can Cytoscape directly import interacton data from BioGrid

[Shaoyu Wang]

Dear All,



I am new to Cytoscape. I wonder if there is any plugin or other way that can automatically convert the interaction data down-loaded from Biogrid to Cytoscape. Any information regarding the "talks" between Cytoscape and Biogrid is appreciated.



Best regards



Shaun

[Michi]

There is a plugin that can import biogrid data
http://wiki.thebiogrid.org/biogridcytoscapeplugin

I have written an importer based on the osprey source code and it
works quite well for our needs.
Unfortunatelle I will not be able to publish it in the near future and
it would probably need some clean up (refactoring and standartisation
of attribute names and properties ...)

The Osprey Source Code is here:
http://sourceforge.net/projects/osprey-network/files/

[Shaoyu Wang]

Thank you Michael. I'll give it a go.
Shaun

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[Keiichiro Ono]

Hi.
It's still in beta status, but from Cytoscape 2.7.0, BioGRID database
will be supported through PSICQUIC web service API. You can try the
feature by installing nightly build:

http://chianti.ucsd.edu:8081/cruisecontrol/buildresults/cytoscape

for more information about PSICQUIC client, please read my last post
in cytoscape-dicscuss mailing list.


http://keiono.tumblr.com/post/285322865/nested-network-feature-used-in-psicquic-client


Thanks.
Kei


2009/12/14 Shaoyu Wang <S.W...@uws.edu.au>:

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Keiichiro Ono ko...@ucsd.edu

Cytoscape Core Developer Team: http://www.cytoscape.org/
UCSD School of Medicine Trey Ideker Lab: http://chianti.ucsd.edu/idekerlab/

[Fadl AlAkwaa]

The are many plug-in to deal with interactions databases like:
Bionetbuilder.
see http://chianti.ucsd.edu/cyto_web/plugins/index.php
Dr Fadhl

[Shaoyu Wang]

Thank you Kei for this an I'll give it a go.

Shaun

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