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
Installing MCL package
download mcl-latest.tar.gz from http://www.micans.org/mcl/src/ to /home/e.skippington/Programs/MCL
tar xzf mcl-latest.tar.gz
./configure
make
make prefix=/home/e.skippington/MCL_test/ install
Now the mcl executable is in /home/e.skippington/MCL_test/bin
Check the PATH variable:
echo $PATH
Need to append /home/e.skippington/MCL_test/bin to the path, do this by editing .bashrc in my home directory
~cd
ls -la
vim .bashrc
Add the following line to the file:
PATH=$PATH:/home/e.skippington/MCL_test/bin; export PATH
BLASTp
Download from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/
blast-2.2.18-x64-linux.tar.gz
All 16 E. coli fasta files are in the directory /home/e.skippington/Phd/LGT/ecoli_fasta
AC_000091.faa NC_002655.faa NC_004337.faa NC_004741.faa NC_007606.faa NC_007946.faa NC_008258.faa NC_009800.faa NC_000913.faa NC_002695.faa NC_004431.faa NC_007384.faa NC_007613.faa NC_008253.faa NC_008563.faa NC_009801.faa