(* 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 = {
Pfr[t], Pi[t], Pr[t], S[t], V[t], Xa[t], Xi[t], Ya[t], Yi[t], preS[t], prepreS[t]
};

initialValues = {
Pfr[0] == 10.0, Pi[0] == 0.0, Pr[0] == 0.0, S[0] == 0.0, V[0] == 30.0, Xa[0] == 0.0, Xi[0] == 6.0, Ya[0] == 0.9, Yi[0] == 0.0, preS[0] == 0.0, prepreS[0] == 200.0
};

rates = {
Glucose\[LetterSpace]sensor\[LetterSpace]inactivation, Photoreceptor\[LetterSpace]activation, Photoreceptor\[LetterSpace]decay, Photoreceptor\[LetterSpace]inactivation, S\[LetterSpace]degradation, S\[LetterSpace]formation, S\[LetterSpace]generation, Transducer\[LetterSpace]activation, Transducer\[LetterSpace]inactivation, V\[LetterSpace]degradation, V\[LetterSpace]formation, preS\[LetterSpace]formation
};

rateEquations = {
Glucose\[LetterSpace]sensor\[LetterSpace]inactivation -> compartment*Gluc*Glucose\[LetterSpace]sensor\[LetterSpace]inactivation\[LetterSpace]kG*Ya[t], Photoreceptor\[LetterSpace]activation -> compartment*Photoreceptor\[LetterSpace]activation\[LetterSpace]IfrSfrPfr*Pfr[t], Photoreceptor\[LetterSpace]decay -> compartment*Photoreceptor\[LetterSpace]decay\[LetterSpace]kd*Pr[t], Photoreceptor\[LetterSpace]inactivation -> compartment*Photoreceptor\[LetterSpace]inactivation\[LetterSpace]IrSrPr*Pr[t], S\[LetterSpace]degradation -> compartment*S\[LetterSpace]degradation\[LetterSpace]kd\[LetterSpace]s*S[t], S\[LetterSpace]formation -> (compartment*S\[LetterSpace]formation\[LetterSpace]alpha1)/(1 + V[t]^3), S\[LetterSpace]generation -> compartment*S\[LetterSpace]generation\[LetterSpace]ky*preS[t]*Ya[t], Transducer\[LetterSpace]activation -> compartment*Transducer\[LetterSpace]activation\[LetterSpace]kia*Pr[t]*Xi[t], Transducer\[LetterSpace]inactivation -> compartment*Transducer\[LetterSpace]inactivation\[LetterSpace]kai*Xa[t], V\[LetterSpace]degradation -> compartment*V\[LetterSpace]degradation\[LetterSpace]kd\[LetterSpace]v*V[t], V\[LetterSpace]formation -> (compartment*V\[LetterSpace]formation\[LetterSpace]alpha2)/(1 + S[t]^3), preS\[LetterSpace]formation -> compartment*preS\[LetterSpace]formation\[LetterSpace]kx*prepreS[t]*Xa[t]
};

parameters = {
Gluc -> 0.0, V\[LetterSpace]degradation\[LetterSpace]kd\[LetterSpace]v -> 1.0, Photoreceptor\[LetterSpace]decay\[LetterSpace]kd -> 0.1, Photoreceptor\[LetterSpace]activation\[LetterSpace]IfrSfrPfr -> 0.1, Photoreceptor\[LetterSpace]inactivation\[LetterSpace]IrSrPr -> 0.0, Transducer\[LetterSpace]activation\[LetterSpace]kia -> 0.1, Transducer\[LetterSpace]inactivation\[LetterSpace]kai -> 0.8, preS\[LetterSpace]formation\[LetterSpace]kx -> 0.2, S\[LetterSpace]generation\[LetterSpace]ky -> 1.0, Glucose\[LetterSpace]sensor\[LetterSpace]inactivation\[LetterSpace]kG -> 0.1, S\[LetterSpace]formation\[LetterSpace]alpha1 -> 30.0, V\[LetterSpace]formation\[LetterSpace]alpha2 -> 50.0, S\[LetterSpace]degradation\[LetterSpace]kd\[LetterSpace]s -> 1.0, compartment -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
Gluc[t]->"http://identifiers.org/chebi/CHEBI:17234", Gluc[t]->"http://identifiers.org/kegg.compound/C00293"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
Pfr'[t] == 1.0*Photoreceptor\[LetterSpace]inactivation -1.0*Photoreceptor\[LetterSpace]activation, Pi'[t] == 1.0*Photoreceptor\[LetterSpace]decay , Pr'[t] == 1.0*Photoreceptor\[LetterSpace]activation -1.0*Photoreceptor\[LetterSpace]inactivation -1.0*Photoreceptor\[LetterSpace]decay, S'[t] == 1.0*S\[LetterSpace]generation +1.0*S\[LetterSpace]formation -1.0*S\[LetterSpace]degradation, V'[t] == 1.0*V\[LetterSpace]formation -1.0*V\[LetterSpace]degradation, Xa'[t] == 1.0*Transducer\[LetterSpace]activation -1.0*Transducer\[LetterSpace]inactivation, Xi'[t] == 1.0*Transducer\[LetterSpace]inactivation -1.0*Transducer\[LetterSpace]activation, Ya'[t] ==  -1.0*Glucose\[LetterSpace]sensor\[LetterSpace]inactivation, Yi'[t] == 1.0*Glucose\[LetterSpace]sensor\[LetterSpace]inactivation , preS'[t] == 1.0*preS\[LetterSpace]formation -1.0*S\[LetterSpace]generation, prepreS'[t] ==  -1.0*preS\[LetterSpace]formation
};
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]}]