(* 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 = {
A00[t], E00[t], E01[t], E02[t], E03[t], E04[t], E05[t], F00[t], F01[t], F02[t], F03[t], F04[t], F05[t], O00[t], O01[t], O02[t], O03[t], O04[t], O05[t], P00[t], P01[t], P02[t], P03[t], P04[t], P05[t], R00[t]
};

initialValues = {
A00[0] == 0.0, E00[0] == 0.0, E01[0] == 0.0, E02[0] == 0.0, E03[0] == 0.0, E04[0] == 0.0, E05[0] == 0.0, F00[0] == 0.0, F01[0] == 0.0, F02[0] == 0.0, F03[0] == 0.0, F04[0] == 0.0, F05[0] == 0.0, O00[0] == 0.0, O01[0] == 0.0, O02[0] == 0.0, O03[0] == 0.0, O04[0] == 0.0, O05[0] == 0.0, P00[0] == 0.0, P01[0] == 0.0, P02[0] == 0.0, P03[0] == 0.0, P04[0] == 0.0, P05[0] == 0.0, R00[0] == 1.0
};

rates = {
v\[LetterSpace]1, v\[LetterSpace]10, v\[LetterSpace]11, v\[LetterSpace]12, v\[LetterSpace]13, v\[LetterSpace]14, v\[LetterSpace]15, v\[LetterSpace]16, v\[LetterSpace]17, v\[LetterSpace]18, v\[LetterSpace]19, v\[LetterSpace]2, v\[LetterSpace]20, v\[LetterSpace]21, v\[LetterSpace]22, v\[LetterSpace]23, v\[LetterSpace]24, v\[LetterSpace]25, v\[LetterSpace]26, v\[LetterSpace]3, v\[LetterSpace]4, v\[LetterSpace]5, v\[LetterSpace]6, v\[LetterSpace]7, v\[LetterSpace]8, v\[LetterSpace]9
};

