(* 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 = {
Auxin[t], CK[t], CTR1\[LetterSpace]star[t], ET[t], PLSm[t], PLSp[t], Ra\[LetterSpace]star[t], Re\[LetterSpace]star[t], X[t]
};

initialValues = {
Auxin[0] == 0.1, CK[0] == 0.1, CTR1\[LetterSpace]star[0] == 0.3, ET[0] == 0.1, PLSm[0] == 0.1, PLSp[0] == 0.1, Ra\[LetterSpace]star[0] == 1.0, Re\[LetterSpace]star[0] == 0.3, X[0] == 0.1
};

rates = {
reaction\[LetterSpace]1, reaction\[LetterSpace]10, reaction\[LetterSpace]11, reaction\[LetterSpace]12, reaction\[LetterSpace]13, reaction\[LetterSpace]14, reaction\[LetterSpace]15, reaction\[LetterSpace]16, reaction\[LetterSpace]17, reaction\[LetterSpace]18, reaction\[LetterSpace]19, reaction\[LetterSpace]2, reaction\[LetterSpace]3, reaction\[LetterSpace]4, reaction\[LetterSpace]5, reaction\[LetterSpace]6, reaction\[LetterSpace]7, reaction\[LetterSpace]8, reaction\[LetterSpace]9, v\[LetterSpace]Auxin, v\[LetterSpace]Cytokinin, v\[LetterSpace]Ethylene
};

rateEquations = {
reaction\[LetterSpace]1 -> compartment\[LetterSpace]1*function\[LetterSpace]2[k1a, X[t], k1], reaction\[LetterSpace]10 -> compartment\[LetterSpace]1*function\[LetterSpace]10[k10, PLSp[t], k10a, Re], reaction\[LetterSpace]11 -> compartment\[LetterSpace]1*function\[LetterSpace]12[Re\[LetterSpace]star[t], ET[t], k11], reaction\[LetterSpace]12 -> compartment\[LetterSpace]1*function\[LetterSpace]13[Auxin[t], CK[t], k12, k12a], reaction\[LetterSpace]13 -> compartment\[LetterSpace]1*function\[LetterSpace]15[ET[t], k13], reaction\[LetterSpace]14 -> compartment\[LetterSpace]1*function\[LetterSpace]16[Re\[LetterSpace]star[t], k14, CTR1], reaction\[LetterSpace]15 -> compartment\[LetterSpace]1*function\[LetterSpace]17[CTR1\[LetterSpace]star[t], k15], reaction\[LetterSpace]16 -> compartment\[LetterSpace]1*function\[LetterSpace]18[CTR1\[LetterSpace]star[t], k16, k16a], reaction\[LetterSpace]17 -> compartment\[LetterSpace]1*function\[LetterSpace]19[X[t], k17], reaction\[LetterSpace]18 -> compartment\[LetterSpace]1*function\[LetterSpace]20[Auxin[t], k18a, k18], reaction\[LetterSpace]19 -> compartment\[LetterSpace]1*function\[LetterSpace]21[CK[t], k19], reaction\[LetterSpace]2 -> compartment\[LetterSpace]1*function\[LetterSpace]3[k2, k2a, ET[t], CK[t], k2b, PLSp[t], k2c], reaction\[LetterSpace]3 -> compartment\[LetterSpace]1*function\[LetterSpace]1[k3, k3a, X[t], Auxin[t]], reaction\[LetterSpace]4 -> compartment\[LetterSpace]1*function\[LetterSpace]4[k4, Auxin[t], Ra], reaction\[LetterSpace]5 -> compartment\[LetterSpace]1*k5*Ra\[LetterSpace]star[t], reaction\[LetterSpace]6 -> compartment\[LetterSpace]1*function\[LetterSpace]6[k6, Ra\[LetterSpace]star[t], ET[t], k6a], reaction\[LetterSpace]7 -> compartment\[LetterSpace]1*function\[LetterSpace]7[k7, PLSm[t]], reaction\[LetterSpace]8 -> compartment\[LetterSpace]1*function\[LetterSpace]8[k8, PLSm[t]], reaction\[LetterSpace]9 -> compartment\[LetterSpace]1*function\[LetterSpace]9[k9, PLSp[t]], v\[LetterSpace]Auxin -> compartment\[LetterSpace]1*IAA*k\[LetterSpace]auxin, v\[LetterSpace]Cytokinin -> CK\[LetterSpace]ex*compartment\[LetterSpace]1*k\[LetterSpace]cytokinin, v\[LetterSpace]Ethylene -> ACC*compartment\[LetterSpace]1*k\[LetterSpace]ethylene
};

