(* 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 = {
CRA[t], DyingBacteria[t], DyingFibr[t], FLC[t], HealthyBacteria[t], HealthyFibr[t], MMP7[t], MMP8[t], MastCells[t], MastCells\[LetterSpace]FLC[t], MastCells\[LetterSpace]FLC\[LetterSpace]CRA[t], Protease[t], TNFalpha[t], washout[t]
};

initialValues = {
CRA[0] == 0.00999412, DyingBacteria[0] == 0.0, DyingFibr[0] == 0.0, FLC[0] == 0.000999412, HealthyBacteria[0] == 1*^-06, HealthyFibr[0] == 999.509, MMP7[0] == 99951.0, MMP8[0] == 999509.0, MastCells[0] == 0.0998992, MastCells\[LetterSpace]FLC[0] == 9.98404*^-05, MastCells\[LetterSpace]FLC\[LetterSpace]CRA[0] == 9.97816000000001*^-07, Protease[0] == 1.0, TNFalpha[0] == 4.75162, washout[0] == 1.0
};

rates = {
R10\[LetterSpace]drug\[LetterSpace]washout, R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding, R12\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]washout, R13\[LetterSpace]CRA\[LetterSpace]Secretion\[LetterSpace]DyingFibr, R14\[LetterSpace]CRAClipOffHealthyFibr, R15\[LetterSpace]DyingFibroblast\[LetterSpace]death, R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast, R17\[LetterSpace]HealthyBacteriaProduction, R18\[LetterSpace]HealthyFibProduction, R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr, R1\[LetterSpace]CRA\[LetterSpace]degradation, R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr, R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria, R22\[LetterSpace]CRA\[LetterSpace]binding, R23\[LetterSpace]FLC\[LetterSpace]binding, R24\[LetterSpace]TNFalpha\[LetterSpace]production, R25\[LetterSpace]Protease\[LetterSpace]production, R26\[LetterSpace]DyingBacteria\[LetterSpace]secrete\[LetterSpace]CRA, R27\[LetterSpace]Dyingbacteria\[LetterSpace]die, R28\[LetterSpace]Proteaseinflux, R2\[LetterSpace]CRA\[LetterSpace]washout, R3\[LetterSpace]CRAinflux, R4\[LetterSpace]FLC\[LetterSpace]washout, R5\[LetterSpace]MMP7\[LetterSpace]washout, R6\[LetterSpace]MMP8\[LetterSpace]washout, R7\[LetterSpace]Protease\[LetterSpace]washout, R8\[LetterSpace]TNFalpha\[LetterSpace]washout, R9\[LetterSpace]FLC\[LetterSpace]production
};

