(* 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 = {
CC[t], CCPT[t], CLK[t], PDP[t], PER[t], PT[t], TIM[t], VRI[t], clkm[t], clkp[t], pdpm[t], pdpp[t], perm[t], perp[t], prcpdp[t], prcper[t], prct[t], prcv[t], prpc[t], prvc[t], timm[t], timp[t], vrim[t], vrip[t]
};

initialValues = {
CC[0] == 0.5566, CCPT[0] == 0.4982, CLK[0] == 3.6628, PDP[0] == 4.1953, PER[0] == 2.7527, PT[0] == 0.4014, TIM[0] == 2.7527, VRI[0] == 3.175, clkm[0] == 0.2583, clkp[0] == 0.003185, pdpm[0] == 0.3175, pdpp[0] == 0.003185, perm[0] == 0.2395, perp[0] == 0.003185, prcpdp[0] == 0.0, prcper[0] == 0.0, prct[0] == 0.0, prcv[0] == 0.0, prpc[0] == 0.0, prvc[0] == 0.0, timm[0] == 0.2395, timp[0] == 0.003185, vrim[0] == 0.2571, vrip[0] == 0.003185
};

rates = {
re1, re10, re15, re17, re2, re20, re28, re3, re30, re31, re32, re35, re37, re38, re39, re4, re42, re43, re44, re45, re46, re47, re48, re51, re53, re54, re55, re56, re57, re58, re59, re60, re61, re62, re63, re64, re65, re66, re68, re69, re9
};

rateEquations = {
re1 -> bccpt*wholeCell*CC[t]*PT[t], re10 -> tlclk*wholeCell*clkm[t], re15 -> dperm*wholeCell*perm[t], re17 -> tlper*wholeCell*perm[t], re2 -> dcc*wholeCell*CC[t], re20 -> wholeCell*perp[t]*(tcccperp*(1 - (1 - prcper[t])^npt) + tcdvpmt*(1 - prcper[t])^npt), re28 -> wholeCell*(tcccvrip*(1 - (1 - prcv[t])^nvri) + tcdvpmt*(1 - prcv[t])^nvri)*vrip[t], re3 -> dccpt*wholeCell*CCPT[t], re30 -> dvrim*wholeCell*vrim[t], re31 -> tlvri*wholeCell*vrim[t], re32 -> dvri*wholeCell*VRI[t], re35 -> wholeCell*pdpp[t]*(tcccpdpp*(1 - (1 - prcpdp[t])^npdp) + tcdvpmt*(1 - prcpdp[t])^npdp), re37 -> dpdpm*wholeCell*pdpm[t], re38 -> tlpdp*wholeCell*pdpm[t], re39 -> dpdp*wholeCell*PDP[t], re4 -> dpt*wholeCell*PT[t], re42 -> wholeCell*clkp[t]*(tcpdpclkp*prpc[t] + tcclkp*(1 - prpc[t] - prvc[t]) + tcvriclkp*prvc[t]), re43 -> bcc*CYC*wholeCell*CLK[t], re44 -> dclk*wholeCell*CLK[t], re45 -> ubcc*wholeCell*CC[t], re46 -> bpt*wholeCell*PER[t]*TIM[t], re47 -> ubpt*wholeCell*PT[t], re48 -> dper*wholeCell*PER[t], re51 -> wholeCell*(tccctimp*(1 - (1 - prct[t])^npt) + tcdvpmt*(1 - prct[t])^npt)*timp[t], re53 -> dtimm*wholeCell*timm[t], re54 -> tltim*wholeCell*timm[t], re55 -> dtim*wholeCell*TIM[t], re56 -> ubccpt*wholeCell*CCPT[t], re57 -> bccperp*wholeCell*CC[t]*(1 - prcper[t]), re58 -> ubccperp*wholeCell*prcper[t], re59 -> ubccvrip*wholeCell*prcv[t], re60 -> bccvrip*wholeCell*CC[t]*(1 - prcv[t]), re61 -> ubccpdpp*wholeCell*prcpdp[t], re62 -> bccpdpp*wholeCell*CC[t]*(1 - prcpdp[t]), re63 -> bvriclkp*wholeCell*(1 - prpc[t] - prvc[t])*VRI[t], re64 -> ubvriclkp*wholeCell*prvc[t], re65 -> bpdpclkp*wholeCell*PDP[t]*(1 - prpc[t] - prvc[t]), re66 -> ubpdpclkp*wholeCell*prpc[t], re68 -> bcctimp*wholeCell*CC[t]*(1 - prct[t]), re69 -> ubcctimp*wholeCell*prct[t], re9 -> dclkm*wholeCell*clkm[t]
};

