(* 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 = {
C[t], CN[t], M\[LetterSpace]P[t], M\[LetterSpace]T[t], P0[t], P1[t], P2[t], T0[t], T1[t], T2[t]
};

initialValues = {
C[0] == 0.18, CN[0] == 1.2, M\[LetterSpace]P[0] == 0.09, M\[LetterSpace]T[0] == 1.41, P0[0] == 0.02, P1[0] == 0.02, P2[0] == 0.01, T0[0] == 0.54, T1[0] == 0.79, T2[0] == 4.65
};

rates = {
CN\[LetterSpace]decay, C\[LetterSpace]decay, C\[LetterSpace]form, C\[LetterSpace]transp, M\[LetterSpace]P\[LetterSpace]decay, M\[LetterSpace]T\[LetterSpace]decay, P1\[LetterSpace]decay, P1\[LetterSpace]depho, P1\[LetterSpace]pho, P2\[LetterSpace]decay, P2\[LetterSpace]depho, P2\[LetterSpace]light\[LetterSpace]deact, PER\[LetterSpace]transl, PO\[LetterSpace]decay, P\[LetterSpace]pho, T0\[LetterSpace]decay, T1\[LetterSpace]decay, T1\[LetterSpace]depho, T1\[LetterSpace]pho, T2\[LetterSpace]decay, T2\[LetterSpace]depho, T2\[LetterSpace]light\[LetterSpace]deact, TIM\[LetterSpace]transl, T\[LetterSpace]pho, per\[LetterSpace]trans, tim\[LetterSpace]trans
};

rateEquations = {
CN\[LetterSpace]decay -> CN\[LetterSpace]decay\[LetterSpace]kd\[LetterSpace]CN*nucleus*CN[t], C\[LetterSpace]decay -> cytoplasm*C\[LetterSpace]decay\[LetterSpace]kd\[LetterSpace]C*C[t], C\[LetterSpace]form -> cytoplasm*(-(C\[LetterSpace]form\[LetterSpace]k4*C[t]) + C\[LetterSpace]form\[LetterSpace]k3*P2[t]*T2[t]), C\[LetterSpace]transp -> cytoplasm*C\[LetterSpace]transp\[LetterSpace]k1*C[t] - C\[LetterSpace]transp\[LetterSpace]k2*nucleus*CN[t], M\[LetterSpace]P\[LetterSpace]decay -> cytoplasm*M\[LetterSpace]P[t]*(kd + M\[LetterSpace]P\[LetterSpace]decay\[LetterSpace]v\[LetterSpace]mP/(M\[LetterSpace]P\[LetterSpace]decay\[LetterSpace]K\[LetterSpace]mP + M\[LetterSpace]P[t])), M\[LetterSpace]T\[LetterSpace]decay -> cytoplasm*M\[LetterSpace]T[t]*(kd + M\[LetterSpace]T\[LetterSpace]decay\[LetterSpace]v\[LetterSpace]mT/(M\[LetterSpace]T\[LetterSpace]decay\[LetterSpace]K\[LetterSpace]mT + M\[LetterSpace]T[t])), P1\[LetterSpace]decay -> cytoplasm*kd*P1[t], P1\[LetterSpace]depho -> (cytoplasm*P1\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]2P*P1[t])/(P1\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]2P + P1[t]), P1\[LetterSpace]pho -> (cytoplasm*P1\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]3P*P1[t])/(P1\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]3P + P1[t]), P2\[LetterSpace]decay -> cytoplasm*kd*P2[t], P2\[LetterSpace]depho -> (cytoplasm*P2\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]4P*P2[t])/(P2\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]4P + P2[t]), P2\[LetterSpace]light\[LetterSpace]deact -> (cytoplasm*P2\[LetterSpace]light\[LetterSpace]deact\[LetterSpace]v\[LetterSpace]dP*P2[t])/(P2\[LetterSpace]light\[LetterSpace]deact\[LetterSpace]K\[LetterSpace]dP + P2[t]), PER\[LetterSpace]transl -> cytoplasm*PER\[LetterSpace]transl\[LetterSpace]k\[LetterSpace]sP*M\[LetterSpace]P[t], PO\[LetterSpace]decay -> cytoplasm*kd*P0[t], P\[LetterSpace]pho -> (cytoplasm*P\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]1P*P0[t])/(P\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]1P + P0[t]), T0\[LetterSpace]decay -> cytoplasm*kd*T0[t], T1\[LetterSpace]decay -> cytoplasm*kd*T1[t], T1\[LetterSpace]depho -> (cytoplasm*T1\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]2T*T1[t])/(T1\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]2T + T1[t]), T1\[LetterSpace]pho -> (cytoplasm*T1\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]3T*T1[t])/(T1\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]3T + T1[t]), T2\[LetterSpace]decay -> cytoplasm*kd*T2[t], T2\[LetterSpace]depho -> (cytoplasm*T2\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]4T*T2[t])/(T2\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]4T + T2[t]), T2\[LetterSpace]light\[LetterSpace]deact -> (cytoplasm*v\[LetterSpace]dT*T2[t])/(T2\[LetterSpace]light\[LetterSpace]deact\[LetterSpace]K\[LetterSpace]dT + T2[t]), TIM\[LetterSpace]transl -> cytoplasm*TIM\[LetterSpace]transl\[LetterSpace]k\[LetterSpace]sT*M\[LetterSpace]T[t], T\[LetterSpace]pho -> (cytoplasm*T\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]1T*T0[t])/(T\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]1T + T0[t]), per\[LetterSpace]trans -> (per\[LetterSpace]trans\[LetterSpace]Ki\[LetterSpace]P^n*per\[LetterSpace]trans\[LetterSpace]v\[LetterSpace]sP)/(per\[LetterSpace]trans\[LetterSpace]Ki\[LetterSpace]P^n + CN[t]^n), tim\[LetterSpace]trans -> (tim\[LetterSpace]trans\[LetterSpace]Ki\[LetterSpace]T^n*tim\[LetterSpace]trans\[LetterSpace]v\[LetterSpace]sT)/(tim\[LetterSpace]trans\[LetterSpace]Ki\[LetterSpace]T^n + CN[t]^n)
};

