(* 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 = {
Inh[t], Inh\[LetterSpace]T1[t], T1[t], T1\[LetterSpace]alpha[t], T2[t], T2\[LetterSpace]beta[t], T3[t], T3\[LetterSpace]Inh[t], alpha[t], alpha\[LetterSpace]T1[t], alpha\[LetterSpace]T1\[LetterSpace]alpha[t], alpha\[LetterSpace]T2[t], alpha\[LetterSpace]T2\[LetterSpace]beta[t], alpha\[LetterSpace]alpha\[LetterSpace]T1[t], alpha\[LetterSpace]beta\[LetterSpace]T2[t], beta[t], beta\[LetterSpace]Inh\[LetterSpace]T3[t], beta\[LetterSpace]T3[t], beta\[LetterSpace]T3\[LetterSpace]Inh[t]
};

initialValues = {
Inh[0] == 0.0, Inh\[LetterSpace]T1[0] == 0.0, T1[0] == 38.5, T1\[LetterSpace]alpha[0] == 0.0, T2[0] == 3.89, T2\[LetterSpace]beta[0] == 0.0, T3[0] == 38.5, T3\[LetterSpace]Inh[0] == 0.0, alpha[0] == 10.0, alpha\[LetterSpace]T1[0] == 0.0, alpha\[LetterSpace]T1\[LetterSpace]alpha[0] == 0.0, alpha\[LetterSpace]T2[0] == 0.0, alpha\[LetterSpace]T2\[LetterSpace]beta[0] == 0.0, alpha\[LetterSpace]alpha\[LetterSpace]T1[0] == 0.0, alpha\[LetterSpace]beta\[LetterSpace]T2[0] == 0.0, beta[0] == 0.0, beta\[LetterSpace]Inh\[LetterSpace]T3[0] == 0.0, beta\[LetterSpace]T3[0] == 0.0, beta\[LetterSpace]T3\[LetterSpace]Inh[0] == 0.0
};

rates = {
ass\[LetterSpace]aa\[LetterSpace]l, ass\[LetterSpace]ab\[LetterSpace]l, ass\[LetterSpace]bc\[LetterSpace]l, ass\[LetterSpace]bc\[LetterSpace]r, ass\[LetterSpace]bc\[LetterSpace]rl, dis\[LetterSpace]aa, dis\[LetterSpace]ab, dis\[LetterSpace]bc, exo\[LetterSpace]a, exo\[LetterSpace]b, exo\[LetterSpace]c, inh\[LetterSpace]ac, inh\[LetterSpace]displ\[LetterSpace]ac, m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]lr, m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]r, m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]rl, m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]lr, m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]r, m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]rl, m\[LetterSpace]ass\[LetterSpace]bc\[LetterSpace]lr, m\[LetterSpace]inh\[LetterSpace]displ\[LetterSpace]ca, nick\[LetterSpace]aa, nick\[LetterSpace]ab, nick\[LetterSpace]bc, pol\[LetterSpace]aa, pol\[LetterSpace]ab, pol\[LetterSpace]bc
};

rateEquations = {
ass\[LetterSpace]aa\[LetterSpace]l -> sample*(-(k0r*alpha\[LetterSpace]T1[t]) + k0d*alpha[t]*T1[t]), ass\[LetterSpace]ab\[LetterSpace]l -> sample*(-(k7r*alpha\[LetterSpace]T2[t]) + k7d*alpha[t]*T2[t]), ass\[LetterSpace]bc\[LetterSpace]l -> sample*(-(k14r*beta\[LetterSpace]T3[t]) + k14d*beta[t]*T3[t]), ass\[LetterSpace]bc\[LetterSpace]r -> sample*(k16d*Inh[t]*T3[t] - k16r*T3\[LetterSpace]Inh[t]), ass\[LetterSpace]bc\[LetterSpace]rl -> sample*(-(k17r*beta\[LetterSpace]T3\[LetterSpace]Inh[t]) + k17d*beta[t]*T3\[LetterSpace]Inh[t]), dis\[LetterSpace]aa -> k5d*sample*alpha\[LetterSpace]T1\[LetterSpace]alpha[t], dis\[LetterSpace]ab -> k12d*sample*alpha\[LetterSpace]T2\[LetterSpace]beta[t], dis\[LetterSpace]bc -> k19d*sample*beta\[LetterSpace]T3\[LetterSpace]Inh[t], exo\[LetterSpace]a -> k24d*sample*alpha[t], exo\[LetterSpace]b -> k25d*sample*beta[t], exo\[LetterSpace]c -> k26d*sample*Inh[t], inh\[LetterSpace]ac -> sample*(-(k21r*Inh\[LetterSpace]T1[t]) + k21d*Inh[t]*T1[t]), inh\[LetterSpace]displ\[LetterSpace]ac -> sample*(-(k22r*alpha[t]*Inh\[LetterSpace]T1[t]) + k22d*Inh[t]*T1\[LetterSpace]alpha[t]), m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]lr -> sample*(-(k1r*alpha[t]*alpha\[LetterSpace]T1[t]) + k1d*alpha\[LetterSpace]T1\[LetterSpace]alpha[t]), m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]r -> sample*(-(k2r*alpha[t]*T1[t]) + k2d*T1\[LetterSpace]alpha[t]), m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]rl -> sample*(k3d*alpha\[LetterSpace]T1\[LetterSpace]alpha[t] - k3r*alpha[t]*T1\[LetterSpace]alpha[t]), m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]lr -> sample*(k8d*alpha\[LetterSpace]T2\[LetterSpace]beta[t] - k8r*alpha\[LetterSpace]T2[t]*beta[t]), m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]r -> sample*(-(k9r*beta[t]*T2[t]) + k9d*T2\[LetterSpace]beta[t]), m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]rl -> sample*(k10d*alpha\[LetterSpace]T2\[LetterSpace]beta[t] - k10r*alpha[t]*T2\[LetterSpace]beta[t]), m\[LetterSpace]ass\[LetterSpace]bc\[LetterSpace]lr -> sample*(k15d*beta\[LetterSpace]T3\[LetterSpace]Inh[t] - k15r*beta\[LetterSpace]T3[t]*Inh[t]), m\[LetterSpace]inh\[LetterSpace]displ\[LetterSpace]ca -> sample*(-(k23r*alpha\[LetterSpace]T1[t]*Inh[t]) + k23d*alpha[t]*Inh\[LetterSpace]T1[t]), nick\[LetterSpace]aa -> k6d*sample*alpha\[LetterSpace]alpha\[LetterSpace]T1[t], nick\[LetterSpace]ab -> k13d*sample*alpha\[LetterSpace]beta\[LetterSpace]T2[t], nick\[LetterSpace]bc -> k20d*sample*beta\[LetterSpace]Inh\[LetterSpace]T3[t], pol\[LetterSpace]aa -> k4d*sample*alpha\[LetterSpace]T1[t], pol\[LetterSpace]ab -> k11d*sample*alpha\[LetterSpace]T2[t], pol\[LetterSpace]bc -> k18d*sample*beta\[LetterSpace]T3[t]
};

parameters = {
k0d -> 0.0294, k0r -> 3.43457943925, k10d -> 3.43457943925, k10r -> 0.0294, k11d -> 11.8408, k12d -> 9.2239832, k13d -> 2.60186, k14d -> 0.0171, k14r -> 0.610714285714, k15d -> 0.00186296832954, k15r -> 0.027, k16d -> 0.027, k16r -> 0.00186296832954, k17d -> 0.0171, k17r -> 0.610714285714, k18d -> 17.024, k19d -> 5.566848, k1d -> 3.43457943925, k1r -> 0.0294, k20d -> 3.2064, k21d -> 0.027, k21r -> 0.00608108108108, k22d -> 0.021546, k22r -> 4.15391351351*^-05, k23d -> 4.15391351351*^-05, k23r -> 0.021546, k24d -> 0.411, k25d -> 0.485802, k26d -> 1.7262, k2d -> 3.43457943925, k2r -> 0.0294, k3d -> 3.43457943925, k3r -> 0.0294, k4d -> 15.2, k5d -> 11.8408, k6d -> 3.34, k7d -> 0.0294, k7r -> 3.43457943925, k8d -> 0.610714285714, k8r -> 0.0171, k9d -> 0.610714285714, k9r -> 0.0171, empty -> 0.0, sample -> 1.0
