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
The Computational Biology Center at Memorial Sloan-Kettering Cancer Center pursues computational biology research projects and the development of bioinformatics resources in the areas of:
- 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.
Credits
Pathway Commons runs on cPath software, and was created by: Gary Bader, Ethan Cerami, Emek Demir, Benjamin Gross, and Chris Sander.
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. |
Web Developer Extension | Another must-have extension to Firefox, used to debug HTML, CSS and Javascript. |
Yahoo! UI Library (YUI) | Web 2.0 / AJAX library. Powers all of our dynamic HTML / AJAX features. Nice work, Yahoo! |
We also gratefully acknowledge Andreas Viklund, who provided the open source stylesheets, used to design the web site.