(* 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 = {
IKK[t], IKK\[LetterSpace]IkBalpha[t], IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB[t], IKK\[LetterSpace]IkBbeta[t], IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB[t], IKK\[LetterSpace]IkBeps[t], IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB[t], IkBalpha[t], IkBalpha\[LetterSpace]NFkB[t], IkBalpha\[LetterSpace]nuc[t], IkBalpha\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t], IkBalpha\[LetterSpace]transcript[t], IkBbeta[t], IkBbeta\[LetterSpace]NFkB[t], IkBbeta\[LetterSpace]nuc[t], IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t], IkBbeta\[LetterSpace]transcript[t], IkBeps[t], IkBeps\[LetterSpace]NFkB[t], IkBeps\[LetterSpace]nuc[t], IkBeps\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t], IkBeps\[LetterSpace]transcript[t], NFkB[t], NFkB\[LetterSpace]nuc[t], fr\[LetterSpace]after\[LetterSpace]trigger[t]
};

initialValues = {
fr\[LetterSpace]after\[LetterSpace]trigger[0] == 0.5, IKK[0] == 0.0, IKK\[LetterSpace]IkBalpha[0] == 0.0, IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB[0] == 0.0, IKK\[LetterSpace]IkBbeta[0] == 0.0, IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB[0] == 0.0, IKK\[LetterSpace]IkBeps[0] == 0.0, IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB[0] == 0.0, IkBalpha[0] == 0.1, IkBalpha\[LetterSpace]NFkB[0] == 0.0, IkBalpha\[LetterSpace]nuc[0] == 0.0, IkBalpha\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[0] == 0.0, IkBalpha\[LetterSpace]transcript[0] == 0.0, IkBbeta[0] == 0.0, IkBbeta\[LetterSpace]NFkB[0] == 0.0, IkBbeta\[LetterSpace]nuc[0] == 0.0, IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[0] == 0.0, IkBbeta\[LetterSpace]transcript[0] == 0.0, IkBeps[0] == 0.0, IkBeps\[LetterSpace]NFkB[0] == 0.0, IkBeps\[LetterSpace]nuc[0] == 0.0, IkBeps\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[0] == 0.0, IkBeps\[LetterSpace]transcript[0] == 0.0, NFkB[0] == 0.1, NFkB\[LetterSpace]nuc[0] == 0.001
};

rates = {
v1, v10, v11, v12, v13, v14, v15, v16, v17, v18, v19, v2, v20, v21, v22, v23, v24, v25, v26, v27, v28, v29, v3, v30, v31, v32, v33, v34, v35, v36, v37, v38, v39, v4, v40, v41, v42, v43, v44, v45, v5, v6, v7, v8, v9
};

