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 email list at 
http://groups.google.com/group/irefindex?hl=en 
to be informed of the official release and updates.

1. 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 leas 128Mb memory (http://cytoscape.org/cgi-bin/moin.cgi/How%20to%20increase%20memory%20for%20Cytoscape)

2. Copy both the IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz files to the plugin directory of Cytoscape.

e.g : Unix /...../Cytoscape_v2.6.0/plugins/

Windows: \.....\Cytoscape_v2.6.0\plugins\

• • you should have write privileges for this directory

3. Start Cytoscape and select IRefIndex_beta3 from plugin menu.

4. First time installation may take up to 5 minutes (while the plugin creates Java index objects).

5. 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 can not see the iRefIndex panel please click on the title iRefIndex, near the Network tab)

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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 form 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
    e.g. #accession:96065
  - There is a sample file available in the following directory
    Unix
    /...../Cytoscape_v2.6.0/plugins/iRefIndex/Sample_batch.txt 
    Windows:
    \.....\Cytoscape_v2.6.0\plugins\iRefIndex\Sample_batch.txt