rateEquations = {
R10\[LetterSpace]drug\[LetterSpace]washout -> compartment*drug*R10\[LetterSpace]drug\[LetterSpace]washout\[LetterSpace]k1*washout[t], R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding -> compartment*(-(FLC\[LetterSpace]drug*R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding\[LetterSpace]k2) + drug*R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding\[LetterSpace]k1*FLC[t]), R12\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]washout -> compartment*FLC\[LetterSpace]drug*R12\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]washout\[LetterSpace]k1*washout[t], R13\[LetterSpace]CRA\[LetterSpace]Secretion\[LetterSpace]DyingFibr -> compartment*R13\[LetterSpace]CRA\[LetterSpace]Secretion\[LetterSpace]DyingFibr\[LetterSpace]k1*DyingFibr[t], R14\[LetterSpace]CRAClipOffHealthyFibr -> compartment*Rate\[LetterSpace]Law\[LetterSpace]for\[LetterSpace]BAFF\[LetterSpace]clipoff[R14\[LetterSpace]CRAClipOffHealthyFibr\[LetterSpace]k1, HealthyFibr[t], MMP7[t]], R15\[LetterSpace]DyingFibroblast\[LetterSpace]death -> compartment*R15\[LetterSpace]DyingFibroblast\[LetterSpace]death\[LetterSpace]k1*DyingFibr[t], R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast -> compartment*R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast\[LetterSpace]k1*HealthyFibr[t]*TNFalpha[t], R17\[LetterSpace]HealthyBacteriaProduction -> compartment*R17\[LetterSpace]HealthyBacteriaProduction\[LetterSpace]k1*HealthyBacteria[t], R18\[LetterSpace]HealthyFibProduction -> compartment*free\[LetterSpace]space*R18\[LetterSpace]HealthyFibProduction\[LetterSpace]k1*HealthyFibr[t], R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr -> compartment*R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr\[LetterSpace]k1*HealthyFibr[t], R1\[LetterSpace]CRA\[LetterSpace]degradation -> compartment*R1\[LetterSpace]CRA\[LetterSpace]degradation\[LetterSpace]k1*CRA[t]*MMP8[t], R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr -> compartment*R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr\[LetterSpace]k1*HealthyFibr[t], R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria -> compartment*R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria\[LetterSpace]k1*HealthyBacteria[t]*Protease[t], R22\[LetterSpace]CRA\[LetterSpace]binding -> compartment*(R22\[LetterSpace]CRA\[LetterSpace]binding\[LetterSpace]k1*CRA[t]*MastCells\[LetterSpace]FLC[t] - R22\[LetterSpace]CRA\[LetterSpace]binding\[LetterSpace]k2*MastCells\[LetterSpace]FLC\[LetterSpace]CRA[t]), R23\[LetterSpace]FLC\[LetterSpace]binding -> compartment*(R23\[LetterSpace]FLC\[LetterSpace]binding\[LetterSpace]k1*FLC[t]*MastCells[t] - R23\[LetterSpace]FLC\[LetterSpace]binding\[LetterSpace]k2*MastCells\[LetterSpace]FLC[t]), R24\[LetterSpace]TNFalpha\[LetterSpace]production -> compartment*R24\[LetterSpace]TNFalpha\[LetterSpace]production\[LetterSpace]k1*MastCells\[LetterSpace]FLC\[LetterSpace]CRA[t], R25\[LetterSpace]Protease\[LetterSpace]production -> compartment*R25\[LetterSpace]Protease\[LetterSpace]production\[LetterSpace]k1*MastCells\[LetterSpace]FLC\[LetterSpace]CRA[t], R26\[LetterSpace]DyingBacteria\[LetterSpace]secrete\[LetterSpace]CRA -> compartment*R26\[LetterSpace]DyingBacteria\[LetterSpace]secrete\[LetterSpace]CRA\[LetterSpace]k1*DyingBacteria[t], R27\[LetterSpace]Dyingbacteria\[LetterSpace]die -> compartment*R27\[LetterSpace]Dyingbacteria\[LetterSpace]die\[LetterSpace]k1*DyingBacteria[t], R28\[LetterSpace]Proteaseinflux -> compartment*Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[k\[LetterSpace]protease\[LetterSpace]influx], R2\[LetterSpace]CRA\[LetterSpace]washout -> compartment*R2\[LetterSpace]CRA\[LetterSpace]washout\[LetterSpace]k1*CRA[t]*washout[t], R3\[LetterSpace]CRAinflux -> compartment*Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[k\[LetterSpace]CRA\[LetterSpace]influx], R4\[LetterSpace]FLC\[LetterSpace]washout -> compartment*R4\[LetterSpace]FLC\[LetterSpace]washout\[LetterSpace]k1*FLC[t]*washout[t], R5\[LetterSpace]MMP7\[LetterSpace]washout -> compartment*R5\[LetterSpace]MMP7\[LetterSpace]washout\[LetterSpace]k1*MMP7[t]*washout[t], R6\[LetterSpace]MMP8\[LetterSpace]washout -> compartment*R6\[LetterSpace]MMP8\[LetterSpace]washout\[LetterSpace]k1*MMP8[t]*washout[t], R7\[LetterSpace]Protease\[LetterSpace]washout -> compartment*R7\[LetterSpace]Protease\[LetterSpace]washout\[LetterSpace]k1*Protease[t]*washout[t], R8\[LetterSpace]TNFalpha\[LetterSpace]washout -> compartment*R8\[LetterSpace]TNFalpha\[LetterSpace]washout\[LetterSpace]k1*TNFalpha[t]*washout[t], R9\[LetterSpace]FLC\[LetterSpace]production -> compartment*Rate\[LetterSpace]Law\[LetterSpace]for\[LetterSpace]B\[LetterSpace]FLC\[LetterSpace]production[R9\[LetterSpace]FLC\[LetterSpace]production\[LetterSpace]k1, CRA[t], Bcells]
};

