BioPax is collaborative effort to create a data exchange format for biological pathway data. BioPax is an open source project.
The Cancer Cell Map contains selected cancer related signaling pathways which you can browse or search.
The Cancer Cell Map was created by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center and the Institute of Bioinformatics. Powered by the cPath pathway database software.
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.
The Mondrian Software enables researchers to visualize complex multi-dimensional genomic profiling data in the context of known biological pathways.
NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.
Currently, NetBox provides the analyzeNet.py method that is fully described in the manuscript: Automated Network Analysis Identifies Core Pathways in Glioblastoma (Currently in Review). This provides a simple command line interface for connecting genes into a network, identifying statistically significant "linker" genes, partitioning the network into modules, and executing two random background models. Results are then made available to the end user as an HTML web page and a series of network and attribute files, which can be loaded into Cytoscape for visualization and further analysis.
Pathguide contains information about hundreds of internet pathway resources.
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.
