Elizabeth Skippington Notes

Liz's Notes

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Useful links

Cytoscape with Power Plugin (via Java WebStart) [1]

Running Java Apps

Currently it appears that only version 1.4.2 of the JRE (Java Runtime Environment) is installed, which is not suitable for all applications. To use the newer version of JRE, you need to specify the full path to the java executable that is installed in the home directory e.g. instead of

 java app.jar

use

 /home/e.skippington/Programs/java/jre1.6.0_07/bin/java app.jar

This has been temporarily fixed by creating a symlink in ~/bin/ of java pointing to the new version of java.

Running Java WebApps

The latest JRE has been installed, but only the 32 bit version, so a separate 32 bit version of firefox has been installed to use the latest 32 bit version of the JRE. The 32 bit, new JRE firefox is at:

 /usr/lib/firefox-3.0.1/firefox

and a symlink called firefox32 has been created to point to it.

Running power graph Program

Run the power graph program by something like:

 java -Xmx1024M -jar Oog.jar -convert -inputfiles=edg -output=bbl -v -writeLog=0 -sortbyfilesize -checkequality -minsim=0.0 -min_max=1 -useGlobalClustering=1 -useGreedyClustering=1

Use the following line for help:

 java -Xmx1024M -jar Oog.jar -?

Making metabolic networks

Metabolic data collected from KEGG 20/4/2009 ftp://ftp.genome.jp/pub/kegg

/home/e.skippington/Phd/Network/KEGG_metabolic_networks

wget ftp://ftp.genome.jp/pub/kegg/ligand/reaction/reaction.lst wget ftp://ftp.genome.jp/pub/kegg/ligand/reaction/reaction_name.lst