User:Vincent Rouilly/Computational Biology With R

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=Computational Biology with R=
=Computational Biology with R=
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==Books==
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* [http://www.crcpress.com/product/isbn/9781420063677;jsessionid=1btcHWVjmXoP9qzHV9Mdzg** R Programming for Bioinformatics, Robert Gentleman, Fred Hutchinson, 2008]
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* [http://www.crcpress.com/product/isbn/9781420068726 Introduction to Scientific Programming and Simulation Using R, Owen Jones et al, 2009]
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* [http://www.r-project.org/doc/bib/R-publications.html More R Books (from R-Project.org)] 
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==Software resources==
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* [http://www.walware.de/goto/statet StatET with Eclipse], develop in R within a great IDE.
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* [http://www.statistik.lmu.de/~leisch/Sweave/ Sweave (literate programming / reproducible science))]
==Tutorials==
==Tutorials==
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=== [http://www.bioconductor.org/packages/2.3/bioc/html/rsbml.html RSBML] lib ===
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* Install library
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** > source("http://bioconductor.org/biocLite.R")
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** > biocLite("rsbml")
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* Load library
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** > library("rsbml")
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* Load SBML model
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* Simulate a SBML model
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** > dom <- rsbml_read("/my_sbml_file.xml") ## e.g. dom <- rsbml_read(system.file("sbml", "GlycolysisLayout.xml", package = "rsbml"))
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** > mod <- model(dom)
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** > sub <- new("SOSSubject", mod)
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** > exp <- new("SOSExperiment", subject=sub)
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** > simulate(exp)  (Warning: it does seem to work for me at the moment)
===Running SBML models in R===
===Running SBML models in R===
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# Load library 'SBMLR' in R by typing:
# Load library 'SBMLR' in R by typing:
## > library("SBMLR")
## > library("SBMLR")
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#
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# Download sample SBML file describing a A-->B reaction: [[media:here]]
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# Read SBML file into R
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## > myModel <- readSBML("AtoB.xml")
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# Simulate model between [0,100] with 100 points
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## > results=simulate(myModel,seq(0,100,1))
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# Plot results
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## > attach(results)
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## > par(mfrow=c(2,1))
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## > plot(time,s1,type="l")
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## > plot(time,s2,type="l")
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## > detach(results)
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===Perturbation analysis on compound concentration===
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# Simulate first section between [0,50], where s1=100 at t=0 (following SBML description)
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## > myModel=readSBML("AtoB.xml")
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## > result_1 = simulate(myModel,seq(0,50,1))
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# Simulate second section between [50,100], where s1=100 at t=50
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## > myModel$species$s1$ic=50
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## > results_2 = simulate(myModel,seq(50,100,1))
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## > results=data.frame(rbind(results_1, results_2))
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## > attach(results)
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## > par(mfrow=c(2,1))
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## > plot(time,IMP,type="l")
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## > plot(time,HX,type="l")
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## > par(mfrow=c(1,1))
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## > detach(results)
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===Perturbation analysis on kinetic rate===

Current revision

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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