parameters = {
kd -> 0.01, l\[LetterSpace]d -> 12.0, n -> 4.0, v\[LetterSpace]dT\[LetterSpace]dark -> 2.0, v\[LetterSpace]dT\[LetterSpace]fac -> 2.0, per\[LetterSpace]trans\[LetterSpace]v\[LetterSpace]sP -> 0.8, per\[LetterSpace]trans\[LetterSpace]Ki\[LetterSpace]P -> 1.0, tim\[LetterSpace]trans\[LetterSpace]v\[LetterSpace]sT -> 1.0, tim\[LetterSpace]trans\[LetterSpace]Ki\[LetterSpace]T -> 1.0, M\[LetterSpace]T\[LetterSpace]decay\[LetterSpace]v\[LetterSpace]mT -> 0.7, M\[LetterSpace]T\[LetterSpace]decay\[LetterSpace]K\[LetterSpace]mT -> 0.2, M\[LetterSpace]P\[LetterSpace]decay\[LetterSpace]v\[LetterSpace]mP -> 0.8, M\[LetterSpace]P\[LetterSpace]decay\[LetterSpace]K\[LetterSpace]mP -> 0.2, PER\[LetterSpace]transl\[LetterSpace]k\[LetterSpace]sP -> 0.9, TIM\[LetterSpace]transl\[LetterSpace]k\[LetterSpace]sT -> 0.9, C\[LetterSpace]form\[LetterSpace]k3 -> 1.2, C\[LetterSpace]form\[LetterSpace]k4 -> 0.6, C\[LetterSpace]decay\[LetterSpace]kd\[LetterSpace]C -> 0.01, CN\[LetterSpace]decay\[LetterSpace]kd\[LetterSpace]CN -> 0.01, C\[LetterSpace]transp\[LetterSpace]k1 -> 1.2, C\[LetterSpace]transp\[LetterSpace]k2 -> 0.2, P\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]1P -> 8.0, P\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]1P -> 2.0, P1\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]3P -> 8.0, P1\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]3P -> 2.0, P1\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]2P -> 2.0, P1\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]2P -> 1.0, P2\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]4P -> 1.0, P2\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]4P -> 2.0, T\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]1T -> 8.0, T\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]1T -> 2.0, T1\[LetterSpace]pho\[LetterSpace]V\[LetterSpace]3T -> 8.0, T1\[LetterSpace]pho\[LetterSpace]K\[LetterSpace]3T -> 2.0, T1\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]2T -> 2.0, T1\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]2T -> 1.0, T2\[LetterSpace]depho\[LetterSpace]V\[LetterSpace]4T -> 1.0, T2\[LetterSpace]depho\[LetterSpace]K\[LetterSpace]4T -> 2.0, T2\[LetterSpace]light\[LetterSpace]deact\[LetterSpace]K\[LetterSpace]dT -> 0.2, P2\[LetterSpace]light\[LetterSpace]deact\[LetterSpace]v\[LetterSpace]dP -> 2.0, P2\[LetterSpace]light\[LetterSpace]deact\[LetterSpace]K\[LetterSpace]dP -> 0.2, cytoplasm -> 1.0, nucleus -> 1.0
};

