(* 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 = {
adp[t], asa[t], asp[t], aspp[t], atp[t], hs[t], hsp[t], nadp[t], nadph[t], phos[t], thr[t]
};

initialValues = {
adp[0] == 0.0, asa[0] == 0.0, asp[0] == 2.0, aspp[0] == 0.0, atp[0] == 10.0, hs[0] == 0.0, hsp[0] == 0.0, nadp[0] == 0.0, nadph[0] == 2.0, phos[0] == 0.0, thr[0] == 2.0
};

rates = {
vak, vasd, vatpase, vhdh, vhk, vnadph\[LetterSpace]endo, vtsy
};

rateEquations = {
vak -> compartment*((vak\[LetterSpace]vm13*(-((adp[t]*aspp[t])/vak\[LetterSpace]keqak) + asp[t]*atp[t]))/((1 + (vak\[LetterSpace]lys/vak\[LetterSpace]k1lys)^vak\[LetterSpace]nak3)*(asp[t] + vak\[LetterSpace]k13*(1 + aspp[t]/vak\[LetterSpace]k13aspp))*(vak\[LetterSpace]k13atp*(1 + adp[t]/vak\[LetterSpace]k13adp) + atp[t])) + (vak\[LetterSpace]vm11*(-((adp[t]*aspp[t])/vak\[LetterSpace]keqak) + asp[t]*atp[t]))/((vak\[LetterSpace]k1atp*(1 + adp[t]/vak\[LetterSpace]k1adp) + atp[t])*(asp[t] + (vak\[LetterSpace]k11*aspp[t])/vak\[LetterSpace]k1aspp + (vak\[LetterSpace]k11*(1 + (thr[t]/vak\[LetterSpace]k1thr)^vak\[LetterSpace]nak1))/(1 + (thr[t]/(vak\[LetterSpace]alpha*vak\[LetterSpace]k1thr))^vak\[LetterSpace]nak1)))), vasd -> (compartment*vasd\[LetterSpace]vm2f*(aspp[t]*nadph[t] - (asa[t]*nadp[t]*phos[t])/vasd\[LetterSpace]k2eq))/((vasd\[LetterSpace]k2nadph*(1 + nadp[t]/vasd\[LetterSpace]k2nadp) + nadph[t])*(aspp[t] + vasd\[LetterSpace]k2aspp*(1 + asa[t]/vasd\[LetterSpace]k2asa)*(1 + phos[t]/vasd\[LetterSpace]k2p))), vatpase -> compartment*vatpase\[LetterSpace]katpase*vatpase\[LetterSpace]prot, vhdh -> (compartment*vhdh\[LetterSpace]vm3f*(-((hs[t]*nadp[t])/vhdh\[LetterSpace]k3eq) + asa[t]*nadph[t])*(1 + (thr[t]/(vhdh\[LetterSpace]alpha3*vhdh\[LetterSpace]k3thr))^vhdh\[LetterSpace]nhdh1))/((vhdh\[LetterSpace]k3asa + asa[t] + (vhdh\[LetterSpace]k3asa*hs[t])/vhdh\[LetterSpace]k3hs)*(vhdh\[LetterSpace]k3nadph*(1 + nadp[t]/vhdh\[LetterSpace]k3nadp) + nadph[t])*(1 + (thr[t]/vhdh\[LetterSpace]k3thr)^vhdh\[LetterSpace]nhdh1)), vhk -> (compartment*vhk\[LetterSpace]vm4f*atp[t]*hs[t])/((1 + vhk\[LetterSpace]lys/vhk\[LetterSpace]k4lys)*(atp[t] + vhk\[LetterSpace]k4atp*(1 + hs[t]/vhk\[LetterSpace]k4ihs))*(hs[t] + vhk\[LetterSpace]k4hs*(1 + atp[t]/vhk\[LetterSpace]k4iatp)*(1 + thr[t]/vhk\[LetterSpace]k4thr))), vnadph\[LetterSpace]endo -> compartment*vnadph\[LetterSpace]endo\[LetterSpace]knadph*vnadph\[LetterSpace]endo\[LetterSpace]prot*nadph[t], vtsy -> (compartment*vtsy\[LetterSpace]vm5*hsp[t])/(vtsy\[LetterSpace]k5hsp + hsp[t])
};

