(* 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], AMP[t], ATP[t], AcAld[t], BPG[t], DHAP[t], F16bP[t], F6P[t], G6P[t], GAP[t], GLC[t], NAD[t], NADH[t], P2G[t], P3G[t], PEP[t], PYR[t]
};

initialValues = {
ADP[0] == 1.29, AMP[0] == 0.44, ATP[0] == 4.29, AcAld[0] == 0.178140579850657, BPG[0] == 0.000736873499865602, DHAP[0] == 0.290344213186674, F16bP[0] == 1.14580464751733, F6P[0] == 0.0588603054728053, G6P[0] == 0.193120800911304, GAP[0] == 0.0789727571926259, GLC[0] == 1.5700004483456, NAD[0] == 1.50329030201531, NADH[0] == 0.0867096979846952, P2G[0] == 0.0169344770274836, P3G[0] == 0.117456252783611, PEP[0] == 0.152501353339511, PYR[0] == 0.527117851793548
};

rates = {
ADH, AK, ATPase, ENO, FBA, GPM, HXKGLK1, HXKHXK1, HXKHXK2, HXT, PDC, PFK, PGI, PGK, PYK, TDH, TPI, glycerolbranch, glycogenbranch, succinatebranch, trehalosebranch
};

rateEquations = {
ADH -> (ADHVmax*(-((EtOH*NAD[t])/(ADHKacald*ADHKeq*ADHKinadh)) + (AcAld[t]*NADH[t])/(ADHKacald*ADHKinadh)))/(1 + (ADHKnad*EtOH)/(ADHKetoh*ADHKinad) + (ADHKnadh*AcAld[t])/(ADHKacald*ADHKinadh) + NAD[t]/ADHKinad + (EtOH*NAD[t])/(ADHKetoh*ADHKinad) + (ADHKnadh*AcAld[t]*NAD[t])/(ADHKacald*ADHKinad*ADHKinadh) + (EtOH*AcAld[t]*NAD[t])/(ADHKetoh*ADHKiacald*ADHKinad) + NADH[t]/ADHKinadh + (ADHKnad*EtOH*NADH[t])/(ADHKetoh*ADHKinad*ADHKinadh) + (AcAld[t]*NADH[t])/(ADHKacald*ADHKinadh) + (EtOH*AcAld[t]*NADH[t])/(ADHKacald*ADHKietoh*ADHKinadh)), AK -> AKk*(ADP[t]^2 - (AMP[t]*ATP[t])/AKKeq), ATPase -> ATPasek*ATP[t], ENO -> (ENOVmax*(P2G[t]/ENOKp2g - PEP[t]/(ENOKeq*ENOKp2g)))/(1 + P2G[t]/ENOKp2g + PEP[t]/ENOKpep), FBA -> (FBAVmax*(F16bP[t]/FBAKf16bp - (DHAP[t]*GAP[t])/(FBAKeq*FBAKf16bp)))/(1 + DHAP[t]/FBAKdhap + F16bP[t]/FBAKf16bp + GAP[t]/FBAKgap + (DHAP[t]*GAP[t])/(FBAKdhap*FBAKgap) + (F16bP[t]*GAP[t])/(FBAKf16bp*FBAKigap)), GPM -> (GPMVmax*(-(P2G[t]/(GPMKeq*GPMKp3g)) + P3G[t]/GPMKp3g))/(1 + P2G[t]/GPMKp2g + P3G[t]/GPMKp3g), HXKGLK1 -> (GLK1*HXKGLK1kcat*(-((ADP[t]*G6P[t])/(HXKGLK1Katp*HXKGLK1Kglc*KeqHXK)) + (ATP[t]*GLC[t])/(HXKGLK1Katp*HXKGLK1Kglc)))/((1 + ADP[t]/HXKGLK1Kadp + ATP[t]/HXKGLK1Katp)*(1 + G6P[t]/HXKGLK1Kg6p + GLC[t]/HXKGLK1Kglc)), HXKHXK1 -> (HXK1*HXKHXK1kcat*(-((ADP[t]*G6P[t])/(HXKHXK1Katp*HXKHXK1Kglc*KeqHXK)) + (ATP[t]*GLC[t])/(HXKHXK1Katp*HXKHXK1Kglc)))/((1 + ADP[t]/HXKHXK1Kadp + ATP[t]/HXKHXK1Katp)*(1 + G6P[t]/HXKHXK1Kg6p + GLC[t]/HXKHXK1Kglc)), HXKHXK2 -> (HXK2*HXKHXK2kcat*(-((ADP[t]*G6P[t])/(HXKHXK2Katp*HXKHXK2Kglc*KeqHXK)) + (ATP[t]*GLC[t])/(HXKHXK2Katp*HXKHXK2Kglc)))/((1 + ADP[t]/HXKHXK2Kadp + ATP[t]/HXKHXK2Katp)*(1 + G6P[t]/HXKHXK2Kg6p + GLC[t]/HXKHXK2Kglc)), HXT -> (HXTVmax*(GLCx - GLC[t]))/(HXTKglc*(1 + GLCx/HXTKglc + GLC[t]/HXTKglc + (GLCx*HXTKi*GLC[t])/HXTKglc^2)), PDC -> (PDCVmax*(PYR[t]/PDCKpyr)^PDCnH)/(1 + (PYR[t]/PDCKpyr)^PDCnH), PFK -> (PFKgR*PFKVmax*ATP[t]*(1 - (ADP[t]*F16bP[t])/(PFKKeq*ATP[t]*F6P[t]))*F6P[t]*(1 + ADP[t]/PFKKadp + ATP[t]/PFKKatp + F16bP[t]/PFKKf16 + (PFKgR*ADP[t]*F16bP[t])/(PFKKadp*PFKKf16) + F6P[t]/PFKKf6p + (PFKgR*ATP[t]*F6P[t])/(PFKKatp*PFKKf6p)))/(PFKKatp*PFKKf6p*((PFKL0*(1 + (PFKCamp*AMP[t])/PFKKamp)^2*(1 + (PFKCatp*ATP[t])/PFKKatp)^2*(1 + (PFKCiatp*ATP[t])/PFKKiatp)^2*(1 + (F26bP*PFKCf26)/PFKKf26 + (PFKCf16*F16bP[t])/PFKKf16)^2)/((1 + AMP[t]/PFKKamp)^2*(1 + ATP[t]/PFKKiatp)^2*(1 + F26bP/PFKKf26 + F16bP[t]/PFKKf16)^2) + (1 + ADP[t]/PFKKadp + ATP[t]/PFKKatp + F16bP[t]/PFKKf16 + (PFKgR*ADP[t]*F16bP[t])/(PFKKadp*PFKKf16) + F6P[t]/PFKKf6p + (PFKgR*ATP[t]*F6P[t])/(PFKKatp*PFKKf6p))^2)), PGI -> (PGIVmax*(-(F6P[t]/(PGIKeq*PGIKg6p)) + G6P[t]/PGIKg6p))/(1 + F6P[t]/PGIKf6p + G6P[t]/PGIKg6p), PGK -> (PGKVmax*((ADP[t]*BPG[t])/(PGKKadp*PGKKbpg) - (ATP[t]*P3G[t])/(PGKKadp*PGKKbpg*PGKKeq)))/((1 + ADP[t]/PGKKadp + ATP[t]/PGKKatp)*(1 + BPG[t]/PGKKbpg + P3G[t]/PGKKp3g)), PYK -> (PYKVmax*((ADP[t]*PEP[t])/(PYKKadp*PYKKpep) - (ATP[t]*PYR[t])/(PYKKadp*PYKKeq*PYKKpep)))/((1 + ADP[t]/PYKKadp + ATP[t]/PYKKatp)*(1 + PEP[t]/PYKKpep + PYR[t]/PYKKpyr)), TDH -> (TDHVmax*((GAP[t]*NAD[t])/(TDHKgap*TDHKnad) - (BPG[t]*NADH[t])/(TDHKeq*TDHKgap*TDHKnad)))/((1 + BPG[t]/TDHKbpg + GAP[t]/TDHKgap)*(1 + NAD[t]/TDHKnad + NADH[t]/TDHKnadh)), TPI -> TPIk*(DHAP[t] - GAP[t]/TPIKeq), glycerolbranch -> (glycerolbranchVmax*(-((GLY*NAD[t])/(glycerolbranchKdhap*glycerolbranchKeq*glycerolbranchKnadh)) + (DHAP[t]*NADH[t])/(glycerolbranchKdhap*glycerolbranchKnadh)))/((1 + GLY/glycerolbranchKgly + DHAP[t]/glycerolbranchKdhap)*(1 + NAD[t]/glycerolbranchKnad + NADH[t]/glycerolbranchKnadh)), glycogenbranch -> glycogenbranchk*ATP[t]*G6P[t], succinatebranch -> succinatebranchk*AcAld[t]*NAD[t], trehalosebranch -> trehalosebranchk*ATP[t]*G6P[t]
