README Cytoscape plugin 3.0 Beta

Date : Nov 21st, 2008 <source> 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/. 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. </source>

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.

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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