Introduction

BiNoM ( Biological Network Manager ) is a Cytoscape plugin developed by the Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

BiNoM software supports the following functions:

• Import of BioPAX, SBML and CellDesigner formats
• Export to BioPAX, SBML and CellDesigner formats after user manipulations
• Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML)
• Full support of BioPAX information (reaction network, interaction network, pathway structure, references), concept of BioPAX index and network interfaces
• Browsing, editing, extracting parts, merging BioPAX files with network graph interface
• Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)
• Support of generating network modular view
• BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)
• Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.)

Downloads

BiNoM can be installed and used in several ways.

Using the Cytoscape plugin manager

1. Launch the Cytoscape plugin manager (menu "Plugins -> Manage Plugins").
2. Go to the category "Other".
3. Select the latest version of BiNoM (currently 2.3).
4. Click "Install".
5. Restart Cytoscape.

As a Cytoscape plug-in file with all libraries included

• Stable (25Mb) release.
• Experimental (25Mb) release.

Installation procedure: just copy the BiNoM jar file into the 'plugin/' folder of Cytoscape (you should also remove all previous BiNoM versions from this folder).

Important note: This version can be used only with versions 2.7.x and 2.8.x of Cytoscape, it not yet compatible with Cytoscape version 3.0.

1. Download the old version of BiNoM.
2. Remove (or, better, rename and keep) xercesImpl.jar from 'lib/' folder of Cytoscape (since it is not compatible with the version of the same jar used by Jena in BiNoM).

Important note: Some browsers automatically rename the BiNoM_all.jar to BiNoM_all.zip after the download. Do not unpack the .zip file but rather rename it back to BiNoM_all.jar and copy into the plugin/ Cytoscape folder.

Using BiNoM as a java library

BiNoM can be linked as a stand-alone java library for file conversions, structural analysis, etc. (examples)

Articles, documentation and goodies

• Bonnet E., Calzone L., Rovera D., Stoll G., Barillot E. and Zinovyev A.. BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. 2013, BMC Systems Biology, 7:18. web link
• Bonnet, E. Standards and formats in systems biology. Seminar "Mathematics and Biology of Cancer", 12.06.2013, Institut Curie. slides
• Bonnet, E. BiNoM 2.0, a versatile tool for accessing and analyzing pathways using standard systems biology formats. NUS - IBENS Workshop "Novel genome-wide approaches to decipher transcriptional and epigenetic regulation in mammalian cells. 30 May 2013. ENS, Paris, France. slides
• Cohen, D. BiNoM and NaviCell: Tools for navigation, curation, maintenance and analysis of complex molecular interaction maps - The 6th International Biocuration Conference, Cambridge, UK, April 8 2013. slides
• Bonnet, E. BiNoM, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. Computational Modeling in Biology Network (COMBINE) 2012. August 2012. The Donnelly Centre, University of Toronto, Canada slides
• Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2008. Bioinformatics 24(6):876-877 manuscript
• BiNoM presentation at the ICSB-2008 workshop Web-services in Systems Biology (Goteborg, Sweden, August 2008) (slides)
• BiNoM poster presentation at the International Conference on Systems Biology (Long Beach, CA, October, 2007) (extended abstract)(poster)

• BiNoM reference card
• BiNoM manual and the files mentioned in it.
• BiNoM tutorial for INSERM training April 2007
• Materials for the training session "Construction, manipulation and navigation through biological networks using CellDesigner, BiNoM, and NaviCell" (04/06/13)
• Materials for the book chapter"Practical use of BiNoM, a Biological Network Manager software" book chapter by Bonnet E. et al (2012)
• BiNoM source code
• BiNoM JavaDoc
• Supplementary material (G1S network file) for the manuscript "BiNoM, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats" by Bonnet E. et al. (2012)
• Example of CellDesigner files prepared for use by NaviCell

Screenshots

   

   

BiNoM working group

• Andrei Zinovyev
• Eric Bonnet
• Laurence Calzone
• Daniel Rovera
• Gautier Stoll
• Paola Vera-Licona
• Stuart Pook
• Eric Viara
• Emmanuel Barillot

Contacts

• Andrei Zinovyev
• Laurence Calzone
• Eric Bonnet
• Emmanuel Barillot

Acknowledgements

This project was partly funded by the EC contract ESBIC-D (LSHG-CT-2005-518192), the PIC Bioinformatique et Biostatistiques from Institut Curie, the Research Networks Program in Bioinformatics from the High Council for Scientific and Technological Cooperation between France and Israel, and the APO-SYS FP7 European program.