parameters = {
Metabolite\[LetterSpace]18 -> 1000.0, k\[LetterSpace]CRA\[LetterSpace]influx -> 0.0, k\[LetterSpace]protease\[LetterSpace]influx -> 0.0, Bcells -> 1.0, FLC\[LetterSpace]drug -> 0.0, drug -> 0.0, R1\[LetterSpace]CRA\[LetterSpace]degradation\[LetterSpace]k1 -> 0.0001, R2\[LetterSpace]CRA\[LetterSpace]washout\[LetterSpace]k1 -> 0.01, R4\[LetterSpace]FLC\[LetterSpace]washout\[LetterSpace]k1 -> 0.01, R5\[LetterSpace]MMP7\[LetterSpace]washout\[LetterSpace]k1 -> 0.01, R6\[LetterSpace]MMP8\[LetterSpace]washout\[LetterSpace]k1 -> 0.01, R7\[LetterSpace]Protease\[LetterSpace]washout\[LetterSpace]k1 -> 0.01, R8\[LetterSpace]TNFalpha\[LetterSpace]washout\[LetterSpace]k1 -> 0.01, R9\[LetterSpace]FLC\[LetterSpace]production\[LetterSpace]k1 -> 0.001, R10\[LetterSpace]drug\[LetterSpace]washout\[LetterSpace]k1 -> 0.0001, R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding\[LetterSpace]k1 -> 1*^-05, R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding\[LetterSpace]k2 -> 1*^-05, R12\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]washout\[LetterSpace]k1 -> 0.0001, R13\[LetterSpace]CRA\[LetterSpace]Secretion\[LetterSpace]DyingFibr\[LetterSpace]k1 -> 0.001, R14\[LetterSpace]CRAClipOffHealthyFibr\[LetterSpace]k1 -> 1*^-08, R15\[LetterSpace]DyingFibroblast\[LetterSpace]death\[LetterSpace]k1 -> 0.2, R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast\[LetterSpace]k1 -> 5*^-07, R17\[LetterSpace]HealthyBacteriaProduction\[LetterSpace]k1 -> 0.01, R18\[LetterSpace]HealthyFibProduction\[LetterSpace]k1 -> 4.85*^-07, R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr\[LetterSpace]k1 -> 1.0, R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr\[LetterSpace]k1 -> 0.1, R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria\[LetterSpace]k1 -> 0.005, R22\[LetterSpace]CRA\[LetterSpace]binding\[LetterSpace]k1 -> 0.1, R22\[LetterSpace]CRA\[LetterSpace]binding\[LetterSpace]k2 -> 0.1, R23\[LetterSpace]FLC\[LetterSpace]binding\[LetterSpace]k1 -> 0.1, R23\[LetterSpace]FLC\[LetterSpace]binding\[LetterSpace]k2 -> 0.1, R24\[LetterSpace]TNFalpha\[LetterSpace]production\[LetterSpace]k1 -> 5000.0, R25\[LetterSpace]Protease\[LetterSpace]production\[LetterSpace]k1 -> 65.0, R26\[LetterSpace]DyingBacteria\[LetterSpace]secrete\[LetterSpace]CRA\[LetterSpace]k1 -> 10.0, R27\[LetterSpace]Dyingbacteria\[LetterSpace]die\[LetterSpace]k1 -> 0.1, compartment -> 1.0
};

assignments = {
Rate\[LetterSpace]Law\[LetterSpace]for\[LetterSpace]BAFF\[LetterSpace]clipoff[k1_,s1_,s2_] -> k1*s1*s2, Rate\[LetterSpace]Law\[LetterSpace]for\[LetterSpace]B\[LetterSpace]FLC\[LetterSpace]production[k1_,s1_,s2_] -> k1*s1*s2, Constant\[LetterSpace]flux\[LetterSpace]\[LetterSpace]irreversible[v_] -> v, free\[LetterSpace]space -> Metabolite\[LetterSpace]18 - DyingFibr[t] - HealthyFibr[t], Total\[LetterSpace]space -> Metabolite\[LetterSpace]18
};

events = {

};

