(* 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 = {
APC[t], APC\[LetterSpace]Cdc20[t], Bub3\[LetterSpace]BubR1[t], Bub3\[LetterSpace]BubR1\[LetterSpace]Cdc20[t], Cdc20[t], Cdc20\[LetterSpace]CMad2[t], MCC[t], MCC\[LetterSpace]APC[t], Mad1\[LetterSpace]CMad2[t], Mad1\[LetterSpace]CMad2\[LetterSpace]OMad2[t], OMad2[t]
};

initialValues = {
APC[0] == 9*^-08, APC\[LetterSpace]Cdc20[0] == 0.0, Bub3\[LetterSpace]BubR1[0] == 1.27*^-07, Bub3\[LetterSpace]BubR1\[LetterSpace]Cdc20[0] == 0.0, Cdc20[0] == 2.2*^-07, Cdc20\[LetterSpace]CMad2[0] == 0.0, MCC[0] == 0.0, MCC\[LetterSpace]APC[0] == 0.0, Mad1\[LetterSpace]CMad2[0] == 5*^-08, Mad1\[LetterSpace]CMad2\[LetterSpace]OMad2[0] == 0.0, OMad2[0] == 1.3*^-07
};

rates = {
R1, R2, R3, R4, R5, R6, R7, R7a, R8
};

rateEquations = {
R1 -> Cytoplasm*(-(k1r*Mad1\[LetterSpace]CMad2\[LetterSpace]OMad2[t]) + k1f*u*Mad1\[LetterSpace]CMad2[t]*OMad2[t]), R2 -> Cytoplasm*k2f*u*Cdc20[t]*Mad1\[LetterSpace]CMad2\[LetterSpace]OMad2[t], R3 -> Cytoplasm*k3f*Cdc20\[LetterSpace]CMad2[t], R4 -> Cytoplasm*(k4f*u*Bub3\[LetterSpace]BubR1[t]*Cdc20\[LetterSpace]CMad2[t] - k4r*MCC[t]), R5 -> Cytoplasm*(-(k5r*Bub3\[LetterSpace]BubR1\[LetterSpace]Cdc20[t]) + k5f*u*Bub3\[LetterSpace]BubR1[t]*Cdc20[t]), R6 -> Cytoplasm*kf6*Cdc20[t]*OMad2[t], R7 -> Cytoplasm*k7f*u*APC[t]*MCC[t], R7a -> Cytoplasm*k7r*u\[LetterSpace]prime*MCC\[LetterSpace]APC[t], R8 -> Cytoplasm*(-(k8r*APC\[LetterSpace]Cdc20[t]) + k8f*APC[t]*Cdc20[t])
};

parameters = {
const\[LetterSpace]val\[LetterSpace]0 -> 0.0, const\[LetterSpace]val\[LetterSpace]1 -> 1.0, k1f -> 200000.0, k1r -> 0.2, k2f -> 100000000.0, k3f -> 0.01, k4f -> 10000000.0, k4r -> 0.02, k5f -> 10000.0, k5r -> 0.2, k7f -> 100000000.0, k7r -> 0.08, k8f -> 5000000.0, k8r -> 0.08, kf6 -> 1000.0, u -> 1.0, u\[LetterSpace]prime -> 0.0, Cytoplasm -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
Cdc20[t]->"http://identifiers.org/uniprot/Q12834", OMad2[t]->"http://identifiers.org/uniprot/Q13257"
};

reactionAnnotations = {

};

units = {
{"time" -> "", "metabolite" -> "mole/<compartment size units>", "extent" -> "mole/<compartment size units>"}
};

(* Time evolution *)
odes = {
APC'[t] == 1.0*R7a -1.0*R7 -1.0*R8, APC\[LetterSpace]Cdc20'[t] == 1.0*R8 , Bub3\[LetterSpace]BubR1'[t] ==  -1.0*R4 -1.0*R5, Bub3\[LetterSpace]BubR1\[LetterSpace]Cdc20'[t] == 1.0*R5 , Cdc20'[t] == 1.0*R3 -1.0*R2 -1.0*R5 -1.0*R6 -1.0*R8, Cdc20\[LetterSpace]CMad2'[t] == 1.0*R2 +1.0*R6 -1.0*R3 -1.0*R4, MCC'[t] == 1.0*R4 +1.0*R7a -1.0*R7, MCC\[LetterSpace]APC'[t] == 1.0*R7 -1.0*R7a, Mad1\[LetterSpace]CMad2'[t] == 1.0*R2 -1.0*R1, Mad1\[LetterSpace]CMad2\[LetterSpace]OMad2'[t] == 1.0*R1 -1.0*R2, OMad2'[t] == 1.0*R3 -1.0*R1 -1.0*R6
};
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]}]