(* 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 = {
APAF1[t], BIR12[t], BIR12\[LetterSpace]C3[t], BIR12\[LetterSpace]SMAC[t], BIR3R[t], BIR3R\[LetterSpace]C9[t], BIR3R\[LetterSpace]SMAC[t], BIR3R\[LetterSpace]p2frag[t], C3[t], C9[t], C9P[t], ClvgPrds[t], CytC\[LetterSpace]cell[t], CytC\[LetterSpace]mit[t], PC3[t], PC9[t], SMAC[t], SMAC\[LetterSpace]mito[t], Substrate[t], XIAP[t], XIAP\[LetterSpace]2SMAC[t], XIAP\[LetterSpace]C3[t], XIAP\[LetterSpace]C9[t], XIAP\[LetterSpace]C9\[LetterSpace]C3[t], XIAP\[LetterSpace]p2frag[t], XIAP\[LetterSpace]p2frag\[LetterSpace]2SMAC[t], XIAP\[LetterSpace]p2frag\[LetterSpace]C3[t]
};

initialValues = {
APAF1[0] == 3.372, BIR12[0] == 0.0, BIR12\[LetterSpace]C3[0] == 0.0, BIR12\[LetterSpace]SMAC[0] == 0.0, BIR3R[0] == 0.0, BIR3R\[LetterSpace]C9[0] == 0.0, BIR3R\[LetterSpace]SMAC[0] == 0.0, BIR3R\[LetterSpace]p2frag[0] == 0.0, C3[0] == 0.0, C9[0] == 0.0, C9P[0] == 0.0, ClvgPrds[0] == 0.0, CytC\[LetterSpace]cell[0] == 0.0, CytC\[LetterSpace]mit[0] == 10.0, PC3[0] == 0.12, PC9[0] == 0.03, SMAC[0] == 0.0, SMAC\[LetterSpace]mito[0] == 0.126, Substrate[0] == 1.0, XIAP[0] == 0.063, XIAP\[LetterSpace]2SMAC[0] == 0.0, XIAP\[LetterSpace]C3[0] == 0.0, XIAP\[LetterSpace]C9[0] == 0.0, XIAP\[LetterSpace]C9\[LetterSpace]C3[0] == 0.0, XIAP\[LetterSpace]p2frag[0] == 0.0, XIAP\[LetterSpace]p2frag\[LetterSpace]2SMAC[0] == 0.0, XIAP\[LetterSpace]p2frag\[LetterSpace]C3[0] == 0.0
};

rates = {
Apo\[LetterSpace]formation, CytC\[LetterSpace]release, SMAC\[LetterSpace]release, reaction1, reaction10, reaction11, reaction12, reaction13, reaction14, reaction15, reaction16, reaction17, reaction18, reaction19, reaction2, reaction20, reaction21, reaction22, reaction23, reaction24, reaction25, reaction26, reaction27, reaction28, reaction29, reaction3, reaction30, reaction31, reaction32, reaction33, reaction34, reaction35, reaction36, reaction37, reaction38, reaction39, reaction4, reaction40, reaction41, reaction42, reaction43, reaction44, reaction45, reaction46, reaction47, reaction48, reaction49, reaction5, reaction50, reaction51, reaction52, reaction53, reaction6, reaction7, reaction8, reaction9
};

rateEquations = {
