README Cytoscape plugin 3.0 Beta

Date : 2008 Nov 21

1. Before start : Make sure Cytoscape is not running. Remove any other installations of iRefIndex_beta# or directories created Make sure Cytoscape has at leas 128Mb memory (http://cytoscape.org/cgi-bin/moin.cgi/How%20to%20increase%20memory%20for%20Cytoscape)

2. Copy both IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz file 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 (Creating Java index objects). 5. If the installation was successful you will see a list of losed indexes in the Results text box in green and if the installation fails you will get 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