parameters = {
vak\[LetterSpace]vm11 -> 0.15, vak\[LetterSpace]keqak -> 0.00064, vak\[LetterSpace]k11 -> 0.97, vak\[LetterSpace]k1thr -> 0.167, vak\[LetterSpace]nak1 -> 4.09, vak\[LetterSpace]alpha -> 2.47, vak\[LetterSpace]k1aspp -> 0.017, vak\[LetterSpace]k1atp -> 0.98, vak\[LetterSpace]k1adp -> 0.25, vak\[LetterSpace]vm13 -> 0.0722, vak\[LetterSpace]lys -> 0.46, vak\[LetterSpace]k1lys -> 0.391, vak\[LetterSpace]nak3 -> 2.8, vak\[LetterSpace]k13 -> 0.32, vak\[LetterSpace]k13aspp -> 0.017, vak\[LetterSpace]k13atp -> 0.22, vak\[LetterSpace]k13adp -> 0.25, vasd\[LetterSpace]vm2f -> 0.1812, vasd\[LetterSpace]k2eq -> 56.4150334574039, vasd\[LetterSpace]k2aspp -> 0.022, vasd\[LetterSpace]k2asa -> 0.11, vasd\[LetterSpace]k2p -> 10.0, vasd\[LetterSpace]k2nadph -> 0.029, vasd\[LetterSpace]k2nadp -> 0.144, vhdh\[LetterSpace]vm3f -> 1.001, vhdh\[LetterSpace]k3eq -> 3162.27766016838, vhdh\[LetterSpace]k3thr -> 0.097, vhdh\[LetterSpace]nhdh1 -> 1.41, vhdh\[LetterSpace]alpha3 -> 3.93, vhdh\[LetterSpace]k3asa -> 0.24, vhdh\[LetterSpace]k3hs -> 3.39, vhdh\[LetterSpace]k3nadph -> 0.037, vhdh\[LetterSpace]k3nadp -> 0.067, vtsy\[LetterSpace]vm5 -> 0.0434, vtsy\[LetterSpace]k5hsp -> 0.31, vhk\[LetterSpace]vm4f -> 0.1, vhk\[LetterSpace]lys -> 0.46, vhk\[LetterSpace]k4lys -> 9.45, vhk\[LetterSpace]k4atp -> 0.072, vhk\[LetterSpace]k4ihs -> 4.7, vhk\[LetterSpace]k4hs -> 0.11, vhk\[LetterSpace]k4thr -> 1.09, vhk\[LetterSpace]k4iatp -> 4.35, vnadph\[LetterSpace]endo\[LetterSpace]knadph -> 5.4*^-06, vnadph\[LetterSpace]endo\[LetterSpace]prot -> 202.0, vatpase\[LetterSpace]katpase -> 4.1*^-05, vatpase\[LetterSpace]prot -> 202.0, compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
adp[t]->"http://identifiers.org/obo.chebi/CHEBI:16761", adp[t]->"http://identifiers.org/kegg.compound/C00008", asa[t]->"http://identifiers.org/obo.chebi/CHEBI:18051", asa[t]->"http://identifiers.org/kegg.compound/C00441", asp[t]->"http://identifiers.org/obo.chebi/CHEBI:17053", asp[t]->"http://identifiers.org/kegg.compound/C00049", aspp[t]->"http://identifiers.org/obo.chebi/CHEBI:15836", aspp[t]->"http://identifiers.org/kegg.compound/C03082", atp[t]->"http://identifiers.org/obo.chebi/CHEBI:15422", atp[t]->"http://identifiers.org/kegg.compound/C00002", hs[t]->"http://identifiers.org/obo.chebi/CHEBI:15699", hs[t]->"http://identifiers.org/kegg.compound/C00263", hsp[t]->"http://identifiers.org/obo.chebi/CHEBI:15961", hsp[t]->"http://identifiers.org/kegg.compound/C01102", nadp[t]->"http://identifiers.org/obo.chebi/CHEBI:18009", nadp[t]->"http://identifiers.org/kegg.compound/C00006", nadph[t]->"http://identifiers.org/obo.chebi/CHEBI:16474", nadph[t]->"http://identifiers.org/kegg.compound/C00005", phos[t]->"http://identifiers.org/obo.chebi/CHEBI:18367", phos[t]->"http://identifiers.org/kegg.compound/C00009", thr[t]->"http://identifiers.org/obo.chebi/CHEBI:16857", thr[t]->"http://identifiers.org/kegg.compound/C00188"
};

reactionAnnotations = {
vak->"http://identifiers.org/kegg.reaction/R00480", vak->"http://identifiers.org/ec-code/2.7.2.4", vak->"http://identifiers.org/obo.go/GO:0004072", vatpase->"http://identifiers.org/obo.go/GO:0016887", vtsy->"http://identifiers.org/kegg.reaction/R01466", vtsy->"http://identifiers.org/ec-code/4.2.3.1", vtsy->"http://identifiers.org/obo.go/GO:0004795"
};

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

(* Time evolution *)
odes = {
adp'[t] == 1.0*vak +1.0*vhk +1.0*vatpase , asa'[t] == 1.0*vasd -1.0*vhdh, asp'[t] ==  -1.0*vak, aspp'[t] == 1.0*vak -1.0*vasd, atp'[t] ==  -1.0*vak -1.0*vhk -1.0*vatpase, hs'[t] == 1.0*vhdh -1.0*vhk, hsp'[t] == 1.0*vhk -1.0*vtsy, nadp'[t] == 1.0*vasd +1.0*vhdh +1.0*vnadph\[LetterSpace]endo , nadph'[t] ==  -1.0*vasd -1.0*vhdh -1.0*vnadph\[LetterSpace]endo, phos'[t] == 1.0*vasd +1.0*vtsy +1.0*vatpase , thr'[t] == 1.0*vtsy 
};
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]}]