User:Vincent Rouilly/Computational Biology With R
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Computational Biology with R
Books
- R Programming for Bioinformatics, Robert Gentleman, Fred Hutchinson, 2008
- Introduction to Scientific Programming and Simulation Using R, Owen Jones et al, 2009
- More R Books (from R-Project.org)
Software resources
- StatET with Eclipse, develop in R within a great IDE.
- Sweave (literate programming / reproducible science))
Tutorials
Running SBML models in R
- Install SBMLR package
- Start R, and enter:
- > source("http://bioconductor.org/biocLite.R")
- > biocLite("SBMLR")
- Load library 'SBMLR' in R by typing:
- > library("SBMLR")
- Download sample SBML file describing a A-->B reaction: media:here
- Read SBML file into R
- > myModel <- readSBML("AtoB.xml")
- Simulate model between [0,100] with 100 points
- > results=simulate(myModel,seq(0,100,1))
- Plot results
- > attach(results)
- > par(mfrow=c(2,1))
- > plot(time,s1,type="l")
- > plot(time,s2,type="l")
- > detach(results)
Perturbation analysis on compound concentration
- Simulate first section between [0,50], where s1=100 at t=0 (following SBML description)
- > myModel=readSBML("AtoB.xml")
- > result_1 = simulate(myModel,seq(0,50,1))
- Simulate second section between [50,100], where s1=100 at t=50
- > myModel$species$s1$ic=50
- > results_2 = simulate(myModel,seq(50,100,1))
- > results=data.frame(rbind(results_1, results_2))
- > attach(results)
- > par(mfrow=c(2,1))
- > plot(time,IMP,type="l")
- > plot(time,HX,type="l")
- > par(mfrow=c(1,1))
- > detach(results)