# User:Vincent Rouilly/Computational Biology With R

(Difference between revisions)
 Revision as of 13:39, 14 December 2009 (view source)← Previous diff Revision as of 13:48, 14 December 2009 (view source)Next diff → Line 23: Line 23: ===Perturbation analysis on compound concentration=== ===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=== ===Perturbation analysis on kinetic rate===

# 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)