rateEquations = {
v1 -> cytoplasm*(-(d4*IkBalpha\[LetterSpace]NFkB[t]) + a4*IkBalpha[t]*NFkB[t]), v10 -> cytoplasm*deg4*IkBalpha\[LetterSpace]NFkB[t], v11 -> cytoplasm*deg4*IkBbeta\[LetterSpace]NFkB[t], v12 -> cytoplasm*deg4*IkBeps\[LetterSpace]NFkB[t], v13 -> cytoplasm*k1*NFkB[t] - k01*nucleus*NFkB\[LetterSpace]nuc[t], v14 -> nucleus*(-(d4*IkBalpha\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t]) + a4*IkBalpha\[LetterSpace]nuc[t]*NFkB\[LetterSpace]nuc[t]), v15 -> nucleus*(-(d5*IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t]) + a5*IkBbeta\[LetterSpace]nuc[t]*NFkB\[LetterSpace]nuc[t]), v16 -> nucleus*(-(d6*IkBeps\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t]) + a6*IkBeps\[LetterSpace]nuc[t]*NFkB\[LetterSpace]nuc[t]), v17 -> nucleus*tr2a, v18 -> nucleus*tr2*NFkB\[LetterSpace]nuc[t]^2, v19 -> nucleus*tr3*IkBalpha\[LetterSpace]transcript[t], v2 -> cytoplasm*(-(d5*IkBbeta\[LetterSpace]NFkB[t]) + a5*IkBbeta[t]*NFkB[t]), v20 -> nucleus*tr2b, v21 -> nucleus*tr3*IkBbeta\[LetterSpace]transcript[t], v22 -> nucleus*tr2e, v23 -> nucleus*tr3*IkBeps\[LetterSpace]transcript[t], v24 -> cytoplasm*(a1*IkBalpha[t]*IKK[t] - d1*IKK\[LetterSpace]IkBalpha[t]), v25 -> nucleus*tr1*IkBalpha\[LetterSpace]transcript[t], v26 -> cytoplasm*deg1*IkBalpha[t], v27 -> cytoplasm*tp1*IkBalpha[t] - nucleus*tp2*IkBalpha\[LetterSpace]nuc[t], v28 -> cytoplasm*(a2*IkBbeta[t]*IKK[t] - d2*IKK\[LetterSpace]IkBbeta[t]), v29 -> nucleus*tr1*IkBbeta\[LetterSpace]transcript[t], v3 -> cytoplasm*(-(d6*IkBeps\[LetterSpace]NFkB[t]) + a6*IkBeps[t]*NFkB[t]), v30 -> cytoplasm*deg1*IkBbeta[t], v31 -> 0.5*cytoplasm*tp1*IkBbeta[t] - 0.5*nucleus*tp2*IkBbeta\[LetterSpace]nuc[t], v32 -> cytoplasm*(a3*IkBeps[t]*IKK[t] - d3*IKK\[LetterSpace]IkBeps[t]), v33 -> nucleus*tr1*IkBeps\[LetterSpace]transcript[t], v34 -> cytoplasm*deg1*IkBeps[t], v35 -> 0.5*cytoplasm*tp1*IkBeps[t] - 0.5*nucleus*tp2*IkBeps\[LetterSpace]nuc[t], v36 -> cytoplasm*(a7*IkBalpha\[LetterSpace]NFkB[t]*IKK[t] - d1*IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB[t]), v37 -> k2*nucleus*IkBalpha\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t], v38 -> cytoplasm*(a8*IkBbeta\[LetterSpace]NFkB[t]*IKK[t] - d2*IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB[t]), v39 -> nucleus*v39\[LetterSpace]k2\[LetterSpace]IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc*(flag\[LetterSpace]for\[LetterSpace]after\[LetterSpace]trigger + fr\[LetterSpace]after\[LetterSpace]trigger[t])*IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t], v4 -> cytoplasm*(-(d4*IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB[t]) + a4*IKK\[LetterSpace]IkBalpha[t]*NFkB[t]), v40 -> cytoplasm*(a9*IkBeps\[LetterSpace]NFkB[t]*IKK[t] - d3*IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB[t]), v41 -> 0.5*k2\[LetterSpace]eps*nucleus*IkBeps\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t], v42 -> cytoplasm*r1*IKK\[LetterSpace]IkBalpha[t], v43 -> cytoplasm*r2*IKK\[LetterSpace]IkBbeta[t], v44 -> cytoplasm*r3*IKK\[LetterSpace]IkBeps[t], v45 -> cytoplasm*k02*IKK[t], v5 -> cytoplasm*r4*IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB[t], v6 -> cytoplasm*(-(d5*IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB[t]) + a5*IKK\[LetterSpace]IkBbeta[t]*NFkB[t]), v7 -> cytoplasm*r5*IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB[t], v8 -> cytoplasm*(-(d6*IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB[t]) + a6*IKK\[LetterSpace]IkBeps[t]*NFkB[t]), v9 -> cytoplasm*r6*IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB[t]
};

parameters = {
a1 -> 1.35, a2 -> 0.36, a3 -> 0.54, a4 -> 30.0, a5 -> 30.0, a6 -> 30.0, a7 -> 11.1, a8 -> 2.88, a9 -> 4.2, d1 -> 0.075, d2 -> 0.105, d3 -> 0.105, d4 -> 0.03, d5 -> 0.03, d6 -> 0.03, deg1 -> 0.00678, deg4 -> 0.00135, flag\[LetterSpace]for\[LetterSpace]after\[LetterSpace]trigger -> 0.5, fr -> 1.0, k01 -> 0.0048, k02 -> 0.0072, k1 -> 5.4, k2 -> 0.828, k2\[LetterSpace]beta -> 0.624, k2\[LetterSpace]eps -> 0.624, r1 -> 0.2442, r2 -> 0.09, r3 -> 0.132, r4 -> 1.224, r5 -> 0.45, r6 -> 0.66, tp1 -> 0.018, tp2 -> 0.012, tr1 -> 0.2448, tr2 -> 0.99, tr2a -> 9.25*^-05, tr2b -> 0.0, tr2e -> 0.0, tr3 -> 0.0168, trigger\[LetterSpace]value -> 0.0, v39\[LetterSpace]k2\[LetterSpace]IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc -> 0.0069, cytoplasm -> 1.0, nucleus -> 1.0
};

