sim: Simulate a model of S3 class SBMLR

In mdnestor/SBMLR: SBML-R Interface and Analysis Tools

Description

This function simulates a model given report times and optional modulators. It uses lsoda of the deSolve package.

Usage

sim(model, times, modulator=NULL,X0=NULL, ...)

Arguments

model	The S3 model object to be simulated. Initial conditions are passed through this object.
times	The sequence of time points to be sampled and provided as rows of the output matrix.
modulator	Null if there are no modulators (default), a vector of numbers if there are steady state Vmax modulators, and a list of interpolating functions if there are time course Vmax modulators.
X0	Override model initial conditions in simulations, particularly piece-wise perturbation simulations.
...	To pass extra args such as event data frames to deSolve.

Details

This is a wrapper for ode.

Value

The data frame output that comes out of ode.

Note

Rules are implemented through time varying boundary conditions updated at each time point as a side effect within the (now internal) function fderiv.

Author(s)

Tom Radivoyevitch

References

For the folate cycle example given below: Morrison PF, Allegra CJ: Folate cycle kinetics in human breast cancer cells. JBiolChem 1989, 264(18):10552-10566.

Examples

##---- The following perturbs PRPP from 5 to 50 uM in Curto et al.'s model.
library(SBMLR) 
curto=readSBML(file.path(system.file(package="SBMLR"), "models/curto.xml"))  
(dPRPP10 <- data.frame(var = "PRPP", time = 0, value = 10,method = "mult"))
(out=sim(curto,times=seq(-20,70,1),events = list(data = dPRPP10) ) )
plot(out,which=c("PRPP","den","IMP","HX","Gua","aprt","XMP","Xa","UA"))

# which should be the same plots as 
curto=readSBMLR(file.path(system.file(package="SBMLR"), "models/curto.r"))  
(dPRPP10 <- data.frame(var = "PRPP", time = 0, value = 10,method = "mult"))
(out=sim(curto,times=seq(-20,70,1),events = list(data = dPRPP10) ) )
plot(out,which=c("PRPP","den","IMP","HX","Gua","aprt","XMP","Xa","UA"))


##---- The following generates Morrison's folate system response to 1uM MTX 
morr=readSBMLR(file.path(system.file(package="SBMLR"), "models/morrison.r"))  
out1=sim(morr,seq(-20,0,1))
morr$species$EMTX$ic=1
out2=sim(morr,0:30)
outs=data.frame(rbind(out1,out2))
attach(outs)
par(mfrow=c(3,4))
plot(time,FH2b,type="l",xlab="Hours")
plot(time,FH2f,type="l",xlab="Hours")
plot(time,DHFRf,type="l",xlab="Hours")
plot(time,DHFRtot,type="l",xlab="Hours")
plot(time,CHOFH4,type="l",xlab="Hours")
plot(time,FH4,type="l",xlab="Hours")
plot(time,CH2FH4,type="l",xlab="Hours")
plot(time,CH3FH4,type="l",xlab="Hours")
plot(time,AICARsyn,type="l",xlab="Hours")
plot(time,MTR,type="l",xlab="Hours")
plot(time,TYMS,type="l",xlab="Hours")
#plot(time,EMTX,type="l",xlab="Hours")
plot(time,DHFReductase,type="l",xlab="Hours")
par(mfrow=c(1,1))
detach(outs)
morr$species$EMTX$ic=0

## Note: This does not work, since EMTX is not a state variable, it is a bc
##(dEMTX1 <- data.frame(var = "EMTX", time = 0, value = 1,method = "add"))
##(out=simulate(morr,times=seq(-20,30,1),events = list(data = dEMTX1) ) )

mdnestor/SBMLR documentation built on Aug. 28, 2020, 12:06 a.m.