assignments = {
v\[LetterSpace]dT -> v\[LetterSpace]dT\[LetterSpace]dark*(1 + (-1 + v\[LetterSpace]dT\[LetterSpace]fac)*Ceiling[0.9*Sin[(Pi*t)/l\[LetterSpace]d]]), Pt -> C[t] + (nucleus*CN[t])/cytoplasm + P0[t] + P1[t] + P2[t], Tt -> C[t] + (nucleus*CN[t])/cytoplasm + T0[t] + T1[t] + T2[t]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {
tim\[LetterSpace]trans->"http://identifiers.org/go/GO:0009299"
};

units = {
{"time" -> "", "metabolite" -> "<substance_units>/litre", "extent" -> "<substance_units>/litre"}
};

(* Time evolution *)
odes = {
C'[t] == 1.0*C\[LetterSpace]form -1.0*C\[LetterSpace]decay -1.0*C\[LetterSpace]transp, CN'[t] == 1.0*C\[LetterSpace]transp -1.0*CN\[LetterSpace]decay, M\[LetterSpace]P'[t] == 1.0*per\[LetterSpace]trans -1.0*M\[LetterSpace]P\[LetterSpace]decay, M\[LetterSpace]T'[t] == 1.0*tim\[LetterSpace]trans -1.0*M\[LetterSpace]T\[LetterSpace]decay, P0'[t] == 1.0*PER\[LetterSpace]transl +1.0*P1\[LetterSpace]depho -1.0*PO\[LetterSpace]decay -1.0*P\[LetterSpace]pho, P1'[t] == 1.0*P\[LetterSpace]pho +1.0*P2\[LetterSpace]depho -1.0*P1\[LetterSpace]decay -1.0*P1\[LetterSpace]pho -1.0*P1\[LetterSpace]depho, P2'[t] == 1.0*P1\[LetterSpace]pho -1.0*P2\[LetterSpace]decay -1.0*C\[LetterSpace]form -1.0*P2\[LetterSpace]depho -1.0*P2\[LetterSpace]light\[LetterSpace]deact, T0'[t] == 1.0*TIM\[LetterSpace]transl +1.0*T1\[LetterSpace]depho -1.0*T0\[LetterSpace]decay -1.0*T\[LetterSpace]pho, T1'[t] == 1.0*T\[LetterSpace]pho +1.0*T2\[LetterSpace]depho -1.0*T1\[LetterSpace]decay -1.0*T1\[LetterSpace]pho -1.0*T1\[LetterSpace]depho, T2'[t] == 1.0*T1\[LetterSpace]pho -1.0*T2\[LetterSpace]decay -1.0*C\[LetterSpace]form -1.0*T2\[LetterSpace]depho -1.0*T2\[LetterSpace]light\[LetterSpace]deact
};
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]}]