BiNoM

BiNoM is a Cytoscape plugin to analyze and manipulate biological networks. BiNoM accepts SBML, SBGN, and BioPAX file formatsand can export to SBML, CellDesigner and BioPAX Level 3 formats. The BiNoM algorithm contains a collection of graph-based functions, such as path analysis, decomposition by involvement of an entity or cyclic decomposition, subnetworks clustering and large network decomposition in modules.

Topic

Systems biology;Molecular interactions, pathways and networks;Data acquisition

Detail

  • Operation: Query and retrieval

  • Software interface: Library;Plug-in

  • Language: Java

  • License: GNU Lesser General Public License v2

  • Cost: Free

  • Version name: 2.3

  • Credit: The European Union Seventh Framework Programme, Projet Incitatif et Collaboratif Computational Systems Biology Approach for Cancer, Institut Curie.

  • Input: -

  • Output: -

  • Contact: Andrei Zinovyev andrei.zinovyev@curie.fr, Laurence Calzone laurence.calzone@curie.fr, Eric Bonnet eric.bonnet@curie.fr, Emmanuel Barillot emmanuel.barillot@curie.fr

  • Collection: -

  • Maturity: Stable

Publications

  • Practical use of BiNoM: a biological network manager software
  • Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. Practical use of BiNoM: a biological network manager software. Methods Mol Biol. 2013;1021:127-46. doi: 10.1007/978-1-62703-450-0_7. PMID: 23715983.
  • https://doi.org/10.1007/978-1-62703-450-0_7
  • PMID: 23715983
  • PMC: -
  • BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
  • Zinovyev A, Viara E, Calzone L, Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics. 2008 Mar 15;24(6):876-7. doi: 10.1093/bioinformatics/btm553. Epub 2007 Nov 16. PMID: 18024474.
  • https://doi.org/10.1093/bioinformatics/btm553
  • PMID: 18024474
  • PMC: -
  • BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
  • Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A. BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18. PMID: 23453054; PMCID: PMC3646686.
  • https://doi.org/10.1186/1752-0509-7-18
  • PMID: 23453054
  • PMC: PMC3646686

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