library(SBMLR) #library(odesolve) curto=readSBML("models/curto.xml") curto summary(curto) # which should be the same plots as curtoR=readSBMLR("models/curto.r") curto==curtoR saveSBML(curto,"models/tmp/curto.xml") saveSBMLR(curto,"models/tmp/curto.r") out1=simulate(curto,seq(-20,0,1)) curto$species$PRPP$ic=50 out2=simulate(curto,0:70) outs=data.frame(rbind(out1,out2)) attach(outs) par(mfrow=c(2,1)) plot(time,IMP,type="l",xlab="minutes",ylab="IMP (uM)") plot(time,HX,type="l",xlab="minutes",ylab="HX (uM)") par(mfrow=c(1,1)) detach(outs) curto$species$PRPP$ic=5 simulate(curto,(-10):10,modulator=rep(2,37)) # bumpless transfer in concentrations since all V increase by 2 simulate(curto,(-10):10,modulator=c(rep(1.1,20),rep(0.9,17))) # half up, half down, not bumpless morr=readSBMLR("models/morrison.r") saveSBML(morr,"models/tmp/morr.xml") saveSBMLR(morr,"models/tmp/morr.r") morrX=readSBML("models/tmp/morr.xml") morr==morrX summary(morr)$reactions["TYMS",2] summary(morrX)$reactions["TYMS",2] out1=simulate(morr,seq(-20,0,1)) morr$species$EMTX$ic=1 out2=simulate(morr,0:30) outs=data.frame(rbind(out1,out2)) attach(outs) par(mfrow=c(3,4)) plot(time,FH2b,type="l",xlab="Hours") plot(time,FH2f,type="l",xlab="Hours") plot(time,DHFRf,type="l",xlab="Hours") plot(time,DHFRtot,type="l",xlab="Hours") plot(time,CHOFH4,type="l",xlab="Hours") plot(time,FH4,type="l",xlab="Hours") plot(time,CH2FH4,type="l",xlab="Hours") plot(time,CH3FH4,type="l",xlab="Hours") plot(time,AICARsyn,type="l",xlab="Hours") plot(time,MTR,type="l",xlab="Hours") plot(time,TYMS,type="l",xlab="Hours") #plot(time,EMTX,type="l",xlab="Hours") plot(time,DHFReductase,type="l",xlab="Hours") par(mfrow=c(1,1)) detach(outs)