k\[LetterSpace]PL -> 801.4, k\[LetterSpace]PT -> 122.9, kcat\[LetterSpace]2 -> 12.4, kcat\[LetterSpace]II -> 43.87, kcat\[LetterSpace]V -> 7.844, kcat\[LetterSpace]X -> 239.1, ki\[LetterSpace]IIaATIII -> 0.7859, ki\[LetterSpace]IIaAlpha2M -> 0.1762, ki\[LetterSpace]Xa -> 4.531, km\[LetterSpace]2 -> 0.06148, km\[LetterSpace]II -> 62.25, km\[LetterSpace]V -> 149.7, km\[LetterSpace]X -> 23.65, compartment\[LetterSpace]1 -> 1.0
};

assignments = {
HenriMichaelisMenten\[LetterSpace]irreversible\[LetterSpace]kcat[kcat_,enzyme_,substrate_,Km_] -> (enzyme*kcat*substrate)/(Km + substrate), AmAct -> IIa[t] + 0.556*IIa\[LetterSpace]alpha2M[t]
};

events = {

};

speciesAnnotations = {
II[t]->"http://identifiers.org/uniprot/P00734", IIa[t]->"http://identifiers.org/uniprot/P00734", V[t]->"http://identifiers.org/uniprot/P12259", Va[t]->"http://identifiers.org/uniprot/P12259", X[t]->"http://identifiers.org/uniprot/P00742", Xa[t]->"http://identifiers.org/uniprot/P00742"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
II'[t] ==  -1.0*R5 -1.0*R6, IIa'[t] == 1.0*R5 +1.0*R6 -1.0*R7 -1.0*R8, IIa\[LetterSpace]ATIII'[t] == 1.0*R8 , IIa\[LetterSpace]alpha2M'[t] == 1.0*R7 , PL'[t] ==  -1.0*R3, PT'[t] == 1.0*R3 , RVV'[t] == 0.0 , V'[t] ==  -1.0*R4, Va'[t] == 1.0*R4 -1.0*R3, X'[t] ==  -1.0*R1, Xa'[t] == 1.0*R1 -1.0*R2 -1.0*R3, Xa\[LetterSpace]ATIII'[t] == 1.0*R2 
};
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]}]