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Bioinformatics Advance Access published online on November 16, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm553
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

Andrei Zinovyev a, Eric Viara a, Laurence Calzone a and Emmanuel Barillot a

aInstitut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France

Dr. Andrei Zinovyev, E-mail: andrei.zinovyev{at}curie.fr


  Abstract

BiNoM (BIological NetwOrk Manager) is a new bioinformatics software which significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX), BiNoM implements a fullfeatured BioPax editor and a method of "interfaces" for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databases. In addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into BioPAX format. BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules,cllipboard operations and others.

Availability: Last version of BiNoM together with documentation, source code and API is available at http://bioinfo.curie.fr/projects/binom

Contact: andrei.zinoyev{at}curie.fr, binom{at}curie.fr

Associate Editor: Dr. Trey Ideker

Received on October 5, 2007; revised on October 5, 2007; accepted on October 31, 2007

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