assignments = {
Total\[LetterSpace]NFkBn -> IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc[t] + NFkB\[LetterSpace]nuc[t], Total\[LetterSpace]IkBeps -> IkBeps[t] + IkBeps\[LetterSpace]NFkB[t] + IKK\[LetterSpace]IkBeps[t] + IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB[t], Total\[LetterSpace]IkBbeta -> IkBbeta[t] + IkBbeta\[LetterSpace]NFkB[t] + IKK\[LetterSpace]IkBbeta[t] + IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB[t], Total\[LetterSpace]IkBalpha -> IkBalpha[t] + IkBalpha\[LetterSpace]NFkB[t] + IKK\[LetterSpace]IkBalpha[t] + IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
IKK'[t] == 1.0*v5 +1.0*v7 +1.0*v9 +1.0*v42 +1.0*v43 +1.0*v44 -1.0*v24 -1.0*v28 -1.0*v32 -1.0*v36 -1.0*v38 -1.0*v40 -1.0*v45, IKK\[LetterSpace]IkBalpha'[t] == 1.0*v24 -1.0*v4 -1.0*v42, IKK\[LetterSpace]IkBalpha\[LetterSpace]NFkB'[t] == 1.0*v4 +1.0*v36 -1.0*v5, IKK\[LetterSpace]IkBbeta'[t] == 1.0*v28 -1.0*v6 -1.0*v43, IKK\[LetterSpace]IkBbeta\[LetterSpace]NFkB'[t] == 1.0*v6 +1.0*v38 -1.0*v7, IKK\[LetterSpace]IkBeps'[t] == 1.0*v32 -1.0*v8 -1.0*v44, IKK\[LetterSpace]IkBeps\[LetterSpace]NFkB'[t] == 1.0*v8 +1.0*v40 -1.0*v9, IkBalpha'[t] == 1.0*v25 -1.0*v1 -1.0*v24 -1.0*v26 -1.0*v27, IkBalpha\[LetterSpace]NFkB'[t] == 1.0*v1 +1.0*v37 -1.0*v10 -1.0*v36, IkBalpha\[LetterSpace]nuc'[t] == 1.0*v27 -1.0*v14, IkBalpha\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc'[t] == 1.0*v14 -1.0*v37, IkBalpha\[LetterSpace]transcript'[t] == 1.0*v17 +1.0*v18 -1.0*v19, IkBbeta'[t] == 1.0*v29 -1.0*v2 -1.0*v28 -1.0*v30 -1.0*v31, IkBbeta\[LetterSpace]NFkB'[t] == 1.0*v2 +1.0*v39 -1.0*v11 -1.0*v38, IkBbeta\[LetterSpace]nuc'[t] == 1.0*v31 -1.0*v15, IkBbeta\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc'[t] == 1.0*v15 -1.0*v39, IkBbeta\[LetterSpace]transcript'[t] == 1.0*v20 -1.0*v21, IkBeps'[t] == 1.0*v33 -1.0*v3 -1.0*v32 -1.0*v34 -1.0*v35, IkBeps\[LetterSpace]NFkB'[t] == 1.0*v3 +1.0*v41 -1.0*v12 -1.0*v40, IkBeps\[LetterSpace]nuc'[t] == 1.0*v35 -1.0*v16, IkBeps\[LetterSpace]nuc\[LetterSpace]NFkB\[LetterSpace]nuc'[t] == 1.0*v16 -1.0*v41, IkBeps\[LetterSpace]transcript'[t] == 1.0*v22 -1.0*v23, NFkB'[t] == 1.0*v5 +1.0*v7 +1.0*v9 +1.0*v10 +1.0*v11 +1.0*v12 -1.0*v1 -1.0*v2 -1.0*v3 -1.0*v4 -1.0*v6 -1.0*v8 -1.0*v13, NFkB\[LetterSpace]nuc'[t] == 1.0*v13 -1.0*v14 -1.0*v15 -1.0*v16, fr\[LetterSpace]after\[LetterSpace]trigger'[t] == (-0.5*trigger\[LetterSpace]value)/(-1999 + t)^2
};
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]}]