parameters = {
k1 -> 1.0, k10 -> 0.0003, k10a -> 0.5, k11 -> 5.0, k12 -> 0.1, k12a -> 0.1, k13 -> 1.0, k14 -> 3.0, k15 -> 0.085, k16 -> 0.3, k16a -> 1.0, k17 -> 0.1, k18 -> 0.1, k18a -> 1.0, k19 -> 1.0, k1a -> 1.0, k2 -> 0.2, k2a -> 2.8, k2b -> 1.0, k2c -> 0.01, k3 -> 2.0, k3a -> 0.45, k4 -> 1.0, k5 -> 1.0, k6 -> 0.3, k6a -> 0.2, k7 -> 1.0, k8 -> 1.0, k9 -> 1.0, k\[LetterSpace]auxin -> 70.0, k\[LetterSpace]cytokinin -> 10.0, k\[LetterSpace]ethylene -> 0.5, ACC -> 0.0, CK\[LetterSpace]ex -> 0.0, CTR1T -> 0.3, IAA -> 0.0, RaT -> 1.0, ReT -> 0.3, compartment\[LetterSpace]1 -> 1.0, extra -> 1.0
};

assignments = {
function\[LetterSpace]16[Re\[LetterSpace]star_,k14_,CTR1_] -> CTR1*k14*Re\[LetterSpace]star, function\[LetterSpace]15[ET_,k13_] -> ET*k13, function\[LetterSpace]3[k2_,k2a_,ET_,CK_,k2b_,PLSp_,k2c_] -> k2 + (ET*k2a*PLSp)/((1 + CK/k2b)*(k2c + PLSp)), function\[LetterSpace]2[k1a_,X_,k1_] -> k1a/(1 + X/k1), function\[LetterSpace]1[k3_,k3a_,X_,Auxin_] -> Auxin*(k3 + k3a*X), function\[LetterSpace]21[CK_,k19_] -> CK*k19, function\[LetterSpace]19[X_,k17_] -> k17*X, function\[LetterSpace]18[CTR1\[LetterSpace]star_,k16_,k16a_] -> k16 - CTR1\[LetterSpace]star*k16a, function\[LetterSpace]20[Auxin_,k18a_,k18_] -> k18a/(1 + Auxin/k18), function\[LetterSpace]17[CTR1\[LetterSpace]star_,k15_] -> CTR1\[LetterSpace]star*k15, function\[LetterSpace]13[Auxin_,CK_,k12_,k12a_] -> k12 + Auxin*CK*k12a, function\[LetterSpace]12[Re\[LetterSpace]star_,ET_,k11_] -> ET*k11*Re\[LetterSpace]star, function\[LetterSpace]10[k10_,PLSp_,k10a_,Re_] -> (k10 + k10a*PLSp)*Re, function\[LetterSpace]9[k9_,PLSp_] -> k9*PLSp, function\[LetterSpace]8[k8_,PLSm_] -> k8*PLSm, function\[LetterSpace]7[k7_,PLSm_] -> k7*PLSm, function\[LetterSpace]6[k6_,Ra\[LetterSpace]star_,ET_,k6a_] -> (k6*Ra\[LetterSpace]star)/(1 + ET/k6a), function\[LetterSpace]4[k4_,Auxin_,Ra_] -> Auxin*k4*Ra, CTR1 -> CTR1T - CTR1\[LetterSpace]star[t], Re -> ReT - Re\[LetterSpace]star[t], Ra -> RaT - Ra\[LetterSpace]star[t]
};

events = {

};

speciesAnnotations = {
ACC[t]->"http://identifiers.org/obo.chebi/CHEBI:18053", ET[t]->"http://identifiers.org/obo.chebi/CHEBI:18153", ET[t]->"http://identifiers.org/kegg.compound/C06547", IAA[t]->"http://identifiers.org/obo.chebi/CHEBI:16411", IAA[t]->"http://identifiers.org/kegg.compound/C00954"
};

reactionAnnotations = {
reaction\[LetterSpace]8->"http://identifiers.org/obo.go/GO:0006412"
};

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

(* Time evolution *)
odes = {
Auxin'[t] == 1.0*reaction\[LetterSpace]1 +1.0*reaction\[LetterSpace]2 +1.0*v\[LetterSpace]Auxin -1.0*reaction\[LetterSpace]3, CK'[t] == 1.0*reaction\[LetterSpace]18 +1.0*v\[LetterSpace]Cytokinin -1.0*reaction\[LetterSpace]19, CTR1\[LetterSpace]star'[t] == 1.0*reaction\[LetterSpace]14 -1.0*reaction\[LetterSpace]15, ET'[t] == 1.0*reaction\[LetterSpace]12 +1.0*v\[LetterSpace]Ethylene -1.0*reaction\[LetterSpace]13, PLSm'[t] == 1.0*reaction\[LetterSpace]6 -1.0*reaction\[LetterSpace]7, PLSp'[t] == 1.0*reaction\[LetterSpace]8 -1.0*reaction\[LetterSpace]9, Ra\[LetterSpace]star'[t] == 1.0*reaction\[LetterSpace]4 -1.0*reaction\[LetterSpace]5, Re\[LetterSpace]star'[t] == 1.0*reaction\[LetterSpace]10 -1.0*reaction\[LetterSpace]11, X'[t] == 1.0*reaction\[LetterSpace]16 -1.0*reaction\[LetterSpace]17
};
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]}]