User:Vincent Rouilly/Computational Biology With R

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Contents

Computational Biology with R

Books

Software resources

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)
    1. > myModel=readSBML("AtoB.xml")
    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)

Perturbation analysis on kinetic rate

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