Genome scale network model

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	:Graph Visualization		:Graph Visualization
		+	;<http://www.bioconductor.org/install/ Bioconductor Install>
		+	;;<http://www.bioconductor.org/packages/release/bioc/ BioC packages>
		+	;<http://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html Rgraphviz>
		+	;<http://www.bioconductor.org/packages/release/bioc/html/rsbml.html rsbml>
		+	;<http://cran.r-project.org/web/packages/BiGGR/index.html BiGGR>
	<pre>		<pre>
	source("http://bioconductor.org/biocLite.R")		source("http://bioconductor.org/biocLite.R")
-	biocLite("rsbml")	+	## requirement: libsbml, graphviz library
-	install.packages("igraph")	+	biocLite("rsbml","Rgraphviz","BiGGR",type="source") # compiling from source code
	###		###
	### visualization of stoichiometric matrix		### visualization of stoichiometric matrix
	###		###
-	library("rsbml")	+	library("BiGGR") # <- related packages automatically ON (graph, igraph,...)
-	library("Rgraphviz")	+	load("shewanella.rdata")
-	library("igraph")	+
-	library("BiGGR")	+
-	graph.adjacency  #! igraph function	+
	</pre>		</pre>

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Revision as of 15:29, 21 July 2011

E-book: Methods in bioengineering : systems analysis of biological networks

Graph Visualization

<http://www.bioconductor.org/install/ Bioconductor Install>

<http://www.bioconductor.org/packages/release/bioc/ BioC packages>

<http://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html Rgraphviz>

<http://www.bioconductor.org/packages/release/bioc/html/rsbml.html rsbml>

<http://cran.r-project.org/web/packages/BiGGR/index.html BiGGR>

source("http://bioconductor.org/biocLite.R")
## requirement: libsbml, graphviz library
biocLite("rsbml","Rgraphviz","BiGGR",type="source") # compiling from source code
###
### visualization of stoichiometric matrix
###
library("BiGGR") # <- related packages automatically ON (graph, igraph,...)
load("shewanella.rdata")