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Bioinformatics Advance Access originally published online on November 16, 2007
Bioinformatics 2008 24(6):876-877; 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 *, Eric Viara , Laurence Calzone and Emmanuel Barillot

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

*To whom correspondence should be addressed.


  Abstract

BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured 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, clipboard operations and others.

Availability: Last version of BiNoM distributed under the LGPL licence together with documentation, source code and API are available at http://bioinfo.curie.fr/projects/binom

Contact: andrei.zinovyev{at}curie.fr

Associate Editor: Trey Ideker

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

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