User:Vincent Rouilly/Computational Biology With R

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===Perturbation analysis on compound concentration===
===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)
===Perturbation analysis on kinetic rate===
===Perturbation analysis on kinetic rate===

Revision as of 13:48, 14 December 2009

Contents

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

  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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