(* 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 = {
A1[t], A2[t], C1[t], C2[t], IPTG[t]
};

initialValues = {
A1[0] == 0.1, A2[0] == 0.1, C1[0] == 20.0, C2[0] == 20.0, IPTG[0] == 5.0
};

rates = {
J0, J1, J2, J3, J4, J5, J6, J7
};

rateEquations = {
J0 -> environment*kc1*C1[t]*(1 - (C1[t] + C2[t])/Cm), J1 -> environment*(D + (d1*K1)/(K1 + A2[t]^2))*C1[t], J2 -> environment*kc2*C2[t]*(1 - (C1[t] + C2[t])/Cm), J3 -> environment*(D + (d2*A1[t]^2)/(K2 + A1[t]^2))*C2[t], J4 -> environment*kA1*C1[t], J5 -> (D + dAA1)*environment*A1[t], J6 -> environment*kA2*C2[t], J7 -> (D + dAA2)*environment*A2[t]
};

parameters = {
Cm -> 100.0, D -> 0.1125, K1 -> 10.0, K2 -> 10.0, d2 -> 0.3, dAA1 -> 0.017, dAA2 -> 0.11, kA1 -> 0.1, kc1 -> 0.8, kc2 -> 0.4, sink -> 0.0, source -> 0.0, environment -> 1.0
};

assignments = {
kA2 -> 0.02 + (0.03*IPTG[t]^2)/(25 + IPTG[t]^2), d1 -> 0.5 + IPTG[t]^2/(25 + IPTG[t]^2)
};

events = {

};

speciesAnnotations = {
A1[t]->"http://identifiers.org/chebi/CHEBI:56080", A2[t]->"http://identifiers.org/chebi/CHEBI:55474", A2[t]->"http://identifiers.org/kegg.compound/C18049", IPTG[t]->"http://identifiers.org/chebi/CHEBI:61448", IPTG[t]->"http://identifiers.org/pubchem.compound/656894"
};

reactionAnnotations = {
J2->"http://identifiers.org/go/GO:0008283", J6->"http://identifiers.org/go/GO:0009058", J6->"http://identifiers.org/ec-code/2.3.1.184"
};

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

(* Time evolution *)
odes = {
A1'[t] == 1.0*J4 -1.0*J5, A2'[t] == 1.0*J6 -1.0*J7, C1'[t] == 1.0*J0 -1.0*J1, C2'[t] == 1.0*J2 -1.0*J3, IPTG'[t] == 0.0 
};
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]}]