BiNoM: Biological Network Manager
Cytoscape plug-in for manipulating and analysing biological networks

Introduction | Download | Documentation | Screenshots | Contacts

Introduction

BiNoM ( Biological Network Manager ) is Cytoscape plugin developed by 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.

The first version of the 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.)

Latest news: BiNoM is now compatible the latest version of Cytoscape (2.6.0). Due to continuous changes in Cytoscape API, only the latest version of Cytoscape will be supported in the future.

More information in

Downloads

BiNoM can be installed and used in several ways:

Easy) As Cytoscape plug-in with all libraries included
Download, 22M

Installation steps:

  1. Copy BiNoM_all.jar into the 'plugin/' folder of Cytoscape

Important note: This version can be used only with the latest version of Cytoscape (2.6.*). If you use Cytoscape version 2.4.* or below, you have to 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.

Pro) As Cytoscape plug-in without Jastor, XmlBeans, Jena libraries (smaller file)
Download, 9M

Installation steps:

  1. Copy BiNoM.jar into the 'plugin/' folder of Cytoscape
  2. Make sure that all jars on which BiNoM is dependent are in CLASSPATH
  3. You can use all the required libraries merged in one big jar file: binomlibext.jar
List of dependencies:
  1. Jastor library (BiNoM uses jastor-1.0.3.jar:jsr173_1.0_api.jar)
  2. XmlBeans library (BiNoM uses xbean.jar:commons-logging.jar:sax.jar)
  3. Jena library (BiNoM uses antlr.jar:concurrent.jar:icu4j_3_4.jar:iri.jar:jakarta-oro-2.0.5.jar:jena.jar:jenatest.jar:junit.jar:rdf-api-2001-01-19.jar:xercesImpl.jar (dated 07/02/07):xml-apis.jar)

Library) As stand-alone jar for file conversions, structural analysis, etc. (Jena, Jastor and XmlBeans are included)
Download, 22M
(examples of use)

Documentation and source code

Screenshots

   

   

BiNoM working group

  • Andrei Zinovyev
  • Eric Viara
  • Emmanuel Barillot
  • Laurence Calzone
  • Philippe La Rosa

Contacts

Acknowledgements

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