Apo\[LetterSpace]formation -> (apo\[LetterSpace]lim*cell*Log[2])/th\[LetterSpace]Apop, CytC\[LetterSpace]release -> (cell*CytC\[LetterSpace]mit[t]*Log[2])/th\[LetterSpace]CytC, SMAC\[LetterSpace]release -> (cell*Log[2]*SMAC\[LetterSpace]mito[t])/th\[LetterSpace]SMAC, reaction1 -> cell*(k1 - k1r*PC3[t]), reaction10 -> cell*(-(k10r*BIR12\[LetterSpace]C3[t]) + k10*BIR12[t]*C3[t]), reaction11 -> cell*k11*C3[t]*XIAP[t], reaction12 -> cell*k12*C3[t]*XIAP\[LetterSpace]C9[t], reaction13 -> cell*k13*C3[t]*XIAP\[LetterSpace]C3[t], reaction14 -> cell*k14*C3[t]*XIAP\[LetterSpace]p2frag[t], reaction15 -> cell*k15*C3[t]*XIAP\[LetterSpace]p2frag\[LetterSpace]C3[t], reaction16 -> cell*k16*C3[t]*XIAP\[LetterSpace]C9\[LetterSpace]C3[t], reaction17 -> cell*k17*C3[t]*XIAP\[LetterSpace]2SMAC[t], reaction18 -> cell*k18*C3[t]*XIAP\[LetterSpace]C9\[LetterSpace]C3[t], reaction19 -> cell*k19*C3[t]*XIAP\[LetterSpace]C9[t], reaction2 -> cell*(k2 - k2r*XIAP[t]), reaction20 -> cell*k20*BIR3R\[LetterSpace]C9[t]*C3[t], reaction21 -> cell*(k21*C9[t]*XIAP[t] - k21r*XIAP\[LetterSpace]C9[t]), reaction22 -> cell*(k22*C9[t]*XIAP\[LetterSpace]C3[t] - k22r*XIAP\[LetterSpace]C9\[LetterSpace]C3[t]), reaction23 -> cell*(-(k23r*BIR3R\[LetterSpace]C9[t]) + k23*BIR3R[t]*C9[t]), reaction24 -> cell*k24*BIR3R\[LetterSpace]p2frag[t], reaction25 -> cell*k25*XIAP\[LetterSpace]p2frag[t], reaction26 -> cell*(k26*SMAC[t]^2*XIAP[t] - k26r*XIAP\[LetterSpace]2SMAC[t]), reaction27 -> cell*(-(k27r*C9[t]*XIAP\[LetterSpace]2SMAC[t]) + k27*SMAC[t]^2*XIAP\[LetterSpace]C9[t]), reaction28 -> cell*(-(k28r*C3[t]*XIAP\[LetterSpace]2SMAC[t]) + k28*SMAC[t]^2*XIAP\[LetterSpace]C3[t]), reaction29 -> cell*(-(k29r*C3[t]*C9[t]*XIAP\[LetterSpace]2SMAC[t]) + k29*SMAC[t]^2*XIAP\[LetterSpace]C9\[LetterSpace]C3[t]), reaction3 -> cell*k3*C9[t]*PC3[t], reaction30 -> cell*(-(k30r*BIR12\[LetterSpace]SMAC[t]) + k30*BIR12[t]*SMAC[t]), reaction31 -> cell*(-(k31r*BIR3R\[LetterSpace]SMAC[t]) + k31*BIR3R[t]*SMAC[t]), reaction32 -> cell*(-(k32r*BIR12\[LetterSpace]SMAC[t]*C3[t]) + k32*BIR12\[LetterSpace]C3[t]*SMAC[t]), reaction33 -> cell*(-(k33r*BIR3R\[LetterSpace]SMAC[t]*C9[t]) + k33*BIR3R\[LetterSpace]C9[t]*SMAC[t]), reaction34 -> cell*(k34*SMAC[t]^2*XIAP\[LetterSpace]p2frag[t] - k34r*XIAP\[LetterSpace]p2frag\[LetterSpace]2SMAC[t]), reaction35 -> cell*k35*C9P[t], reaction36 -> cell*k36*C9[t], reaction37 -> cell*k37*C3[t], reaction38 -> cell*k38*XIAP\[LetterSpace]C3[t], reaction39 -> cell*k39*XIAP\[LetterSpace]C9\[LetterSpace]C3[t], reaction4 -> cell*k4*C3[t]*C9[t], reaction40 -> cell*k40*XIAP\[LetterSpace]C9[t], reaction41 -> cell*k41*XIAP\[LetterSpace]p2frag[t], reaction42 -> cell*k42*XIAP\[LetterSpace]p2frag\[LetterSpace]C3[t], reaction43 -> cell*k43*XIAP\[LetterSpace]p2frag\[LetterSpace]2SMAC[t], reaction44 -> cell*k44*XIAP\[LetterSpace]2SMAC[t], reaction45 -> cell*k45*BIR12[t], reaction46 -> cell*k46*BIR3R[t], reaction47 -> cell*k47*BIR12\[LetterSpace]SMAC[t], reaction48 -> cell*k48*BIR3R\[LetterSpace]SMAC[t], reaction49 -> cell*k49*BIR12\[LetterSpace]C3[t], reaction5 -> cell*k5*C9P[t]*PC3[t], reaction50 -> cell*k50*BIR3R\[LetterSpace]C9[t], reaction51 -> cell*k51*BIR3R\[LetterSpace]p2frag[t], reaction52 -> cell*k52*SMAC[t], reaction53 -> cell*k53*C3[t]*Substrate[t], reaction6 -> cell*k6*C3[t]*PC3[t], reaction7 -> cell*(k7*C3[t]*XIAP[t] - k7r*XIAP\[LetterSpace]C3[t]), reaction8 -> cell*(k8*C3[t]*XIAP\[LetterSpace]C9[t] - k8r*XIAP\[LetterSpace]C9\[LetterSpace]C3[t]), reaction9 -> cell*(k9*C3[t]*XIAP\[LetterSpace]p2frag[t] - k9r*XIAP\[LetterSpace]p2frag\[LetterSpace]C3[t])
};

parameters = {
APAF1\[LetterSpace]tot -> APAF1, C3\[LetterSpace]tot -> PC3, C9\[LetterSpace]tot -> PC9, CytC\[LetterSpace]tot -> CytC\[LetterSpace]mit, SMAC\[LetterSpace]tot -> SMAC\[LetterSpace]mito, S\[LetterSpace]breakdown -> 0.01, XIAP\[LetterSpace]ini -> XIAP, k1 -> 0.000468, k10 -> 156.0, k10r -> 0.144, k11 -> 12.0, k12 -> 12.0, k13 -> 12.0, k14 -> 12.0, k15 -> 12.0, k16 -> 12.0, k17 -> 12.0, k18 -> 12.0, k19 -> 12.0, k1r -> 0.0039, k2 -> 0.0007308, k20 -> 12.0, k21 -> 156.0, k21r -> 0.144, k22 -> 156.0, k22r -> 0.144, k23 -> 156.0, k23r -> 0.144, k24 -> 0.0, k25 -> 0.0, k26 -> 420.0, k26r -> 0.133, k27 -> 420.0, k27r -> 156.0, k28 -> 420.0, k28r -> 156.0, k29 -> 420.0, k29r -> 156.0, k2r -> 0.0116, k3 -> 6.0, k30 -> 4.45, k30r -> 31.9, k31 -> 0.33, k31r -> 14.2, k32 -> 4.45, k32r -> 156.0, k33 -> 0.33, k33r -> 156.0, k34 -> 420.0, k34r -> 156.0, k35 -> 0.0058, k36 -> 0.0058, k37 -> 0.0058, k38 -> 0.0347, k39 -> 0.0347, k4 -> 12.0, k40 -> 0.0347, k41 -> 0.0058, k42 -> 0.0347, k43 -> 0.0347, k44 -> 0.0347, k45 -> 0.0058, k46 -> 0.0347, k47 -> 0.0058, k48 -> 0.0347, k49 -> 0.0058, k5 -> 48.0, k50 -> 0.0058, k51 -> 0.0347, k52 -> 0.0058, k53 -> 12.0, k6 -> 2.4, k7 -> 156.0, k7r -> 0.144, k8 -> 156.0, k8r -> 0.144, k9 -> 156.0, k9r -> 0.144, th\[LetterSpace]Apop -> 2.3, th\[LetterSpace]CytC -> 1.5, th\[LetterSpace]SMAC -> 7.0, cell -> 1.0, mito -> 1.0
