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 --enable-blast

 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

 vim mcxdeblast

Change the first line to: #!/usr/bin/perl -w

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

Concatenate into one big file

 cat  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 > all_16_ecoli.faa

 /home/e.skippington/Programs/BLAST/blast-2.2.18/bin/formatdb -i all_16_ecoli.faa -o T -n all_16_ecoli_db

 /home/e.skippington/Programs/BLAST/blast-2.2.18/bin/blastpgp -i all_16_ecoli.faa -d all_16_ecoli_db -o all_ecoli.m9 -m9