(* 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 = {
E[t], E\[LetterSpace]M[t], E\[LetterSpace]M1[t], E\[LetterSpace]P1[t], E\[LetterSpace]P2[t], E\[LetterSpace]P21[t], E\[LetterSpace]P\[LetterSpace]1[t], E\[LetterSpace]P\[LetterSpace]2[t], M[t], M1[t], P[t], P2[t], P21[t], T[t]
};

initialValues = {
E[0] == 0.00015, E\[LetterSpace]M[0] == 0.0, E\[LetterSpace]M1[0] == 0.0, E\[LetterSpace]P1[0] == 0.0, E\[LetterSpace]P2[0] == 0.0, E\[LetterSpace]P21[0] == 0.0, E\[LetterSpace]P\[LetterSpace]1[0] == 0.0, E\[LetterSpace]P\[LetterSpace]2[0] == 0.0, M[0] == 0.0, M1[0] == 0.0, P[0] == 1.0, P2[0] == 0.0, P21[0] == 0.0, T[0] == 0.0
};

rates = {
r1, r10, r11, r12, r13, r14, r15, r16, r2, r3, r4, r5, r6, r7, r8, r9
};

rateEquations = {
r1 -> compartment*(-(j1*E\[LetterSpace]P\[LetterSpace]1[t]) + k1*E[t]*P[t]), r10 -> compartment*k10*P2[t], r11 -> compartment*(-(j7*E\[LetterSpace]P21[t]) + k7*E[t]*P21[t]), r12 -> compartment*(-(j7a*E\[LetterSpace]P2[t]) + k7a*E[t]*P2[t]), r13 -> compartment*k8*E\[LetterSpace]P21[t], r14 -> compartment*k8a*E\[LetterSpace]P2[t], r15 -> compartment*kC1*E\[LetterSpace]P\[LetterSpace]1[t], r16 -> compartment*kC2*E\[LetterSpace]P\[LetterSpace]2[t], r2 -> compartment*k2*E\[LetterSpace]P\[LetterSpace]1[t], r3 -> compartment*k9*M[t], r4 -> compartment*(-(j3*E\[LetterSpace]M1[t]) + k3*E[t]*M1[t]), r5 -> compartment*(-(j3a*E\[LetterSpace]M[t]) + k3a*E[t]*M[t]), r6 -> compartment*k4*E\[LetterSpace]M1[t], r7 -> compartment*k4a*E\[LetterSpace]M[t], r8 -> compartment*(-(j5*E\[LetterSpace]P\[LetterSpace]2[t]) + k5*E[t]*P[t]), r9 -> compartment*k6*E\[LetterSpace]P\[LetterSpace]2[t]
};

parameters = {
j1 -> 33.4, j3 -> 1.58*^-06, j3a -> 0.185, j5 -> 21.8, j7 -> 4.46*^-09, j7a -> 2.66*^-05, k1 -> 91.8, k10 -> 7.23*^-10, k2 -> 82.4, k3 -> 38.1, k3a -> 151.5, k4 -> 38.1, k4a -> 209.9, k5 -> 5.16, k6 -> 32.3, k7 -> 6.76*^-08, k7a -> 4.7, k8 -> 0.00599, k8a -> 42.6, k9 -> 3.12*^-08, kC1 -> 2.39*^-06, kC2 -> 0.031, compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
T[t]->"http://identifiers.org/chebi/CHEBI:9574"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
E'[t] == 1.0*r2 +1.0*r6 +1.0*r7 +1.0*r9 +1.0*r13 +1.0*r14 -1.0*r1 -1.0*r4 -1.0*r5 -1.0*r8 -1.0*r11 -1.0*r12, E\[LetterSpace]M'[t] == 1.0*r5 -1.0*r7, E\[LetterSpace]M1'[t] == 1.0*r4 -1.0*r6, E\[LetterSpace]P1'[t] == 0.0 , E\[LetterSpace]P2'[t] == 1.0*r12 -1.0*r14, E\[LetterSpace]P21'[t] == 1.0*r11 -1.0*r13, E\[LetterSpace]P\[LetterSpace]1'[t] == 1.0*r1 -1.0*r2 -1.0*r15, E\[LetterSpace]P\[LetterSpace]2'[t] == 1.0*r8 -1.0*r9 -1.0*r16, M'[t] == 1.0*r2 -1.0*r3 -1.0*r5, M1'[t] == 1.0*r3 -1.0*r4, P'[t] ==  -1.0*r1 -1.0*r8, P2'[t] == 1.0*r9 -1.0*r10 -1.0*r12, P21'[t] == 1.0*r10 -1.0*r11, T'[t] == 1.0*r6 +1.0*r7 +1.0*r13 +1.0*r14 +1.0*r15 +1.0*r16 
};
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]}]