(* 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 = {
x1[t], x10[t], x11[t], x12[t], x13[t], x14[t], x15[t], x16[t], x17[t], x18[t], x19[t], x2[t], x20[t], x21[t], x22[t], x23[t], x24[t], x25[t], x3[t], x4[t], x5[t], x6[t], x7[t], x8[t], x9[t]
};

initialValues = {
x1[0] == 0.001, x10[0] == 0.001, x11[0] == 0.001, x12[0] == 0.001, x13[0] == 0.001, x14[0] == 0.001, x15[0] == 1.5, x16[0] == 1.5, x17[0] == 0.5, x18[0] == 0.2, x19[0] == 0.5, x2[0] == 0.001, x20[0] == 0.5, x21[0] == 5.0, x22[0] == 0.76, x23[0] == 0.07, x24[0] == 0.8, x25[0] == 0.0, x3[0] == 0.001, x4[0] == 0.001, x5[0] == 0.001, x6[0] == 0.001, x7[0] == 0.001, x8[0] == 0.001, x9[0] == 0.001
};

rates = {
R1, R10, R11, R12, R13, R14, R16, R17, R18, R19, R2, R20, R21, R22, R23, R24, R25, R26, R27, R28, R29, R3, R30, R31, R32, R34, R4, R5, R6, R7, R8, R9
};

rateEquations = {
R1 -> (cell*K15*lin*x15[t]*(1 + x11[t]/KI22 + x13[t]/KI21 + x2[t]/KI20 + x4[t]/KI19))/(lin + k15*(1 + x1[t]/ks)), R10 -> (cell*K21*x1[t]*x21[t])/(x1[t] + k21*(1 + x10[t]/ks + x11[t]/ki12 + x3[t]/ki8 + x5[t]/ki7 + x7[t]/ki11)), R11 -> (cell*K24*x10[t]*x24[t])/(x10[t] + k24*(1 + x11[t]/ks)), R12 -> (cell*K21*x10[t]*x21[t])/(x10[t] + k21*(1 + x11[t]/ki12 + x12[t]/ks + x3[t]/ki8 + x5[t]/ki7 + x7[t]/ki11)), R13 -> (cell*K22*x12[t]*x22[t])/(x12[t] + k22*(1 + x13[t]/ks)), R14 -> (cell*K23*x13[t]*x23[t])/(x13[t] + k23*(1 + x11[t]/ki15 + x14[t]/ks + x5[t]/ki14)), R16 -> (a24*cell*x7[t]^2)/(KI24^2 + x7[t]^2), R17 -> cell*ki17*x17[t]*x2[t], R18 -> cell*kd9*x9[t], R19 -> cell*ki5*x20[t]*x6[t], R2 -> (cell*K16*x1[t]*x16[t])/(x1[t] + k16*(1 + x2[t]/ks)), R20 -> cell*ki4*x2[t]*x20[t], R21 -> cell*KI23*x13[t]*x21[t], R22 -> (cell*K22*x12[t]*x22[t])/(129*(k22 + x12[t])), R23 -> cell*kd12*x12[t], R24 -> cell*kd13*x13[t], R25 -> cell*kd8*x8[t], R26 -> cell*kd3*x3[t], R27 -> cell*kd2*x2[t], R28 -> cell*kd16*x16[t], R29 -> cell*kd11*x11[t], R3 -> (cell*K24*x2[t]*x24[t])/(x2[t] + k24*(1 + x3[t]/ks)), R30 -> cell*ki9*x12[t]*x21[t], R31 -> cell*ki10*x10[t]*x21[t], R32 -> cell*ki6*x2[t]*x21[t], R34 -> 0.1*cell*x1[t], R4 -> (cell*K17*x1[t]*x17[t])/(x1[t] + k17*(1 + x3[t]/ki16 + x4[t]/ki18 + x4[t]/ks)), R5 -> (cell*K24*x24[t]*x4[t])/(x4[t] + k24*(1 + x5[t]/ks)), R6 -> (cell*K18*x1[t]*x18[t])/(x1[t] + k18*(1 + x6[t]/ks + x7[t]/ki3)), R7 -> (cell*K19*x19[t]*x6[t])/(x6[t] + k19*(1 + x1[t]/ki1 + x3[t]/ki2 + x7[t]/ks)), R8 -> (cell*K20*x20[t]*x6[t])/(x6[t] + k20*(1 + x8[t]/ks)), R9 -> cell*kd8*x8[t]
};

