(* 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 = {
IPTG[t], ia1\[LetterSpace]ActiveTF[t], ia1\[LetterSpace]InactiveTF[t], p1[t], p2[t], p3[t], pAUR1[t], pSLS1[t], pSLS4[t], proAUR1[t], proLACI[t], proLAMDAR[t], proSLS1[t], proSLS4[t], proTETR[t], ter1[t], ter2[t], ter3[t], ter4[t], ter5[t], ter6[t]
};

initialValues = {
IPTG[0] == 10000.0, ia1\[LetterSpace]ActiveTF[0] == 100.0, ia1\[LetterSpace]InactiveTF[0] == 100.0, p1[0] == 10.0, p2[0] == 10.0, p3[0] == 10.0, pAUR1[0] == 10.0, pSLS1[0] == 10.0, pSLS4[0] == 10.0, proAUR1[0] == 0.0, proLACI[0] == 0.0, proLAMDAR[0] == 0.0, proSLS1[0] == 0.0, proSLS4[0] == 0.0, proTETR[0] == 0.0, ter1[0] == 10.0, ter2[0] == 10.0, ter3[0] == 10.0, ter4[0] == 10.0, ter5[0] == 10.0, ter6[0] == 10.0
};

rates = {
ia1\[LetterSpace]bind\[LetterSpace]forward, ia1\[LetterSpace]bind\[LetterSpace]reverse, pp1\[LetterSpace]v1, pp1\[LetterSpace]v2, pp2\[LetterSpace]v1, pp2\[LetterSpace]v2, pp3\[LetterSpace]v1, pp3\[LetterSpace]v2, pp4\[LetterSpace]v1, pp4\[LetterSpace]v2, pp5\[LetterSpace]v1, pp5\[LetterSpace]v2, pp6\[LetterSpace]v1, pp6\[LetterSpace]v2
};

rateEquations = {
ia1\[LetterSpace]bind\[LetterSpace]forward -> ia1\[LetterSpace]ActiveTF[t]*IPTG[t], ia1\[LetterSpace]bind\[LetterSpace]reverse -> ia1\[LetterSpace]Kd*ia1\[LetterSpace]InactiveTF[t], pp1\[LetterSpace]v1 -> 1, pp1\[LetterSpace]v2 -> proSLS1\[LetterSpace]degradation\[LetterSpace]rate*proSLS1[t], pp2\[LetterSpace]v1 -> AUR1*pAUR1\[LetterSpace]strength*pp2\[LetterSpace]translation\[LetterSpace]rate, pp2\[LetterSpace]v2 -> proAUR1\[LetterSpace]degradation\[LetterSpace]rate*proAUR1[t], pp3\[LetterSpace]v1 -> pp3\[LetterSpace]translation\[LetterSpace]rate*pSLS4\[LetterSpace]strength*SLS4, pp3\[LetterSpace]v2 -> proSLS4\[LetterSpace]degradation\[LetterSpace]rate*proSLS4[t], pp4\[LetterSpace]v1 -> LACI*p2\[LetterSpace]strength*pp4\[LetterSpace]translation\[LetterSpace]rate, pp4\[LetterSpace]v2 -> proLACI\[LetterSpace]degradation\[LetterSpace]rate*proLACI[t], pp5\[LetterSpace]v1 -> LAMDAR*p1\[LetterSpace]strength*pp5\[LetterSpace]translation\[LetterSpace]rate, pp5\[LetterSpace]v2 -> proLAMDAR\[LetterSpace]degradation\[LetterSpace]rate*proLAMDAR[t], pp6\[LetterSpace]v1 -> p3\[LetterSpace]strength*pp6\[LetterSpace]translation\[LetterSpace]rate*TETR, pp6\[LetterSpace]v2 -> proTETR\[LetterSpace]degradation\[LetterSpace]rate*proTETR[t]
};

parameters = {
ia1\[LetterSpace]Kd -> 0.001, ia1\[LetterSpace]repression\[LetterSpace]Kd -> 1.0, ia1\[LetterSpace]repression\[LetterSpace]h -> 2.0, p1\[LetterSpace]strength -> 2.5, p2\[LetterSpace]strength -> 2.4, p3\[LetterSpace]strength -> 2.5, pAUR1\[LetterSpace]strength -> 2.014, pSLS1\[LetterSpace]strength -> 2.5, pSLS4\[LetterSpace]strength -> 2.57, pp2\[LetterSpace]translation\[LetterSpace]rate -> 1.0, pp3\[LetterSpace]translation\[LetterSpace]rate -> 1.0, pp4\[LetterSpace]translation\[LetterSpace]rate -> 1.0, pp5\[LetterSpace]translation\[LetterSpace]rate -> 1.0, pp6\[LetterSpace]translation\[LetterSpace]rate -> 1.0, proAUR1\[LetterSpace]degradation\[LetterSpace]rate -> 0.1, proLACI\[LetterSpace]degradation\[LetterSpace]rate -> 0.07, proLAMDAR\[LetterSpace]degradation\[LetterSpace]rate -> 0.0415, proSLS1\[LetterSpace]degradation\[LetterSpace]rate -> 0.07, proSLS4\[LetterSpace]degradation\[LetterSpace]rate -> 0.04, proTETR\[LetterSpace]degradation\[LetterSpace]rate -> 0.08, ta1\[LetterSpace]Kd -> 1.0, ta1\[LetterSpace]h -> 2.0, tr1\[LetterSpace]Kd -> 1.0, tr1\[LetterSpace]h -> 2.0, tr2\[LetterSpace]Kd -> 1.0, tr2\[LetterSpace]h -> 2.0, tr3\[LetterSpace]Kd -> 1.0, tr3\[LetterSpace]h -> 2.0, tr4\[LetterSpace]Kd -> 1.0, tr4\[LetterSpace]h -> 2.0, tr5\[LetterSpace]Kd -> 1.0, tr5\[LetterSpace]h -> 2.0, tr6\[LetterSpace]Kd -> 1.0, tr6\[LetterSpace]h -> 2.0, DefaultCompartment -> 1.0
};

