iRefScape plugin for Cytoscape

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Ian Donaldson

Jun 25, 2010, 10:39:38 AM6/25/10

Dear iRefIndex users:

We are pleased to announce the most recent versions of the iRefScape plugin for Cytoscape.

iRefScape allows users to search protein interaction data that has been consolidated from multiple databases including BIND, BioGrid, IntAct, MINT,  MPPI and OPHID (MPACT, CORUM, and Imex records from DIP will be made available in the next iRefIndex release.  HPRD records are also available on request – see

Cytoscape 2.7 users:
Install iRefScape 0.90 beta from the Plugins menu.
This version is not backwards compatible with Cytoscape 2.6.3.
Linux users with Java 1.6 (not 1.5) will not be able to install the plugin using the Plugin manager (instead, install manually – see link below)
Details on plugin installation and use are available at  

Cytoscape 2.6.3 users:
Install iRefScape 0.89 beta from the Plugins menu
This will be the last iRefScape that supports Cytoscape 2.6.3
Details on plugin installation and use are available at

iRefScape is based on version 7.0 of the iRefIndex (see for details).

Best regards,

Paul Boddie
Ian Donaldson

Details about the plugin
1)      Each node in the iRefScape view represents a distinct protein sequence from a distinct taxon.
2)      Each node is also assigned a canonical group identifier which groups together related proteins.
3)   Each edge represents evidence from some source database that supports this interaction.  Multiple edges between nodes are possible.
       This multi-edge view can be toggled on and off under the iRefScape/View Tools/Toggle selected multi-edges.
4)      Complex data are represented separately from binary data using a bi-partite graph representation (hexagonal nodes represent complexes).
5)      The iRefScape plugin downloads all data locally when first installed (about 300 Mb). Searching thereafter is independent of a network connection.
6)      An extensive set of node and edge attributes are loaded with search results.

Google group for announcements and feedback:
Source data for build 7.0:
Statistics for build 7.0:
iRefWeb interface to release 6.0 of the data: (will be updated to 7.0 once the paper is reviewed).





Brian Turner

Jun 25, 2010, 10:45:23 AM6/25/10
Post this on cytoscape discuss as well.

Brian Turner
416 813 7810

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