parameters = {
K15 -> 3600.0, K16 -> 1000.0, K17 -> 1000.0, K18 -> 1000.0, K19 -> 3000.0, K20 -> 1599.0, K21 -> 5000.0, K22 -> 125.0, K23 -> 150.0, K24 -> 500.0, KI19 -> 500.0, KI20 -> 200.0, KI21 -> 500.0, KI22 -> 500.0, KI23 -> 0.053, KI24 -> 2.3*^-05, a24 -> 0.15, k15 -> 2600.0, k16 -> 70.0, k17 -> 50.0, k18 -> 50.0, k19 -> 160.0, k20 -> 4.0, k21 -> 5.0, k22 -> 20.0, k23 -> 3.9, k24 -> 70.0, kd11 -> 0.001, kd12 -> 0.07, kd13 -> 0.01, kd16 -> 0.01, kd2 -> 0.05, kd3 -> 0.01, kd8 -> 0.1, kd9 -> 0.001, ki1 -> 0.3, ki10 -> 0.01, ki11 -> 15.0, ki12 -> 6.3, ki14 -> 0.2, ki15 -> 0.86, ki16 -> 10.0, ki17 -> 10.0, ki18 -> 10.0, ki2 -> 30.0, ki3 -> 30.0, ki4 -> 0.6, ki5 -> 0.1, ki6 -> 0.01, ki7 -> 30.0, ki8 -> 4.0, ki9 -> 0.175, ks -> 500.0, lin -> 12.0, cell -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
x1[t]->"http://identifiers.org/obo.chebi/CHEBI:15843", x1[t]->"http://identifiers.org/kegg.compound/C00219", x10[t]->"http://identifiers.org/obo.chebi/CHEBI:15632", x10[t]->"http://identifiers.org/kegg.compound/C05356", x11[t]->"http://identifiers.org/obo.chebi/CHEBI:28209", x11[t]->"http://identifiers.org/kegg.compound/C04805", x12[t]->"http://identifiers.org/obo.chebi/CHEBI:15651", x13[t]->"http://identifiers.org/obo.chebi/CHEBI:15647", x14[t]->"http://identifiers.org/obo.chebi/CHEBI:15646", x15[t]->"http://identifiers.org/uniprot/P04054", x16[t]->"http://identifiers.org/uniprot/P16050", x17[t]->"http://identifiers.org/uniprot/P18054", x19[t]->"http://identifiers.org/uniprot/Q9H7Z7", x2[t]->"http://identifiers.org/obo.chebi/CHEBI:15628", x2[t]->"http://identifiers.org/kegg.compound/C05966", x20[t]->"http://identifiers.org/uniprot/P24557", x21[t]->"http://identifiers.org/uniprot/P09917", x22[t]->"http://identifiers.org/uniprot/P09960", x23[t]->"http://identifiers.org/uniprot/Q08477", x24[t]->"http://identifiers.org/uniprot/P36969", x3[t]->"http://identifiers.org/obo.chebi/CHEBI:15558", x3[t]->"http://identifiers.org/kegg.compound/C04742", x4[t]->"http://identifiers.org/obo.chebi/CHEBI:15626", x4[t]->"http://identifiers.org/kegg.compound/C05965", x5[t]->"http://identifiers.org/obo.chebi/CHEBI:34146", x5[t]->"http://identifiers.org/kegg.compound/C14777", x6[t]->"http://identifiers.org/obo.chebi/CHEBI:15554", x6[t]->"http://identifiers.org/kegg.compound/C00427", x7[t]->"http://identifiers.org/obo.chebi/CHEBI:15551", x7[t]->"http://identifiers.org/kegg.compound/C00584", x8[t]->"http://identifiers.org/obo.chebi/CHEBI:15627", x8[t]->"http://identifiers.org/kegg.compound/C02198", x9[t]->"http://identifiers.org/obo.chebi/CHEBI:28728", x9[t]->"http://identifiers.org/kegg.compound/C05963"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
x1'[t] == 1.0*R1 -1.0*R2 -1.0*R4 -1.0*R6 -1.0*R10 -1.0*R34, x10'[t] == 1.0*R10 -1.0*R11 -1.0*R12, x11'[t] == 1.0*R11 -1.0*R29, x12'[t] == 1.0*R12 -1.0*R13 -1.0*R23, x13'[t] == 1.0*R13 -1.0*R14 -1.0*R24, x14'[t] == 1.0*R14 , x15'[t] == 0.0 , x16'[t] == 1.0*R16 -1.0*R28, x17'[t] ==  -1.0*R17, x18'[t] == 0.0 , x19'[t] == 0.0 , x2'[t] == 1.0*R2 -1.0*R3 -1.0*R27, x20'[t] ==  -1.0*R20 -1.0*R19, x21'[t] == 1.0*R21 -1.0*R30 -1.0*R31 -1.0*R32, x22'[t] ==  -1.0*R22, x23'[t] == 0.0 , x24'[t] == 0.0 , x25'[t] == 0.0 , x3'[t] == 1.0*R3 -1.0*R26, x4'[t] == 1.0*R4 -1.0*R5, x5'[t] == 1.0*R5 , x6'[t] == 1.0*R6 -1.0*R7 -1.0*R8, x7'[t] == 1.0*R7 , x8'[t] == 1.0*R8 -1.0*R25, x9'[t] == 1.0*R9 -1.0*R18
};
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]}]