parameters = {
bcc -> 2.349, bccpdpp -> 0.062, bccperp -> 0.069, bccpt -> 51.0, bcctimp -> 0.069, bccvrip -> 0.1, bpdpclkp -> 1.155, bpt -> 1.1, bvriclkp -> 1.858, dcc -> 0.184, dccpt -> 15.06, dclk -> 0.2, dclkm -> 0.643, dpdp -> 0.156, dpdpm -> 0.06, dper -> 0.62, dperm -> 0.053, dpt -> 0.279, dtim -> 0.62, dtimm -> 0.053, dvri -> 1.226, dvrim -> 0.07, npdp -> 6.0, npt -> 5.0, nvri -> 4.0, tcccpdpp -> 9.831, tcccperp -> 11.0, tccctimp -> 11.0, tcccvrip -> 16.86, tcclkp -> 1.42, tcdvpmt -> 0.028, tcpdpclkp -> 125.54, tcvriclkp -> 0.053, tlclk -> 35.0, tlpdp -> 1.87, tlper -> 36.0, tltim -> 36.0, tlvri -> 14.68, ubcc -> 0.89, ubccpdpp -> 0.145, ubccperp -> 0.262, ubccpt -> 7.89, ubcctimp -> 0.262, ubccvrip -> 0.276, ubpdpclkp -> 0.952, ubpt -> 2.93, ubvriclkp -> 1.043, CYC -> 1.0, wholeCell -> 1.0
};

assignments = {

};

events = {

};

speciesAnnotations = {
VRI[t]->"http://identifiers.org/uniprot/Q9VMS4"
};

reactionAnnotations = {

};

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

(* Time evolution *)
odes = {
CC'[t] == 1.0*re43 +1.0*re56 -1.0*re1 -1.0*re2 -1.0*re45, CCPT'[t] == 1.0*re1 -1.0*re3 -1.0*re56, CLK'[t] == 1.0*re10 +1.0*re45 -1.0*re43 -1.0*re44, PDP'[t] == 1.0*re38 -1.0*re39, PER'[t] == 1.0*re17 +1.0*re47 -1.0*re46 -1.0*re48, PT'[t] == 1.0*re46 +1.0*re56 -1.0*re1 -1.0*re4 -1.0*re47, TIM'[t] == 1.0*re47 +1.0*re54 -1.0*re46 -1.0*re55, VRI'[t] == 1.0*re31 -1.0*re32, clkm'[t] == 1.0*re42 -1.0*re9, clkp'[t] == 0.0 , pdpm'[t] == 1.0*re35 -1.0*re37, pdpp'[t] == 0.0 , perm'[t] == 1.0*re20 -1.0*re15, perp'[t] == 0.0 , prcpdp'[t] == 1.0*re62 -1.0*re61, prcper'[t] == 1.0*re57 -1.0*re58, prct'[t] == 1.0*re68 -1.0*re69, prcv'[t] == 1.0*re60 -1.0*re59, prpc'[t] == 1.0*re65 -1.0*re66, prvc'[t] == 1.0*re63 -1.0*re64, timm'[t] == 1.0*re51 -1.0*re53, timp'[t] == 0.0 , vrim'[t] == 1.0*re28 -1.0*re30, vrip'[t] == 0.0 
};
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]}]