title: BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
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.
  
  
  BACKGROUND
  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
authors.affiliation: Institut Curie, Service de Bioinformatique, 26 rue d'Ulm, F-75248 Paris Cedex 05, France. andrei.zinovyev@curie.fr
authors.forename: Andrei
authors.initials: A
authors.lastname: Zinovyev
authors.forename: Eric
authors.initials: E
authors.lastname: Viara
authors.forename: Laurence
authors.initials: L
authors.lastname: Calzone
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome