Cytoscape Links
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
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
Documentation in Other Languages
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) .
ISB | UCSD | MSKCC | Pasteur | Agilent | UCSF | Unilever | Toronto | NCIBI
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