# Computational Biology with R

## Tutorials

### RSBML lib

• Load SBML model
• Simulate a SBML model
• > dom <- rsbml_read("/my_sbml_file.xml") ## e.g. dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"))
• > mod <- model(dom)
• > sub <- new("SOSSubject", mod)
• > exp <- new("SOSExperiment", subject=sub)
• > simulate(exp) (Warning: it does seem to work for me at the moment)

### Running SBML models in R

1. Install SBMLR package
1. Start R, and enter:
2. > source("http://bioconductor.org/biocLite.R")
3. > biocLite("SBMLR")
2. Load library 'SBMLR' in R by typing:
1. > library("SBMLR")
3. Download sample SBML file describing a A-->B reaction: media:here
4. Read SBML file into R
1. > myModel <- readSBML("AtoB.xml")
5. Simulate model between [0,100] with 100 points
1. > results=simulate(myModel,seq(0,100,1))
6. Plot results
1. > attach(results)
2. > par(mfrow=c(2,1))
3. > plot(time,s1,type="l")
4. > plot(time,s2,type="l")
5. > detach(results)

### Perturbation analysis on compound concentration

1. Simulate first section between [0,50], where s1=100 at t=0 (following SBML description)
2. > result_1 = simulate(myModel,seq(0,50,1))
2. Simulate second section between [50,100], where s1=100 at t=50
1. > myModel\$species\$s1\$ic=50
2. > results_2 = simulate(myModel,seq(50,100,1))
3. > results=data.frame(rbind(results_1, results_2))
4. > attach(results)
5. > par(mfrow=c(2,1))
6. > plot(time,IMP,type="l")
7. > plot(time,HX,type="l")
8. > par(mfrow=c(1,1))
9. > detach(results)