Description

Chinook is a peer-to-peer (P2P) bioinformatics service. The goal of the Chinook platform is to facilitate exchange of analysis techniques within a local community and/or worldwide. Chinook operates by turning command-line applications into services which are broadcast over a virtual network. Currently, there are over 10 analysis services that have been made "Chinook-ready". These range from alignment to regulation prediction algorithms. Furthermore, Chinook is designed to make it extremely easy to add new services. This is facilitated using XML.

Currently, there is no source code available for Chinook. The source though is licenced under Creative Common's Attribution-NonCommercial license and is freely available on request to chinook@bcgsc.bc.ca. As interested parties emerge, we will move this to the bioinformatics.org cvs.

Citing Chinook (temporary):

Chinook Internal:

Chinook External:

Chinook is funded by Genome Canada as part of the Bioinformatics of Mammalian Gene Regulation grant. Stephen Montgomery is a Ph.D. graduate student in Genetics at the University of British Columbia. He is funded by the Michael Smith Foundation for Health Research. His work is performed primarily at Canada's Michael Smith Genome Sciences Centre as part of the Gene Regulation Informatics team. Steven Jones is the Head of Bioinformatics for the CMSGSC. He is a Scholar of the Michael Smith Foundation for Health Research.

Chinook License

This work is licensed under a Creative Commons License.

Mailing List

The Chinook mailing list is a low-volume regulated list that broadcasts weekly development announcements.

Sign-up at http://www.bcgsc.ca/mailman/listinfo/chinook
Visit archives at http://www.bcgsc.ca/pipermail/chinook/

Documentation

Chinook User Documentation CUD: This documentation is designed to help users configure, develop, and run the Chinook server
NEW (May 25th, 2004) Running Chinook Running Chinook (for developers)
Adding New Services (PDF) Adding new Chinook servcies
Creating JBuilder Development Environment for Chinook Dev (PDF) Setting up Chinook for your IDE
Intro to Packages and External Directories (PDF) The Java packages
Chinook Advertisements (PDF) Generating JXTA advertisements in Chinook

Chinook Guides: This documentation consists of coding guides for Chinook developers
Auto-Configuration (PDF) Chinook / JXTA hybrid configuration utilities

Adding New Services Note

If you are interested in putting your algorithm into Chinook, please e-mail the chinook mailing list at chinook@bcgsc.bc.ca. Currently, we are working on making this process easier and the release version of chinook (available soon) will have facilitated mechanisms for helping you to publish your service without our assistance. If you are interested in what we do to integrate your algorithms, read the Adding New Services document above.

Presentations on Chinook

Development Issues

Chinook development will be geared up in early 2004 to support GENEREG and CMMT usage.
The following issues are outstanding in productotype II (the current implementation).
Chinook Bug List (PDF)

Web start client

Chinook Client Web Start Try it out and e-mail chinook@bcgsc.bc.ca with your comments. (There may be a problem with the bootstrapping over webstart right now.)

Chinook Images (Screenshots)

Chinook client user interface on start-up. Services are separated by ontology in the service tree. Service statistics appear in the service table. Clicking on a service, displays its 3rd party website. When a service is selected to run a job, the parameter entry panel appears. Job status will appear in the jobs table (bottom-left). From the jobs table, reports can be viewed. As the client is running new P2P services are continually being discovered.

Chinook CVS