};

parameters = {
ADH1 -> 0.0409771277320022, ADH5 -> 0.00106249605621922, ADHKacald -> 1.11, ADHKeq -> 14492.7536231884, ADHKetoh -> 17.0, ADHKiacald -> 1.1, ADHKietoh -> 90.0, ADHKinad -> 0.92, ADHKinadh -> 0.031, ADHKnad -> 0.17, ADHKnadh -> 0.11, ADHVmax -> 111.334973497906, AKKeq -> 0.45, AKk -> 0.75, ATPasek -> 0.658333333333333, CDC19 -> 0.512097526792801, ENO1 -> 0.171592988538958, ENO2 -> 0.493611573294543, ENOKeq -> 6.7, ENOKp2g -> 0.04, ENOKpep -> 0.5, ENOVmax -> 3.36, EXTERNAL -> 0.0, F26bP -> 0.003, FBA1 -> 0.0367018202831552, FBAKdhap -> 2.0, FBAKeq -> 0.069, FBAKf16bp -> 0.3, FBAKgap -> 2.4, FBAKigap -> 10.0, FBAVmax -> 1.57816666666667, GLK1 -> 0.0112717406104807, GPM1 -> 0.182500074724267, GPMKeq -> 0.19, GPMKp2g -> 0.08, GPMKp3g -> 1.2, GPMVmax -> 43.0833333333333, HXK1 -> 0.0041951864287446, HXK2 -> 0.0153328384926289, HXKGLK1Kadp -> 0.23, HXKGLK1Katp -> 0.865, HXKGLK1Kg6p -> 30.0, HXKGLK1Kglc -> 0.0106, HXKGLK1kcat -> 0.0721, HXKHXK1Kadp -> 0.23, HXKHXK1Katp -> 0.293, HXKHXK1Kg6p -> 30.0, HXKHXK1Kglc -> 0.15, HXKHXK1kcat -> 10.2, HXKHXK2Kadp -> 0.23, HXKHXK2Katp -> 0.195, HXKHXK2Kg6p -> 30.0, HXKHXK2Kglc -> 0.2, HXKHXK2kcat -> 63.1, HXTKglc -> 0.9, HXTKi -> 0.91, HXTVmax -> 3.35, KeqHXK -> 2000.0, NA -> 6.02214*^+20, PDC1 -> 0.266952694557084, PDC5 -> 0.00308868608169189, PDC6 -> 0.0016352160527653, PDCKpyr -> 4.33, PDCVmax -> 14.2966666666667, PDCnH -> 1.9, PFK1 -> 0.0116962574765781, PFK2 -> 0.00975915538330228, PFKCamp -> 0.0845, PFKCatp -> 3.0, PFKCf16 -> 0.397, PFKCf26 -> 0.0174, PFKCiatp -> 100.0, PFKKadp -> 1.0, PFKKamp -> 0.0995, PFKKatp -> 0.71, PFKKeq -> 800.0, PFKKf16 -> 0.111, PFKKf26 -> 0.000682, PFKKf6p -> 0.1, PFKKiatp -> 0.65, PFKL0 -> 0.66, PFKVmax -> 1.83333333333333, PFKgR -> 5.12, PGI1 -> 0.0345726768225249, PGIKeq -> 0.29, PGIKf6p -> 0.3, PGIKg6p -> 1.4, PGIVmax -> 17.6, PGK1 -> 0.0644142281647388, PGKKadp -> 0.2, PGKKatp -> 0.3, PGKKbpg -> 0.003, PGKKeq -> 3200.0, PGKKp3g -> 0.53, PGKVmax -> 259.220125786164, PYK2 -> 0.00151748381804475, PYKKadp -> 0.53, PYKKatp -> 1.5, PYKKeq -> 6500.0, PYKKpep -> 0.14, PYKKpyr -> 21.0, PYKVmax -> 16.6666666666667, TDH1 -> 0.087716160700349, TDH2 -> 0.0, TDH3 -> 1.05110118662137, TDHKbpg -> 0.0098, TDHKeq -> 0.00533412710224736, TDHKgap -> 0.21, TDHKnad -> 0.09, TDHKnadh -> 0.06, TDHVmax -> 19.2, TPI1 -> 0.073589454911377, TPIKeq -> 0.045, TPIk -> 7500.0, cell -> 1.0, extracellular -> 1.0, glycerolbranchKdhap -> 0.4, glycerolbranchKeq -> 4300.0, glycerolbranchKgly -> 1.0, glycerolbranchKnad -> 0.93, glycerolbranchKnadh -> 0.023, glycerolbranchVmax -> 0.785166666666667, glycogenbranchk -> 0.01480424934314, succinatebranchk -> 0.237257345562943, sumAXP -> 6.02, sumNAD -> 1.59, trehalosebranchk -> 0.00592169973725601, volume -> 2*^-14, EtOH -> 55.472577854384, GLCx -> 74.0, GLY -> 0.15, SUC -> 0.0, TRH -> 0.00384697134241316, glycogen -> 0.0, default\[LetterSpace]compartment -> 1.0
};

assignments = {
sumPXG -> P2G[t] + P3G[t], energycharge -> (ADP[t]/2 + ATP[t])/sumAXP, fitconc -> Sqrt[(1 - (NA*sumPXG*volume)/1618640)^2 + (1 - (NA*volume*DHAP[t])/3496987)^2 + (1 - (NA*volume*F16bP[t])/13800392)^2 + (1 - (NA*volume*F6P[t])/708930)^2 + (1 - (NA*volume*G6P[t])/2326001)^2 + (1 - (NA*volume*GAP[t])/951170)^2 + (1 - (NA*volume*GLC[t])/18909525)^2 + (1 - (NA*volume*PEP[t])/1836769)^2 + (1 - (NA*volume*PYR[t])/6348755)^2]/3
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
ADP'[t] == 1.0*HXKHXK2 +1.0*glycogenbranch +1.0*trehalosebranch +1.0*HXKGLK1 +1.0*PFK +1.0*ATPase +1.0*HXKHXK1 -2.0*AK -1.0*PYK -1.0*PGK, AMP'[t] == 1.0*AK , ATP'[t] == 1.0*AK +1.0*PYK +1.0*PGK -1.0*HXKHXK2 -1.0*glycogenbranch -1.0*trehalosebranch -1.0*HXKGLK1 -1.0*PFK -1.0*ATPase -1.0*HXKHXK1, AcAld'[t] == 1.0*PDC -2.0*succinatebranch -1.0*ADH, BPG'[t] == 1.0*TDH -1.0*PGK, DHAP'[t] == 1.0*FBA -1.0*glycerolbranch -1.0*TPI, F16bP'[t] == 1.0*PFK -1.0*FBA, F6P'[t] == 1.0*PGI -1.0*PFK, G6P'[t] == 1.0*HXKHXK2 +1.0*HXKGLK1 +1.0*HXKHXK1 -1.0*glycogenbranch -2.0*trehalosebranch -1.0*PGI, GAP'[t] == 1.0*FBA +1.0*TPI -1.0*TDH, GLC'[t] == 1.0*HXT -1.0*HXKHXK2 -1.0*HXKGLK1 -1.0*HXKHXK1, NAD'[t] == 1.0*glycerolbranch +1.0*ADH -3.0*succinatebranch -1.0*TDH, NADH'[t] == 3.0*succinatebranch +1.0*TDH -1.0*glycerolbranch -1.0*ADH, P2G'[t] == 1.0*GPM -1.0*ENO, P3G'[t] == 1.0*PGK -1.0*GPM, PEP'[t] == 1.0*ENO -1.0*PYK, PYR'[t] == 1.0*PYK -1.0*PDC
};
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]}]