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Bioinformatics Advance Access published online on April 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn208
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Cytoscape ESP: simple search of complex biological networks

Maital Ashkenazi 1,*, Gary D. Bader 2, Allan Kuchinsky 3, Menachem Moshelion 1 and David J. States 4

1Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, IL
2Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON
3Agilent Technologies, Santa Clara, CA
4Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI

*To whom correspondence should be addressed. Maital Ashkenazi, E-mail: ashkenaz{at}agri.huji.ac.il


  Abstract

Summary: Cytoscape ESP enables searching complex biological networks on multiple attribute fields using logical operators and wildcards. Queries use an intuitive syntax and simple search line interface. ESP is implemented as a Cytoscape plugin and complements existing search functions in the Cytoscape network visualization and analysis software, allowing users to easily identify nodes, edges and subgraphs of interest, even for very large networks.

Availability: http://conklinwolf.ucsf.edu/genmappwiki/Google_Summer_of_Code_2007/Maital

Contact: ashkenaz{at}agri.huji.ac.il

Associate Editor: Dr. Trey Ideker

Received on November 14, 2007; revised on January 17, 2008; accepted on April 23, 2008

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