User:Vincent Rouilly/Computational Biology With R - Revision history

Vincent Rouilly: /* Tutorials */

2009-12-17T18:11:13Z

Tutorials

←Older revision		Revision as of 18:11, 17 December 2009
Line 11:		Line 11:

	==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===

Vincent Rouilly at 15:04, 15 December 2009

2009-12-15T15:04:58Z

←Older revision		Revision as of 15:04, 15 December 2009
Line 1:		Line 1:
	=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==

Vincent Rouilly at 17:48, 14 December 2009

2009-12-14T17:48:11Z

←Older revision		Revision as of 17:48, 14 December 2009
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===

Vincent Rouilly at 17:39, 14 December 2009

2009-12-14T17:39:29Z

←Older revision		Revision as of 17:39, 14 December 2009
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===

Vincent Rouilly: /* Running SBML models in R */

2009-12-10T15:50:10Z

Running SBML models in R

←Older revision		Revision as of 15:50, 10 December 2009
Line 4:		Line 4:

	===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")
-	# ~~Dowload this SBML file that describes a simple Enzymatic reaction with Michaelis-Menten reaction~~	+	# Load library 'SBMLR' in R by typing:
-	# ~~...~~	+	## > library("SBMLR")
		+	#

Vincent Rouilly: 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...

2009-12-10T14:32:31Z

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...

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")
## biocLite("SBMLR")
# Dowload this SBML file that describes a simple Enzymatic reaction with Michaelis-Menten reaction
# ...