User:Vincent Rouilly/Computational Biology With R

(Difference between revisions)
 Revision as of 13:48, 14 December 2009 (view source)← Previous diff Revision as of 11:04, 15 December 2009 (view source)Next diff → Line 1: Line 1: =Computational Biology with R= =Computational Biology with R= + + ==Books== + * [http://www.crcpress.com/product/isbn/9781420063677;jsessionid=1btcHWVjmXoP9qzHV9Mdzg** R Programming for Bioinformatics, Robert Gentleman, Fred Hutchinson, 2008] + * [http://www.crcpress.com/product/isbn/9781420068726 Introduction to Scientific Programming and Simulation Using R, Owen Jones et al, 2009] + * [http://www.r-project.org/doc/bib/R-publications.html More R Books (from R-Project.org)] + + ==Software resources== + * [http://www.walware.de/goto/statet StatET with Eclipse], develop in R within a great IDE. + * [http://www.statistik.lmu.de/~leisch/Sweave/ Sweave (literate programming / reproducible science))] ==Tutorials== ==Tutorials==

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")
4. Read SBML file into R
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)