User:Vincent Rouilly/Computational Biology With R: Difference between revisions
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(New page: =Computational Biology with R= ==Tutorials== ===Running SBML models in R=== # Install '''SBMLR''' package ## Start R, and enter: ## source("http://bioconductor.org/biocLite.R") ## biocLi...) |
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=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== | ||
=== [http://www.bioconductor.org/packages/2.3/bioc/html/rsbml.html RSBML] lib === | |||
* Install library | |||
** > source("http://bioconductor.org/biocLite.R") | |||
** > biocLite("rsbml") | |||
* Load library | |||
** > library("rsbml") | |||
* 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=== | ===Running SBML models in R=== | ||
# Install '''SBMLR''' package | # Install '''[http://www.bioconductor.org/packages/bioc/html/SBMLR.html SBMLR]''' package | ||
## Start R, and enter: | ## Start R, and enter: | ||
## source("http://bioconductor.org/biocLite.R") | ## > source("http://bioconductor.org/biocLite.R") | ||
## biocLite("SBMLR") | ## > 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) | |||
===Perturbation analysis on kinetic rate=== |
Latest revision as of 11:11, 17 December 2009
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
RSBML lib
- Install library
- > source("http://bioconductor.org/biocLite.R")
- > biocLite("rsbml")
- Load library
- > library("rsbml")
- 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
- 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)