rateEquations = {
v\[LetterSpace]1 -> -(kb01*A00[t]) + kf01*O2*R00[t], v\[LetterSpace]10 -> (kf10*F01[t])/2.718281828^(19.46188812245315*deltapsi*q2) - 2.718281828^(19.46188812245315*deltapsi*q2)*kb10*F02[t], v\[LetterSpace]11 -> (kf11*F02[t])/(2.718281828^(19.46188812245315*deltapsi*q3)*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*q3)*kb11*F03[t], v\[LetterSpace]12 -> kf12*F03[t] - kb12*F04[t], v\[LetterSpace]13 -> (kf13*F04[t])/(2.718281828^(19.46188812245315*deltapsi*(1 - q2))*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*(1 - q2))*kb13*F05[t], v\[LetterSpace]14 -> (kf14*F05[t])/2.718281828^(19.46188812245315*deltapsi*(1 - q3)) - (2.718281828^(19.46188812245315*deltapsi*(1 - q3))*kb14*O00[t])/10^pHC, v\[LetterSpace]15 -> cred*kf15*O00[t] - (1 - cred)*kb15*O01[t], v\[LetterSpace]16 -> (kf16*O01[t])/2.718281828^(19.46188812245315*deltapsi*q2) - 2.718281828^(19.46188812245315*deltapsi*q2)*kb16*O02[t], v\[LetterSpace]17 -> (kf17*O02[t])/(2.718281828^(19.46188812245315*deltapsi*q3)*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*q3)*kb17*O03[t], v\[LetterSpace]18 -> kf18*O03[t] - kb18*O04[t], v\[LetterSpace]19 -> (kf19*O04[t])/(2.718281828^(19.46188812245315*deltapsi*(1 - q2))*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*(1 - q2))*kb19*O05[t], v\[LetterSpace]2 -> kf02*A00[t] - kb02*P00[t], v\[LetterSpace]20 -> -((2.718281828^(19.46188812245315*deltapsi*(1 - q3))*kb20*E00[t])/10^pHC) + (kf20*O05[t])/2.718281828^(19.46188812245315*deltapsi*(1 - q3)), v\[LetterSpace]21 -> cred*kf21*E00[t] - (1 - cred)*kb21*E01[t], v\[LetterSpace]22 -> (kf22*E01[t])/2.718281828^(19.46188812245315*deltapsi*q2) - 2.718281828^(19.46188812245315*deltapsi*q2)*kb22*E02[t], v\[LetterSpace]23 -> (kf23*E02[t])/(2.718281828^(19.46188812245315*deltapsi*q3)*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*q3)*kb23*E03[t], v\[LetterSpace]24 -> kf24*E03[t] - kb24*E04[t], v\[LetterSpace]25 -> (kf25*E04[t])/(2.718281828^(19.46188812245315*deltapsi*(1 - q2))*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*(1 - q2))*kb25*E05[t], v\[LetterSpace]26 -> (kf26*E05[t])/2.718281828^(19.46188812245315*deltapsi*(1 - q3)) - (2.718281828^(19.46188812245315*deltapsi*(1 - q3))*kb26*R00[t])/10^pHC, v\[LetterSpace]3 -> cred*kf03*P00[t] - (1 - cred)*kb03*P01[t], v\[LetterSpace]4 -> (kf04*P01[t])/2.718281828^(19.46188812245315*deltapsi*q2) - 2.718281828^(19.46188812245315*deltapsi*q2)*kb04*P02[t], v\[LetterSpace]5 -> (kf05*P02[t])/(2.718281828^(19.46188812245315*deltapsi*q3)*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*q3)*kb05*P03[t], v\[LetterSpace]6 -> kf06*P03[t] - kb06*P04[t], v\[LetterSpace]7 -> (kf07*P04[t])/(2.718281828^(19.46188812245315*deltapsi*(1 - q2))*10^pHM) - 2.718281828^(19.46188812245315*deltapsi*(1 - q2))*kb07*P05[t], v\[LetterSpace]8 -> -((2.718281828^(19.46188812245315*deltapsi*(1 - q3))*kb08*F00[t])/10^pHC) + (kf08*P05[t])/2.718281828^(19.46188812245315*deltapsi*(1 - q3)), v\[LetterSpace]9 -> cred*kf09*F00[t] - (1 - cred)*kb09*F01[t]
};

parameters = {
EmaccE -> 0.65, EmaccF -> 0.35, EmaccP -> 0.25, Emcyta -> 0.27, O2 -> 0.0001, cred -> 0.04, deltapsi -> 0.18, kb01 -> 19200.0, kb02 -> 64.0363912, kb15 -> 111548.6393, kb16 -> 31464.85383, kb17 -> 55.55555556, kb18 -> 400000000.0, kb19 -> 0.078120117, kb20 -> 72727272.73, kf01 -> 192000000.0, kf02 -> 28000.0, kf15 -> 200000.0, kf16 -> 68535.14617, kf17 -> 66666666667.0, kf18 -> 600000000.0, kf19 -> 12499218799.0, kf20 -> 400.0, pHC -> 7.0, pHM -> 7.0, pKaE -> 6.0, pKaF -> 7.0, phiE03 -> 0.0, phiE04 -> 0.0, phiF03 -> 0.0, phiF04 -> 0.0, phiP03 -> 0.0, phiP04 -> 0.0, q2 -> 0.33, q3 -> 0.67, rtotal -> 0.002581067, default\[LetterSpace]compartment -> 1.0
};

