User:Vincent Rouilly/Computational Biology With R

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (Running SBML models in R)
Line 10: Line 10:
# Load library 'SBMLR' in R by typing:
# Load library 'SBMLR' in R by typing:
## > library("SBMLR")
## > 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===
 +
 
 +
===Perturbation analysis on kinetic rate===

Revision as of 12:39, 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

Perturbation analysis on kinetic rate

Personal tools