(* 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 = {
a[t], b[t]
};

initialValues = {
a[0] == 50.0, b[0] == 0.0
};

rates = {
Abeta\[LetterSpace]formation\[LetterSpace]from\[LetterSpace]APP, Decrease\[LetterSpace]in\[LetterSpace]the\[LetterSpace]extracellular\[LetterSpace]concentration\[LetterSpace]of\[LetterSpace]beta\[LetterSpace]amyloid, Effect\[LetterSpace]of\[LetterSpace]extracellular\[LetterSpace]ACh, Loss\[LetterSpace]of\[LetterSpace]intracellular\[LetterSpace]choline
};

rateEquations = {
Abeta\[LetterSpace]formation\[LetterSpace]from\[LetterSpace]APP -> Brain*Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[k2], Decrease\[LetterSpace]in\[LetterSpace]the\[LetterSpace]extracellular\[LetterSpace]concentration\[LetterSpace]of\[LetterSpace]beta\[LetterSpace]amyloid -> Brain*Decrease\[LetterSpace]in\[LetterSpace]the\[LetterSpace]extracellular\[LetterSpace]concentration\[LetterSpace]of\[LetterSpace]beta\[LetterSpace]amyloid\[LetterSpace]0[k4, b[t]], Effect\[LetterSpace]of\[LetterSpace]extracellular\[LetterSpace]ACh -> Brain*Effect\[LetterSpace]of\[LetterSpace]extracellular\[LetterSpace]ACh\[LetterSpace]0[k3, a[t]], Loss\[LetterSpace]of\[LetterSpace]intracellular\[LetterSpace]choline -> Brain*Loss\[LetterSpace]of\[LetterSpace]intracellular\[LetterSpace]choline\[LetterSpace]0[k1, a[t], b[t]]
};

parameters = {
k1 -> 0.007, k2 -> 0.33, k3 -> 0.0042, k4 -> 0.01, Brain -> 1.0
};

assignments = {
Decrease\[LetterSpace]in\[LetterSpace]the\[LetterSpace]extracellular\[LetterSpace]concentration\[LetterSpace]of\[LetterSpace]beta\[LetterSpace]amyloid\[LetterSpace]0[k4_,b_] -> b*k4, Effect\[LetterSpace]of\[LetterSpace]extracellular\[LetterSpace]ACh\[LetterSpace]0[k3_,a_] -> a*k3, Loss\[LetterSpace]of\[LetterSpace]intracellular\[LetterSpace]choline\[LetterSpace]0[k1_,a_,b_] -> a*b*k1, Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[v_] -> v, aRel -> a[t]/50
};

events = {

};

speciesAnnotations = {
a[t]->"http://identifiers.org/chebi/CHEBI:15355", aRel[t]->"http://identifiers.org/chebi/CHEBI:15355", b[t]->"http://identifiers.org/uniprot/P05067"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
a'[t] ==  -1.0*Loss\[LetterSpace]of\[LetterSpace]intracellular\[LetterSpace]choline, b'[t] == 1.0*Abeta\[LetterSpace]formation\[LetterSpace]from\[LetterSpace]APP -1.0*Effect\[LetterSpace]of\[LetterSpace]extracellular\[LetterSpace]ACh -1.0*Decrease\[LetterSpace]in\[LetterSpace]the\[LetterSpace]extracellular\[LetterSpace]concentration\[LetterSpace]of\[LetterSpace]beta\[LetterSpace]amyloid
};
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]}]