};

assignments = {
alpha\[LetterSpace]total -> alpha[t] + alpha\[LetterSpace]T1[t] + 2*alpha\[LetterSpace]T1\[LetterSpace]alpha[t] + 2*alpha\[LetterSpace]T2[t] + alpha\[LetterSpace]T2\[LetterSpace]beta[t] + T1\[LetterSpace]alpha[t], beta\[LetterSpace]total -> alpha\[LetterSpace]T2\[LetterSpace]beta[t] + beta[t] + beta\[LetterSpace]T3[t] + beta\[LetterSpace]T3\[LetterSpace]Inh[t] + T2\[LetterSpace]beta[t], Inh\[LetterSpace]total -> beta\[LetterSpace]T3\[LetterSpace]Inh[t] + Inh[t] + Inh\[LetterSpace]T1[t] + T3\[LetterSpace]Inh[t], fluorescence -> -0.38 + 0.00093*(22*(alpha\[LetterSpace]alpha\[LetterSpace]T1[t] + alpha\[LetterSpace]beta\[LetterSpace]T2[t] + alpha\[LetterSpace]T1\[LetterSpace]alpha[t] + alpha\[LetterSpace]T2\[LetterSpace]beta[t]) + 27*(beta\[LetterSpace]Inh\[LetterSpace]T3[t] + beta\[LetterSpace]T3\[LetterSpace]Inh[t]) + 11*(alpha\[LetterSpace]T1[t] + alpha\[LetterSpace]T2[t] + beta\[LetterSpace]T3[t] + T1\[LetterSpace]alpha[t] + T2\[LetterSpace]beta[t]) + 16*(Inh\[LetterSpace]T1[t] + T3\[LetterSpace]Inh[t])), Bp\[LetterSpace]concentration -> 22*(alpha\[LetterSpace]alpha\[LetterSpace]T1[t] + alpha\[LetterSpace]beta\[LetterSpace]T2[t] + alpha\[LetterSpace]T1\[LetterSpace]alpha[t] + alpha\[LetterSpace]T2\[LetterSpace]beta[t]) + 27*(beta\[LetterSpace]Inh\[LetterSpace]T3[t] + beta\[LetterSpace]T3\[LetterSpace]Inh[t]) + 11*(alpha\[LetterSpace]T1[t] + alpha\[LetterSpace]T2[t] + beta\[LetterSpace]T3[t] + T1\[LetterSpace]alpha[t] + T2\[LetterSpace]beta[t]) + 16*(Inh\[LetterSpace]T1[t] + T3\[LetterSpace]Inh[t])
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
Inh'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]bc\[LetterSpace]lr +1.0*dis\[LetterSpace]bc +1.0*m\[LetterSpace]inh\[LetterSpace]displ\[LetterSpace]ca -1.0*ass\[LetterSpace]bc\[LetterSpace]r -1.0*inh\[LetterSpace]ac -1.0*inh\[LetterSpace]displ\[LetterSpace]ac -1.0*exo\[LetterSpace]c, Inh\[LetterSpace]T1'[t] == 1.0*inh\[LetterSpace]ac +1.0*inh\[LetterSpace]displ\[LetterSpace]ac -1.0*m\[LetterSpace]inh\[LetterSpace]displ\[LetterSpace]ca, T1'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]r -1.0*ass\[LetterSpace]aa\[LetterSpace]l -1.0*inh\[LetterSpace]ac, T1\[LetterSpace]alpha'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]rl -1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]r -1.0*inh\[LetterSpace]displ\[LetterSpace]ac, T2'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]r -1.0*ass\[LetterSpace]ab\[LetterSpace]l, T2\[LetterSpace]beta'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]rl -1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]r, T3'[t] ==  -1.0*ass\[LetterSpace]bc\[LetterSpace]l -1.0*ass\[LetterSpace]bc\[LetterSpace]r, T3\[LetterSpace]Inh'[t] == 1.0*ass\[LetterSpace]bc\[LetterSpace]r -1.0*ass\[LetterSpace]bc\[LetterSpace]rl, alpha'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]lr +1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]r +1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]rl +1.0*dis\[LetterSpace]aa +1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]rl +1.0*inh\[LetterSpace]displ\[LetterSpace]ac -1.0*ass\[LetterSpace]aa\[LetterSpace]l -1.0*ass\[LetterSpace]ab\[LetterSpace]l -1.0*m\[LetterSpace]inh\[LetterSpace]displ\[LetterSpace]ca -1.0*exo\[LetterSpace]a, alpha\[LetterSpace]T1'[t] == 1.0*m\[LetterSpace]inh\[LetterSpace]displ\[LetterSpace]ca +1.0*ass\[LetterSpace]aa\[LetterSpace]l +1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]lr -1.0*pol\[LetterSpace]aa, alpha\[LetterSpace]T1\[LetterSpace]alpha'[t] == 1.0*nick\[LetterSpace]aa -1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]lr -1.0*m\[LetterSpace]ass\[LetterSpace]aa\[LetterSpace]rl -1.0*dis\[LetterSpace]aa, alpha\[LetterSpace]T2'[t] == 1.0*ass\[LetterSpace]ab\[LetterSpace]l +1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]lr -1.0*pol\[LetterSpace]ab, alpha\[LetterSpace]T2\[LetterSpace]beta'[t] == 1.0*nick\[LetterSpace]ab -1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]lr -1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]rl -1.0*dis\[LetterSpace]ab, alpha\[LetterSpace]alpha\[LetterSpace]T1'[t] == 1.0*pol\[LetterSpace]aa +1.0*dis\[LetterSpace]aa -1.0*nick\[LetterSpace]aa, alpha\[LetterSpace]beta\[LetterSpace]T2'[t] == 1.0*pol\[LetterSpace]ab +1.0*dis\[LetterSpace]ab -1.0*nick\[LetterSpace]ab, beta'[t] == 1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]lr +1.0*m\[LetterSpace]ass\[LetterSpace]ab\[LetterSpace]r +1.0*dis\[LetterSpace]ab -1.0*ass\[LetterSpace]bc\[LetterSpace]l -1.0*ass\[LetterSpace]bc\[LetterSpace]rl -1.0*exo\[LetterSpace]b, beta\[LetterSpace]Inh\[LetterSpace]T3'[t] == 1.0*pol\[LetterSpace]bc +1.0*dis\[LetterSpace]bc -1.0*nick\[LetterSpace]bc, beta\[LetterSpace]T3'[t] == 1.0*ass\[LetterSpace]bc\[LetterSpace]l +1.0*m\[LetterSpace]ass\[LetterSpace]bc\[LetterSpace]lr -1.0*pol\[LetterSpace]bc, beta\[LetterSpace]T3\[LetterSpace]Inh'[t] == 1.0*ass\[LetterSpace]bc\[LetterSpace]rl +1.0*nick\[LetterSpace]bc -1.0*m\[LetterSpace]ass\[LetterSpace]bc\[LetterSpace]lr -1.0*dis\[LetterSpace]bc
};
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]}]