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Computational Biology with R

Tutorials

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

Perturbation analysis on kinetic rate