assignments = {
kb24 -> kb18*rE03^((-1 + phiE03)/2), kf12 -> kf18*rF03^((1 + phiF03)/2), rF03 -> (2.718281828^(38.9237762449063*(EmaccF - Emcyta))*kb18)/kf18, kb04 -> kb16, kf06 -> kf18*rP03^((1 + phiP03)/2), kf13 -> kf19*rF04^((1 + phiF04)/2), kf24 -> kf18*rE03^((1 + phiE03)/2), kf04 -> kf16, kf26 -> kf20, kf22 -> kf16, rP04 -> rtotal/(rE03*rE04*rF03*rF04*rP03), rP03 -> (2.718281828^(38.9237762449063*(EmaccP - Emcyta))*kb18)/kf18, kb03 -> kb15, rE03 -> (2.718281828^(38.9237762449063*(EmaccE - Emcyta))*kb18)/kf18, kf14 -> kf20, kb12 -> kb18*rF03^((-1 + phiF03)/2), kf07 -> kf19*rP04^((1 + phiP04)/2), kf10 -> kf16, kb13 -> kb19*rF04^((-1 + phiF04)/2), kf08 -> kf20, kf21 -> kf15, kb11 -> kb17, kb09 -> kb15, kb10 -> kb16, kb05 -> kb17, rF04 -> (10^pKaF*kb19)/kf19, kf11 -> kf17, kb22 -> kb16, kb21 -> kb15, kf09 -> kf15, kb26 -> kb20, kb14 -> kb20, kb08 -> kb20, kb07 -> kb19*rP04^((-1 + phiP04)/2), kb23 -> kb17, kf03 -> kf15, kf25 -> kf19*rE04^((1 + phiE04)/2), kf05 -> kf17, kf23 -> kf17, rE04 -> (10^pKaE*kb19)/kf19, kb06 -> kb18*rP03^((-1 + phiP03)/2), kb25 -> kb19*rE04^((-1 + phiE04)/2)
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
A00'[t] == 1.0*v\[LetterSpace]1 -1.0*v\[LetterSpace]2, E00'[t] == 1.0*v\[LetterSpace]20 -1.0*v\[LetterSpace]21, E01'[t] == 1.0*v\[LetterSpace]21 -1.0*v\[LetterSpace]22, E02'[t] == 1.0*v\[LetterSpace]22 -1.0*v\[LetterSpace]23, E03'[t] == 1.0*v\[LetterSpace]23 -1.0*v\[LetterSpace]24, E04'[t] == 1.0*v\[LetterSpace]24 -1.0*v\[LetterSpace]25, E05'[t] == 1.0*v\[LetterSpace]25 -1.0*v\[LetterSpace]26, F00'[t] == 1.0*v\[LetterSpace]8 -1.0*v\[LetterSpace]9, F01'[t] == 1.0*v\[LetterSpace]9 -1.0*v\[LetterSpace]10, F02'[t] == 1.0*v\[LetterSpace]10 -1.0*v\[LetterSpace]11, F03'[t] == 1.0*v\[LetterSpace]11 -1.0*v\[LetterSpace]12, F04'[t] == 1.0*v\[LetterSpace]12 -1.0*v\[LetterSpace]13, F05'[t] == 1.0*v\[LetterSpace]13 -1.0*v\[LetterSpace]14, O00'[t] == 1.0*v\[LetterSpace]14 -1.0*v\[LetterSpace]15, O01'[t] == 1.0*v\[LetterSpace]15 -1.0*v\[LetterSpace]16, O02'[t] == 1.0*v\[LetterSpace]16 -1.0*v\[LetterSpace]17, O03'[t] == 1.0*v\[LetterSpace]17 -1.0*v\[LetterSpace]18, O04'[t] == 1.0*v\[LetterSpace]18 -1.0*v\[LetterSpace]19, O05'[t] == 1.0*v\[LetterSpace]19 -1.0*v\[LetterSpace]20, P00'[t] == 1.0*v\[LetterSpace]2 -1.0*v\[LetterSpace]3, P01'[t] == 1.0*v\[LetterSpace]3 -1.0*v\[LetterSpace]4, P02'[t] == 1.0*v\[LetterSpace]4 -1.0*v\[LetterSpace]5, P03'[t] == 1.0*v\[LetterSpace]5 -1.0*v\[LetterSpace]6, P04'[t] == 1.0*v\[LetterSpace]6 -1.0*v\[LetterSpace]7, P05'[t] == 1.0*v\[LetterSpace]7 -1.0*v\[LetterSpace]8, R00'[t] == 1.0*v\[LetterSpace]26 -1.0*v\[LetterSpace]1
};
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]}]