About Pathway Commons
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search.
- Biologists can browse and search Pathway Commons pathways.
- Computational biologists can download all pathways in BioPAX format for global analysis.
- Software developers can build software on top of Pathway Commons using our web service API. You can also download and install the cPath software to create a local mirror of Pathway Commons.
All data is freely available, under the license terms of each contributing database.
About cBio @ MSKCC
- sequence-structure analysis
- gene regulation
- molecular pathways and networks
- diagnostic and prognostic indicators
The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components -- the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources.
About the University of Toronto
The University of Toronto is Canada's largest university, with a strong focus on research. Pathway Commons work is done in the Bader Lab.
Pathway Commons is built entirely on open source software. We gratefully acknowledge the following open source projects.
|Apache Tomcat||Servlet / Java Server Pages (JSP) Engine.|
|Apache Commons||Multiple Apache Commons projects, including DBCP: database connection pooling services.|
|Apache Log4j||Java logging framework. Helps us track down bugs.|
|Apache Lucene||Full-featured text search engine library. Powers all our search functionality.|
|Apache Struts||Extensible framework for creating Java web applications. Powers all or our web pages.|
|ARP: Another RDF Parser||RDF/XML Parser. Parses and validates all our BioPAX files.|
|Cruise Control||Framework for running continuous builds. Re-compiles and re-tests all Pathway Commons code after every check in.|
|CVS||Version control system.|
|EhCache||Java caching library. Helps keep Pathway Commons running fast.|
|Firebug||A must-have extension to Firefox, used to debug Web 2.0 applications.|
|JDOM||Our favorite library for parsing XML in Java.|
|JUnit||Unit test framework for regression testing.|
|MySQL||Relational database system.|
|Yahoo! UI Library (YUI)||Web 2.0 / AJAX library. Powers all of our dynamic HTML / AJAX features. Nice work, Yahoo!|