(* 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 = {
ATP[t], DHAP[t], DPGA[t], E4P[t], F6P[t], FBP[t], G1P[t], G6P[t], GAP[t], PGA[t], R5P[t], Ru5P[t], RuBP[t], S7P[t], SBP[t], X5P[t]
};

initialValues = {
ATP[0] == 0.68, DHAP[0] == 0.48, DPGA[0] == 0.0011, E4P[0] == 0.05, F6P[0] == 0.640764257004719, FBP[0] == 0.669999999999999, G1P[0] == 0.0854779518844294, G6P[0] == 1.47375779111085, GAP[0] == 0.02, PGA[0] == 2.4, R5P[0] == 0.125186846038864, Ru5P[0] == 0.0500747384155456, RuBP[0] == 2.0, S7P[0] == 2.0, SBP[0] == 0.3, X5P[0] == 0.0747384155455904
};

rates = {
ATP\[LetterSpace]S, F6P\[LetterSpace]TK, FBP\[LetterSpace]A, FBPase, GAP\[LetterSpace]DH, PGA\[LetterSpace]K, PG\[LetterSpace]I, PG\[LetterSpace]M, R5P\[LetterSpace]I, Ru5P\[LetterSpace]E, Ru5P\[LetterSpace]K, RuBisCO, S7P\[LetterSpace]TK, SBP\[LetterSpace]A, SBPase, Starch\[LetterSpace]P, Starch\[LetterSpace]S, TPT\[LetterSpace]DHAP, TPT\[LetterSpace]GAP, TPT\[LetterSpace]PGA, TP\[LetterSpace]I
};

rateEquations = {
ATP\[LetterSpace]S -> chloroplast*function\[LetterSpace]6[ATP\[LetterSpace]S\[LetterSpace]Vm, ADP, Pi, ATP\[LetterSpace]S\[LetterSpace]K1, ATP\[LetterSpace]S\[LetterSpace]K2], F6P\[LetterSpace]TK -> chloroplast*(F6P\[LetterSpace]TK\[LetterSpace]k1*F6P[t]*GAP[t] - F6P\[LetterSpace]TK\[LetterSpace]k2*E4P[t]*X5P[t]), FBP\[LetterSpace]A -> chloroplast*(-(FBP\[LetterSpace]A\[LetterSpace]k2*FBP[t]) + FBP\[LetterSpace]A\[LetterSpace]k1*DHAP[t]*GAP[t]), FBPase -> chloroplast*function\[LetterSpace]2[FBPase\[LetterSpace]Vm, FBP[t], FBPase\[LetterSpace]K, F6P[t], FBPase\[LetterSpace]KR1, Pi, FBPase\[LetterSpace]KR2], GAP\[LetterSpace]DH -> chloroplast*(GAP\[LetterSpace]DH\[LetterSpace]k1*H*NADPH*DPGA[t] - GAP\[LetterSpace]DH\[LetterSpace]k2*NADP*Pi*GAP[t]), PGA\[LetterSpace]K -> chloroplast*(-(ADP*PGA\[LetterSpace]K\[LetterSpace]k2*DPGA[t]) + PGA\[LetterSpace]K\[LetterSpace]k1*ATP[t]*PGA[t]), PG\[LetterSpace]I -> chloroplast*(PG\[LetterSpace]I\[LetterSpace]k1*F6P[t] - PG\[LetterSpace]I\[LetterSpace]k2*G6P[t]), PG\[LetterSpace]M -> chloroplast*(-(PG\[LetterSpace]M\[LetterSpace]k2*G1P[t]) + PG\[LetterSpace]M\[LetterSpace]k1*G6P[t]), R5P\[LetterSpace]I -> chloroplast*(R5P\[LetterSpace]I\[LetterSpace]k1*R5P[t] - R5P\[LetterSpace]I\[LetterSpace]k2*Ru5P[t]), Ru5P\[LetterSpace]E -> chloroplast*(-(Ru5P\[LetterSpace]E\[LetterSpace]k2*Ru5P[t]) + Ru5P\[LetterSpace]E\[LetterSpace]k1*X5P[t]), Ru5P\[LetterSpace]K -> chloroplast*function\[LetterSpace]4[Ru5P\[LetterSpace]K\[LetterSpace]Vm, Ru5P[t], ATP[t], Ru5P\[LetterSpace]K\[LetterSpace]K1, PGA[t], Ru5P\[LetterSpace]K\[LetterSpace]KR1, RuBP[t], Ru5P\[LetterSpace]K\[LetterSpace]KR2, Pi, Ru5P\[LetterSpace]K\[LetterSpace]KR3, ADP, Ru5P\[LetterSpace]K\[LetterSpace]KR41, Ru5P\[LetterSpace]K\[LetterSpace]K2, Ru5P\[LetterSpace]K\[LetterSpace]KR42], RuBisCO -> chloroplast*function\[LetterSpace]1[RuBisCO\[LetterSpace]Vm, RuBP[t], RuBisCO\[LetterSpace]K, PGA[t], RuBisCO\[LetterSpace]KR1, FBP[t], RuBisCO\[LetterSpace]KR2, SBP[t], RuBisCO\[LetterSpace]KR3, Pi, RuBisCO\[LetterSpace]KR4, NADPH, RuBisCO\[LetterSpace]KR5], S7P\[LetterSpace]TK -> chloroplast*(S7P\[LetterSpace]TK\[LetterSpace]k1*GAP[t]*S7P[t] - S7P\[LetterSpace]TK\[LetterSpace]k2*R5P[t]*X5P[t]), SBP\[LetterSpace]A -> chloroplast*(SBP\[LetterSpace]A\[LetterSpace]k1*DHAP[t]*E4P[t] - SBP\[LetterSpace]A\[LetterSpace]k2*SBP[t]), SBPase -> chloroplast*function\[LetterSpace]3[SBPase\[LetterSpace]Vm, SBP[t], SBPase\[LetterSpace]K, Pi, SBPase\[LetterSpace]KR1], Starch\[LetterSpace]P -> chloroplast*function\[LetterSpace]3[Starch\[LetterSpace]P\[LetterSpace]Vm, Pi, Starch\[LetterSpace]P\[LetterSpace]K, G1P[t], Starch\[LetterSpace]P\[LetterSpace]KR1], Starch\[LetterSpace]S -> chloroplast*function\[LetterSpace]5[Starch\[LetterSpace]S\[LetterSpace]Vm, G1P[t], ATP[t], Starch\[LetterSpace]S\[LetterSpace]K1, Starch\[LetterSpace]S\[LetterSpace]K2, ADP, Starch\[LetterSpace]S\[LetterSpace]KR1, Pi, Starch\[LetterSpace]S\[LetterSpace]KA1, PGA[t], Starch\[LetterSpace]S\[LetterSpace]KA2, F6P[t], Starch\[LetterSpace]S\[LetterSpace]KA3, FBP[t]], TPT\[LetterSpace]DHAP -> chloroplast*function\[LetterSpace]7[TPT\[LetterSpace]DHAP\[LetterSpace]Vm, DHAP[t], TPT\[LetterSpace]DHAP\[LetterSpace]KA, Pext, TPT\[LetterSpace]DHAP\[LetterSpace]K, Pi, TPT\[LetterSpace]DHAP\[LetterSpace]KR1, PGA[t], TPT\[LetterSpace]DHAP\[LetterSpace]KR2, GAP[t], TPT\[LetterSpace]DHAP\[LetterSpace]KR3], TPT\[LetterSpace]GAP -> chloroplast*function\[LetterSpace]7[TPT\[LetterSpace]GAP\[LetterSpace]Vm, GAP[t], TPT\[LetterSpace]GAP\[LetterSpace]KA, Pext, TPT\[LetterSpace]GAP\[LetterSpace]K, Pi, TPT\[LetterSpace]GAP\[LetterSpace]KR1, PGA[t], TPT\[LetterSpace]GAP\[LetterSpace]KR2, DHAP[t], TPT\[LetterSpace]GAP\[LetterSpace]KR3], TPT\[LetterSpace]PGA -> chloroplast*function\[LetterSpace]7[TPT\[LetterSpace]PGA\[LetterSpace]Vm, PGA[t], TPT\[LetterSpace]PGA\[LetterSpace]KA, Pext, TPT\[LetterSpace]PGA\[LetterSpace]K, Pi, TPT\[LetterSpace]PGA\[LetterSpace]KR1, GAP[t], TPT\[LetterSpace]PGA\[LetterSpace]KR2, DHAP[t], TPT\[LetterSpace]PGA\[LetterSpace]KR3], TP\[LetterSpace]I -> chloroplast*(-(TP\[LetterSpace]I\[LetterSpace]k2*DHAP[t]) + TP\[LetterSpace]I\[LetterSpace]k1*GAP[t])
};

parameters = {
H -> 1.25892541179417*^-05, NADP -> 0.29, NADPH -> 0.21, Pext -> 0.5, RuBisCO\[LetterSpace]Vm -> 340.0, RuBisCO\[LetterSpace]K -> 0.02, RuBisCO\[LetterSpace]KR1 -> 0.84, RuBisCO\[LetterSpace]KR2 -> 0.04, RuBisCO\[LetterSpace]KR3 -> 0.0075, RuBisCO\[LetterSpace]KR4 -> 0.9, RuBisCO\[LetterSpace]KR5 -> 0.07, PGA\[LetterSpace]K\[LetterSpace]k1 -> 500000000.0, PGA\[LetterSpace]K\[LetterSpace]k2 -> 1612900000000.0, GAP\[LetterSpace]DH\[LetterSpace]k1 -> 500000000.0, GAP\[LetterSpace]DH\[LetterSpace]k2 -> 31.25, TP\[LetterSpace]I\[LetterSpace]k1 -> 500000000.0, TP\[LetterSpace]I\[LetterSpace]k2 -> 22727000.0, FBP\[LetterSpace]A\[LetterSpace]k1 -> 500000000.0, FBP\[LetterSpace]A\[LetterSpace]k2 -> 70423000.0, FBPase\[LetterSpace]Vm -> 200.0, FBPase\[LetterSpace]K -> 0.03, FBPase\[LetterSpace]KR1 -> 0.7, FBPase\[LetterSpace]KR2 -> 12.0, F6P\[LetterSpace]TK\[LetterSpace]k1 -> 500000000.0, F6P\[LetterSpace]TK\[LetterSpace]k2 -> 5952400000.0, SBP\[LetterSpace]A\[LetterSpace]k1 -> 500000000.0, SBP\[LetterSpace]A\[LetterSpace]k2 -> 38461500.0, SBPase\[LetterSpace]Vm -> 40.0, SBPase\[LetterSpace]K -> 0.02, SBPase\[LetterSpace]KR1 -> 12.0, S7P\[LetterSpace]TK\[LetterSpace]k1 -> 500000000.0, S7P\[LetterSpace]TK\[LetterSpace]k2 -> 588240000.0, R5P\[LetterSpace]I\[LetterSpace]k1 -> 500000000.0, R5P\[LetterSpace]I\[LetterSpace]k2 -> 1250000000.0, Ru5P\[LetterSpace]E\[LetterSpace]k1 -> 500000000.0, Ru5P\[LetterSpace]E\[LetterSpace]k2 -> 746269000.0, Ru5P\[LetterSpace]K\[LetterSpace]Vm -> 1000.0, Ru5P\[LetterSpace]K\[LetterSpace]K1 -> 0.05, Ru5P\[LetterSpace]K\[LetterSpace]KR1 -> 2.0, Ru5P\[LetterSpace]K\[LetterSpace]KR2 -> 0.7, Ru5P\[LetterSpace]K\[LetterSpace]KR3 -> 4.0, Ru5P\[LetterSpace]K\[LetterSpace]KR41 -> 2.5, Ru5P\[LetterSpace]K\[LetterSpace]K2 -> 0.05, Ru5P\[LetterSpace]K\[LetterSpace]KR42 -> 0.4, PG\[LetterSpace]I\[LetterSpace]k1 -> 500000000.0, PG\[LetterSpace]I\[LetterSpace]k2 -> 217400000.0, PG\[LetterSpace]M\[LetterSpace]k1 -> 500000000.0, PG\[LetterSpace]M\[LetterSpace]k2 -> 8621000000.0, Starch\[LetterSpace]S\[LetterSpace]Vm -> 40.0, Starch\[LetterSpace]S\[LetterSpace]K1 -> 0.08, Starch\[LetterSpace]S\[LetterSpace]K2 -> 0.08, Starch\[LetterSpace]S\[LetterSpace]KR1 -> 10.0, Starch\[LetterSpace]S\[LetterSpace]KA1 -> 0.1, Starch\[LetterSpace]S\[LetterSpace]KA2 -> 0.02, Starch\[LetterSpace]S\[LetterSpace]KA3 -> 0.02, Starch\[LetterSpace]P\[LetterSpace]Vm -> 40.0, Starch\[LetterSpace]P\[LetterSpace]K -> 0.1, Starch\[LetterSpace]P\[LetterSpace]KR1 -> 0.05, ATP\[LetterSpace]S\[LetterSpace]Vm -> 350.0, ATP\[LetterSpace]S\[LetterSpace]K1 -> 0.014, ATP\[LetterSpace]S\[LetterSpace]K2 -> 0.3, TPT\[LetterSpace]PGA\[LetterSpace]Vm -> 250.0, TPT\[LetterSpace]PGA\[LetterSpace]KA -> 0.74, TPT\[LetterSpace]PGA\[LetterSpace]K -> 0.25, TPT\[LetterSpace]PGA\[LetterSpace]KR1 -> 0.63, TPT\[LetterSpace]PGA\[LetterSpace]KR2 -> 0.075, TPT\[LetterSpace]PGA\[LetterSpace]KR3 -> 0.077, TPT\[LetterSpace]GAP\[LetterSpace]Vm -> 250.0, TPT\[LetterSpace]GAP\[LetterSpace]KA -> 0.74, TPT\[LetterSpace]GAP\[LetterSpace]K -> 0.075, TPT\[LetterSpace]GAP\[LetterSpace]KR1 -> 0.63, TPT\[LetterSpace]GAP\[LetterSpace]KR2 -> 0.25, TPT\[LetterSpace]GAP\[LetterSpace]KR3 -> 0.077, TPT\[LetterSpace]DHAP\[LetterSpace]Vm -> 250.0, TPT\[LetterSpace]DHAP\[LetterSpace]KA -> 0.74, TPT\[LetterSpace]DHAP\[LetterSpace]K -> 0.077, TPT\[LetterSpace]DHAP\[LetterSpace]KR1 -> 0.63, TPT\[LetterSpace]DHAP\[LetterSpace]KR2 -> 0.25, TPT\[LetterSpace]DHAP\[LetterSpace]KR3 -> 0.075, chloroplast -> 1.0, cytosol -> 1.0
};

assignments = {
function\[LetterSpace]5[Vm_,S1_,S2_,K1_,K2_,R1_,KR1_,R2_,KA1_,A1_,KA2_,A2_,KA3_,A3_] -> (S1*S2*Vm)/((1 + R1/KR1)*(K1 + S1)*(K2*(1 + (K2*R2)/(A1*KA1 + A2*KA2 + A3*KA3)) + S2)), function\[LetterSpace]3[Vm_,S_,K_,R1_,KR1_] -> (S*Vm)/(K*(1 + R1/KR1) + S), function\[LetterSpace]1[Vm_,S_,K_,R1_,KR1_,R2_,KR2_,R3_,KR3_,R4_,KR4_,R5_,KR5_] -> (S*Vm)/(K*(1 + R1/KR1 + R2/KR2 + R3/KR3 + R4/KR4 + R5/KR5) + S), function\[LetterSpace]6[Vm_,s1_,s2_,K1_,K2_] -> (s1*s2*Vm)/((K1 + s1)*(K2 + s2)), function\[LetterSpace]4[Vm_,S1_,S2_,K1_,R1_,KR1_,R2_,KR2_,R3_,KR3_,R4_,KR41_,K2_,KR42_] -> (S1*S2*Vm)/((K1*(1 + R1/KR1 + R2/KR2 + R3/KR3) + S1)*(K2*(1 + R4/KR42) + (1 + R4/KR41)*S2)), function\[LetterSpace]7[Vm_,S_,KA_,A_,K_,R1_,KR1_,R2_,KR2_,R3_,KR3_] -> (S*Vm)/(K*(1 + (1 + KA/A)*(R1/KR1 + R2/KR2 + R3/KR3)) + (1 + KA/A)*S), function\[LetterSpace]2[Vm_,S_,K_,R1_,KR1_,R2_,KR2_] -> (S*Vm)/(K*(1 + R1/KR1 + R2/KR2) + S), ADP -> 1.5 - ATP[t], Pi -> 15 - ATP[t] - DHAP[t] - E4P[t] - F6P[t] - G1P[t] - G6P[t] - GAP[t] - PGA[t] - R5P[t] - Ru5P[t] - S7P[t] - 2*(DPGA[t] + FBP[t] + RuBP[t] + SBP[t]) - X5P[t]
};

events = {

};

speciesAnnotations = {
G6P[t]->"http://identifiers.org/pubchem.compound/439958", NADP[t]->"http://identifiers.org/chebi/CHEBI:25523", NADPH[t]->"http://identifiers.org/chebi/CHEBI:16474"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
ATP'[t] == 1.0*ATP\[LetterSpace]S -1.0*PGA\[LetterSpace]K -1.0*Ru5P\[LetterSpace]K -1.0*Starch\[LetterSpace]S, DHAP'[t] == 1.0*TP\[LetterSpace]I -1.0*FBP\[LetterSpace]A -1.0*SBP\[LetterSpace]A -1.0*TPT\[LetterSpace]DHAP, DPGA'[t] == 1.0*PGA\[LetterSpace]K -1.0*GAP\[LetterSpace]DH, E4P'[t] == 1.0*F6P\[LetterSpace]TK -1.0*SBP\[LetterSpace]A, F6P'[t] == 1.0*FBPase -1.0*F6P\[LetterSpace]TK -1.0*PG\[LetterSpace]I, FBP'[t] == 1.0*FBP\[LetterSpace]A -1.0*FBPase, G1P'[t] == 1.0*PG\[LetterSpace]M +1.0*Starch\[LetterSpace]P -1.0*Starch\[LetterSpace]S, G6P'[t] == 1.0*PG\[LetterSpace]I -1.0*PG\[LetterSpace]M, GAP'[t] == 1.0*GAP\[LetterSpace]DH -1.0*TP\[LetterSpace]I -1.0*FBP\[LetterSpace]A -1.0*F6P\[LetterSpace]TK -1.0*S7P\[LetterSpace]TK -1.0*TPT\[LetterSpace]GAP, PGA'[t] == 2.0*RuBisCO -1.0*PGA\[LetterSpace]K -1.0*TPT\[LetterSpace]PGA, R5P'[t] == 1.0*S7P\[LetterSpace]TK -1.0*R5P\[LetterSpace]I, Ru5P'[t] == 1.0*R5P\[LetterSpace]I +1.0*Ru5P\[LetterSpace]E -1.0*Ru5P\[LetterSpace]K, RuBP'[t] == 1.0*Ru5P\[LetterSpace]K -1.0*RuBisCO, S7P'[t] == 1.0*SBPase -1.0*S7P\[LetterSpace]TK, SBP'[t] == 1.0*SBP\[LetterSpace]A -1.0*SBPase, X5P'[t] == 1.0*F6P\[LetterSpace]TK +1.0*S7P\[LetterSpace]TK -1.0*Ru5P\[LetterSpace]E
};
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]}]