BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

by: Andrei Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot

Bioinformatics (16 November 2007), btm553.

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摘要

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@curie.fr, binom@curie.fr 10.1093/bioinformatics/btm553

@article{citeulike:1992269, 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@curie.fr, binom@curie.fr 10.1093/bioinformatics/btm553}, author = {Zinovyev, Andrei and Viara, Eric and Calzone, Laurence and Barillot, Emmanuel }, citeulike-article-id = {1992269}, doi = {10.1093/bioinformatics/btm553}, journal = {Bioinformatics}, keywords = {interactome}, month = {November}, pages = {btm553+}, posted-at = {2007-11-27 10:47:12}, priority = {2}, title = {BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks}, url = {http://dx.doi.org/10.1093/bioinformatics/btm553}, year = {2007} }

RIS record

TY - JOUR ID - citeulike:1992269 L3 - citeulike-article-id:1992269 TI - BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks JF - Bioinformatics SP - btm553 N2 - 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@curie.fr, binom@curie.fr 10.1093/bioinformatics/btm553 KW - interactome AU - Zinovyev, Andrei AU - Viara, Eric AU - Calzone, Laurence AU - Barillot, Emmanuel PY - 2007/11/16/ UR - http://dx.doi.org/10.1093/bioinformatics/btm553 ER -

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