speciesAnnotations = {

};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CRA'[t] == 1000.0*R26\[LetterSpace]DyingBacteria\[LetterSpace]secrete\[LetterSpace]CRA +1.0*R3\[LetterSpace]CRAinflux +1.0*R9\[LetterSpace]FLC\[LetterSpace]production +1.0*R13\[LetterSpace]CRA\[LetterSpace]Secretion\[LetterSpace]DyingFibr +1.0*R14\[LetterSpace]CRAClipOffHealthyFibr -1.0*R9\[LetterSpace]FLC\[LetterSpace]production -1.0*R1\[LetterSpace]CRA\[LetterSpace]degradation -1.0*R2\[LetterSpace]CRA\[LetterSpace]washout -1.0*R22\[LetterSpace]CRA\[LetterSpace]binding, DyingBacteria'[t] == 1.0*R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria -1.0*R26\[LetterSpace]DyingBacteria\[LetterSpace]secrete\[LetterSpace]CRA -1.0*R27\[LetterSpace]Dyingbacteria\[LetterSpace]die, DyingFibr'[t] == 1.0*R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast -1.0*R13\[LetterSpace]CRA\[LetterSpace]Secretion\[LetterSpace]DyingFibr -1.0*R15\[LetterSpace]DyingFibroblast\[LetterSpace]death, FLC'[t] == 1.0*R9\[LetterSpace]FLC\[LetterSpace]production -1.0*R11\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]binding -1.0*R4\[LetterSpace]FLC\[LetterSpace]washout -1.0*R23\[LetterSpace]FLC\[LetterSpace]binding, HealthyBacteria'[t] == 2.0*R17\[LetterSpace]HealthyBacteriaProduction -1.0*R17\[LetterSpace]HealthyBacteriaProduction -1.0*R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria, HealthyFibr'[t] == 2.0*R18\[LetterSpace]HealthyFibProduction +1.0*R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr +1.0*R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr +1.0*R14\[LetterSpace]CRAClipOffHealthyFibr -1.0*R14\[LetterSpace]CRAClipOffHealthyFibr -1.0*R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast -1.0*R18\[LetterSpace]HealthyFibProduction -1.0*R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr -1.0*R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr, MMP7'[t] == 1.0*R19\[LetterSpace]MMP7\[LetterSpace]release\[LetterSpace]HealthyFibr +1.0*R14\[LetterSpace]CRAClipOffHealthyFibr -1.0*R5\[LetterSpace]MMP7\[LetterSpace]washout -1.0*R14\[LetterSpace]CRAClipOffHealthyFibr, MMP8'[t] == 100.0*R20\[LetterSpace]MMP8\[LetterSpace]release\[LetterSpace]HealthyFibr +1.0*R1\[LetterSpace]CRA\[LetterSpace]degradation -1.0*R6\[LetterSpace]MMP8\[LetterSpace]washout -1.0*R1\[LetterSpace]CRA\[LetterSpace]degradation, MastCells'[t] ==  -1.0*R23\[LetterSpace]FLC\[LetterSpace]binding, MastCells\[LetterSpace]FLC'[t] == 1.0*R23\[LetterSpace]FLC\[LetterSpace]binding -1.0*R22\[LetterSpace]CRA\[LetterSpace]binding, MastCells\[LetterSpace]FLC\[LetterSpace]CRA'[t] == 1.0*R22\[LetterSpace]CRA\[LetterSpace]binding +1.0*R24\[LetterSpace]TNFalpha\[LetterSpace]production +1.0*R25\[LetterSpace]Protease\[LetterSpace]production -1.0*R24\[LetterSpace]TNFalpha\[LetterSpace]production -1.0*R25\[LetterSpace]Protease\[LetterSpace]production, Protease'[t] == 1.0*R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria +1.0*R25\[LetterSpace]Protease\[LetterSpace]production +1.0*R28\[LetterSpace]Proteaseinflux -1.0*R7\[LetterSpace]Protease\[LetterSpace]washout -1.0*R21\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]Bacteria, TNFalpha'[t] == 1.0*R24\[LetterSpace]TNFalpha\[LetterSpace]production +1.0*R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast -1.0*R8\[LetterSpace]TNFalpha\[LetterSpace]washout -1.0*R16\[LetterSpace]Healthy\[LetterSpace]to\[LetterSpace]Dying\[LetterSpace]fibroblast, washout'[t] == 1.0*R2\[LetterSpace]CRA\[LetterSpace]washout +1.0*R4\[LetterSpace]FLC\[LetterSpace]washout +1.0*R5\[LetterSpace]MMP7\[LetterSpace]washout +1.0*R6\[LetterSpace]MMP8\[LetterSpace]washout +1.0*R7\[LetterSpace]Protease\[LetterSpace]washout +1.0*R8\[LetterSpace]TNFalpha\[LetterSpace]washout +1.0*R10\[LetterSpace]drug\[LetterSpace]washout +1.0*R12\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]washout -1.0*R5\[LetterSpace]MMP7\[LetterSpace]washout -1.0*R6\[LetterSpace]MMP8\[LetterSpace]washout -1.0*R7\[LetterSpace]Protease\[LetterSpace]washout -1.0*R8\[LetterSpace]TNFalpha\[LetterSpace]washout -1.0*R10\[LetterSpace]drug\[LetterSpace]washout -1.0*R12\[LetterSpace]FLC\[LetterSpace]drug\[LetterSpace]washout -1.0*R2\[LetterSpace]CRA\[LetterSpace]washout -1.0*R4\[LetterSpace]FLC\[LetterSpace]washout
};
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]}]