Difference between revisions of "README Cytoscape plugin 3.0 Beta"

From irefindex
Line 19: Line 19:
  
 
3. Start Cytoscape and select  IRefIndex_beta3 from plugin menu.
 
3. Start Cytoscape and select  IRefIndex_beta3 from plugin menu.
 +
 
4. First time installation may take up to 5 minutes (Creating Java index objects).
 
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  
 
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.
 
and if the installation fails you will get errors in red text.

Revision as of 11:14, 21 November 2008

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.



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