BioPax is collaborative effort to create a data exchange format for biological pathway data. BioPax is an open source project.
cPath aims to be a freely available cancer pathway database. Currently, only information about protein-protein interactions collected from major interaction databases that support the PSI-MI format is available. cPath is open-source and is easy to locally install for private management of protein-protein interactions. Future directions include support for the BioPAX format so that entire pathways can be stored, queried and presented.
Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.
