Cytoscape Dependencies

Piccolo provides the graphics engine used by Cytoscape, has a Zoomable User Interface(ZUI)
and provides a powerful framework for user interaction and data display.

Software

• GenMAPP
• Osprey
• Cyclone
• eXpanda (Network visualization/analysis Perl library supporting sif/gml file I/O)
• pyNetConv - Interconverts network file formats e.g. .net, .gml, .sif
• BiologicalNetworks

Network Databases

• Biomolecular Interaction Network Database (BIND)
• BioPAX Directory (Pathguide)

Data Exchange Formats

• BioPAX (Biological Pathway Exchange)
• SBML (Systems Biology Markup Language)
• PSI-MI (Proteomics Standards Initiative - Molecular Interaction)
• GML (non-XML graph markup language)
• XGMML (eXtensible Graph Markup and Modeling Language)
• The Gene Ontology (for data anotation)
• Open Biomedical Ontologies

Projects Using Cytoscape

• T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers
• caWorkBench2.0 - A Platform for Integrated Genomics
• GENPAC - NLP (Natural Language Processing) based information extraction system for life science domain.
• National Center for Integrative Biomedical Informatics (NCIBI)
• GeneGo
  

Support

• NIH NIGMS grant 1 R01 GM070743-01
• Unilever
• National Science Foundation (NSF)

Documentation in Other Languages

• CyDoc - Cytoscape Japanese Documentation Project

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743-01 and the U.S. National Science Foundation (NSF) . Corporate funding is provided through a contract from Unilever PLC.

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