README Cytoscape plugin 3.0 Beta

Date : Nov 21st, 2008

The iRefIndex plugin for Cytoscape has not been officially released. If you are looking at this page, you have probably been directed here from the Cytoscape plugin directory at ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin . This plugin is for testing purposes only. Join the Google groups e-mail list at http://groups.google.com/group/irefindex?hl=en to be informed of the official release and updates.

Installation

1. Obtain Cytoscape from http://cytoscape.org/ and follow the installation instructions for that software.
2. Before starting:
   • Make sure that Cytoscape is not running.
   • Remove any other installations of iRefIndex beta or directories created by iRefIndex.
   • Make sure Cytoscape has at least 128MB memory (http://cytoscape.org/cgi-bin/moin.cgi/How%20to%20increase%20memory%20for%20Cytoscape)
3. Copy both the IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz files to the plugins directory of Cytoscape. For example:
   • On Unix: /...../Cytoscape_v2.6.0/plugins/
   • On Windows: \.....\Cytoscape_v2.6.0\plugins\
   • (You should have write privileges for this directory.)
4. Start Cytoscape and select IRefIndex_beta3 from plugin menu.
5. First time installation may take up to 5 minutes (while the plugin creates Java index objects).
6. If the installation is successful, you will see a list of indices in the Results text box in green and if the installation fails you will see errors in red text. (If you cannot see the iRefIndex panel please click on the title iRefIndex, near the Network tab.)

Windows Vista users 

Cytoscape installation inside "Program files" directory is not recommended. Use C:\Cytoscape_v2.6.1\ instead. The iRefIndex plugin requires unrestricted hard disk drive access in its installation folder for low level operations.

MacOS users 

The plugin will not work unless Java 1.6X is installed (and there is no official release of this version available from Sun yet). But the following approach was tested and can be recommended.

If you are running MACOSX 10.4, a Java environment that works (in the absence of version 6 for that OS version) is this one: http://landonf.bikemonkey.org/static/soylatte/

1)Downloading the binary here: http://hg.bikemonkey.org/archive/javasrc_1_6_jrl_darwin/soylatte16-i386-1.0.3.tar.bz

2)Making sure that you override the default 1.5 Java of the MacOSX by modifying the PATH statement in /etc/profile

3)Increasing a bit the Xmx (512m) and Xms (512m) settings in the startup cytoscape 2.6.1 shell file (cytoscape.sh)

should produce a workable irefindex Cytoscape plugin on a 10.4.11 (8.11.1) system.

Q&A

1. How do I search all the interactions involving the protein NP:477306?
   • Type NP_477306 on the search text box.
   • Select ACCESSION from type drop down menu.
   • (Optional) Restrict the search within a certain taxon identifier by selecting the id from Taxon.
   • Click Search & load.
2. How do I load a list of identifiers from a file?
   • For this you need to create plain text file with the list of identifiers.
   • First line of the file should be the type of search and the taxonomy identifier. For example:
     #accession:9606
   • There is a sample file available in the following directory:
     • On Unix: /...../Cytoscape_v2.6.0/plugins/iRefIndex/Sample_batch.txt
     • On Windows: \.....\Cytoscape_v2.6.0\plugins\iRefIndex\Sample_batch.txt
3. What is the result showing?
   • The blue nodes are the query nodes, while the green nodes are the first interactors of the query nodes.
   • Hexagons represent pseudo-nodes (indication that proteins linked to it belong to the same complex) and not interactors.
   • Multiple edges between two nodes are due to several sources containing the same interaction.