};

assignments = {
BIR3R\[LetterSpace]p2frag\[LetterSpace]norm -> BIR3R\[LetterSpace]p2frag[t]/XIAP\[LetterSpace]ini, BIR3R\[LetterSpace]C9\[LetterSpace]norm -> BIR3R\[LetterSpace]C9[t]/XIAP\[LetterSpace]ini, BIR12\[LetterSpace]C3\[LetterSpace]norm -> BIR12\[LetterSpace]C3[t]/XIAP\[LetterSpace]ini, BIR3R\[LetterSpace]norm -> BIR3R[t]/XIAP\[LetterSpace]ini, BIR12\[LetterSpace]norm -> BIR12[t]/XIAP\[LetterSpace]ini, XIAP\[LetterSpace]p2frag\[LetterSpace]norm -> (XIAP\[LetterSpace]p2frag[t] + XIAP\[LetterSpace]p2frag\[LetterSpace]C3[t])/XIAP\[LetterSpace]ini, XIAP\[LetterSpace]C9\[LetterSpace]norm -> (XIAP\[LetterSpace]C9[t] + XIAP\[LetterSpace]C9\[LetterSpace]C3[t])/XIAP\[LetterSpace]ini, XIAP\[LetterSpace]C3\[LetterSpace]norm -> (XIAP\[LetterSpace]C3[t] + XIAP\[LetterSpace]C9\[LetterSpace]C3[t])/XIAP\[LetterSpace]ini, XIAP\[LetterSpace]norm -> XIAP[t]/XIAP\[LetterSpace]ini, Apoform -> 1 - PC9[t]/C9\[LetterSpace]tot, SMAC\[LetterSpace]rel -> 1 - SMAC\[LetterSpace]mito[t]/SMAC\[LetterSpace]tot, PC3norm -> PC3[t]/C3\[LetterSpace]tot, C3norm -> C3[t]/C3\[LetterSpace]tot, C9Pnorm -> C9P[t]/C9\[LetterSpace]tot, C9norm -> C9[t]/C9\[LetterSpace]tot, XIAP\[LetterSpace]2SMAC\[LetterSpace]norm -> XIAP\[LetterSpace]2SMAC[t]/XIAP\[LetterSpace]ini, SMAC\[LetterSpace]norm -> SMAC[t]/XIAP\[LetterSpace]ini, apo\[LetterSpace]lim -> Piecewise[{{PC9[t], PC9[t] < APAF1[t]}}, APAF1[t]]
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
APAF1'[t] ==  -1.0*Apo\[LetterSpace]formation, BIR12'[t] == 1.0*reaction11 +1.0*reaction12 +1.0*reaction14 -1.0*reaction10 -1.0*reaction30 -1.0*reaction45, BIR12\[LetterSpace]C3'[t] == 1.0*reaction10 +1.0*reaction13 +1.0*reaction15 +1.0*reaction16 -1.0*reaction32 -1.0*reaction49, BIR12\[LetterSpace]SMAC'[t] == 1.0*reaction17 +1.0*reaction30 +1.0*reaction32 -1.0*reaction47, BIR3R'[t] == 1.0*reaction11 +1.0*reaction13 +1.0*reaction24 -1.0*reaction23 -1.0*reaction31 -1.0*reaction46, BIR3R\[LetterSpace]C9'[t] == 1.0*reaction12 +1.0*reaction16 +1.0*reaction23 -1.0*reaction20 -1.0*reaction33 -1.0*reaction50, BIR3R\[LetterSpace]SMAC'[t] == 1.0*reaction17 +1.0*reaction31 +1.0*reaction33 -1.0*reaction48, BIR3R\[LetterSpace]p2frag'[t] == 1.0*reaction14 +1.0*reaction15 +1.0*reaction20 -1.0*reaction24 -1.0*reaction51, C3'[t] == 1.0*reaction3 +1.0*reaction4 +1.0*reaction5 +2.0*reaction6 +1.0*reaction11 +1.0*reaction12 +1.0*reaction13 +1.0*reaction14 +1.0*reaction15 +1.0*reaction16 +1.0*reaction17 +1.0*reaction18 +1.0*reaction19 +1.0*reaction20 +1.0*reaction28 +1.0*reaction29 +1.0*reaction32 +1.0*reaction53 -1.0*reaction4 -1.0*reaction6 -1.0*reaction7 -1.0*reaction8 -1.0*reaction9 -1.0*reaction10 -1.0*reaction11 -1.0*reaction12 -1.0*reaction13 -1.0*reaction14 -1.0*reaction15 -1.0*reaction16 -1.0*reaction17 -1.0*reaction18 -1.0*reaction19 -1.0*reaction20 -1.0*reaction37 -1.0*reaction53, C9'[t] == 1.0*reaction3 +1.0*reaction27 +1.0*reaction29 +1.0*reaction33 +1.0*Apo\[LetterSpace]formation -1.0*reaction3 -1.0*reaction4 -1.0*reaction21 -1.0*reaction22 -1.0*reaction23 -1.0*reaction36, C9P'[t] == 1.0*reaction4 +1.0*reaction5 +1.0*reaction18 +1.0*reaction19 +1.0*reaction20 -1.0*reaction5 -1.0*reaction35, ClvgPrds'[t] == 1.0*reaction53 , CytC\[LetterSpace]cell'[t] == 1.0*CytC\[LetterSpace]release , CytC\[LetterSpace]mit'[t] ==  -1.0*CytC\[LetterSpace]release, PC3'[t] == 1.0*reaction1 -1.0*reaction3 -1.0*reaction5 -1.0*reaction6, PC9'[t] ==  -1.0*Apo\[LetterSpace]formation, SMAC'[t] == 1.0*SMAC\[LetterSpace]release -2.0*reaction26 -2.0*reaction27 -2.0*reaction28 -2.0*reaction29 -1.0*reaction30 -1.0*reaction31 -1.0*reaction32 -1.0*reaction33 -2.0*reaction34 -1.0*reaction52, SMAC\[LetterSpace]mito'[t] ==  -1.0*SMAC\[LetterSpace]release, Substrate'[t] ==  -1.0*reaction53, XIAP'[t] == 1.0*reaction2 +1.0*reaction25 -1.0*reaction7 -1.0*reaction11 -1.0*reaction21 -1.0*reaction26, XIAP\[LetterSpace]2SMAC'[t] == 1.0*reaction26 +1.0*reaction27 +1.0*reaction28 +1.0*reaction29 -1.0*reaction17 -1.0*reaction44, XIAP\[LetterSpace]C3'[t] == 1.0*reaction7 -1.0*reaction13 -1.0*reaction22 -1.0*reaction28 -1.0*reaction38, XIAP\[LetterSpace]C9'[t] == 1.0*reaction21 -1.0*reaction8 -1.0*reaction12 -1.0*reaction19 -1.0*reaction27 -1.0*reaction40, XIAP\[LetterSpace]C9\[LetterSpace]C3'[t] == 1.0*reaction8 +1.0*reaction22 -1.0*reaction16 -1.0*reaction18 -1.0*reaction29 -1.0*reaction39, XIAP\[LetterSpace]p2frag'[t] == 1.0*reaction19 -1.0*reaction9 -1.0*reaction14 -1.0*reaction25 -1.0*reaction34 -1.0*reaction41, XIAP\[LetterSpace]p2frag\[LetterSpace]2SMAC'[t] == 1.0*reaction34 -1.0*reaction43, XIAP\[LetterSpace]p2frag\[LetterSpace]C3'[t] == 1.0*reaction9 +1.0*reaction18 -1.0*reaction15 -1.0*reaction42
};
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]}]