Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.
BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. <ul><li>Import of BioPAX 3, SBML and CellDesigner formats<li>Export to BioPAX 3, SBML and CellDesigner formats after user manipulations<li>Conversion between standards (CellDesigner-&gt;BioPAX 3, BioPAX 3 -&gt;SBML)<li>Full support of BioPAX 3 information (reaction network, interaction network, pathway structure, references), concept of BioPAX 3 index and network interfaces<li>Browsing, editing, extracting parts, merging BioPAX 3 files with network graph interface<li>Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)<li>Support of generating network modular view<li>BioPAX 3 network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)<li>Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.) </ul>

Version 2.5

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Released 22 Jul 2013

Works with Cytoscape 2.7, 2.8

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