assignments = {
rs6 -> (1 + (proTETR[t]/tr4\[LetterSpace]Kd)^tr4\[LetterSpace]h)^(-1), rs4 -> (1 + (proLAMDAR[t]/tr5\[LetterSpace]Kd)^tr5\[LetterSpace]h)^(-1), AUR1 -> pAUR1\[LetterSpace]strength/(1 + (proSLS1[t]/tr1\[LetterSpace]Kd)^tr1\[LetterSpace]h), LACI -> p2\[LetterSpace]strength/(1 + (proLAMDAR[t]/tr5\[LetterSpace]Kd)^tr5\[LetterSpace]h), SLS4 -> pSLS4\[LetterSpace]strength/(1 + (proAUR1[t]/tr2\[LetterSpace]Kd)^tr2\[LetterSpace]h), rs5 -> (1 + (proLACI[t]/tr3\[LetterSpace]Kd)^tr3\[LetterSpace]h)^(-1), rs1 -> (1 + (proSLS1[t]/tr1\[LetterSpace]Kd)^tr1\[LetterSpace]h)^(-1), rs2 -> (1 + (proAUR1[t]/tr2\[LetterSpace]Kd)^tr2\[LetterSpace]h)^(-1), ope1 -> (1 + (ia1\[LetterSpace]ActiveTF[t]/ia1\[LetterSpace]repression\[LetterSpace]Kd)^ia1\[LetterSpace]repression\[LetterSpace]h)^(-1), SLS1 -> (pSLS1\[LetterSpace]strength*(proSLS4[t]/ta1\[LetterSpace]Kd)^ta1\[LetterSpace]h)/((1 + (ia1\[LetterSpace]ActiveTF[t]/ia1\[LetterSpace]repression\[LetterSpace]Kd)^ia1\[LetterSpace]repression\[LetterSpace]h)*(1 + (proLACI[t]/tr6\[LetterSpace]Kd)^tr6\[LetterSpace]h)*(1 + (proSLS4[t]/ta1\[LetterSpace]Kd)^ta1\[LetterSpace]h)), as1 -> (proSLS4[t]/ta1\[LetterSpace]Kd)^ta1\[LetterSpace]h/(1 + (proSLS4[t]/ta1\[LetterSpace]Kd)^ta1\[LetterSpace]h), TETR -> p3\[LetterSpace]strength/(1 + (proLACI[t]/tr3\[LetterSpace]Kd)^tr3\[LetterSpace]h), LAMDAR -> p1\[LetterSpace]strength/(1 + (proTETR[t]/tr4\[LetterSpace]Kd)^tr4\[LetterSpace]h), rs3 -> (1 + (proLACI[t]/tr6\[LetterSpace]Kd)^tr6\[LetterSpace]h)^(-1)
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
IPTG'[t] == 1.0*ia1\[LetterSpace]bind\[LetterSpace]reverse -1.0*ia1\[LetterSpace]bind\[LetterSpace]forward, ia1\[LetterSpace]ActiveTF'[t] == 1.0*ia1\[LetterSpace]bind\[LetterSpace]reverse -1.0*ia1\[LetterSpace]bind\[LetterSpace]forward, ia1\[LetterSpace]InactiveTF'[t] == 1.0*ia1\[LetterSpace]bind\[LetterSpace]forward -1.0*ia1\[LetterSpace]bind\[LetterSpace]reverse, p1'[t] == 0.0 , p2'[t] == 0.0 , p3'[t] == 0.0 , pAUR1'[t] == 0.0 , pSLS1'[t] == 0.0 , pSLS4'[t] == 0.0 , proAUR1'[t] == 1.0*pp2\[LetterSpace]v1 -1.0*pp2\[LetterSpace]v2, proLACI'[t] == 1.0*pp4\[LetterSpace]v1 -1.0*pp4\[LetterSpace]v2, proLAMDAR'[t] == 1.0*pp5\[LetterSpace]v1 -1.0*pp5\[LetterSpace]v2, proSLS1'[t] == 1.0*pp1\[LetterSpace]v1 -1.0*pp1\[LetterSpace]v2, proSLS4'[t] == 1.0*pp3\[LetterSpace]v1 -1.0*pp3\[LetterSpace]v2, proTETR'[t] == 1.0*pp6\[LetterSpace]v1 -1.0*pp6\[LetterSpace]v2, ter1'[t] == 0.0 , ter2'[t] == 0.0 , ter3'[t] == 0.0 , ter4'[t] == 0.0 , ter5'[t] == 0.0 , ter6'[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]}]