1. Chinook: A collaborative system for bioinformatics analysis. UBIC/CMMT Talk October 2004 Stephen Montgomery

2. How is bioinformatics done? Data and Innovation Innovation Requirements Organization and Interpretation

3. Each community has its own culture

4. An interaction map of biologists and bioinformaticians

5. Things get more complicated…  Each individual has: Access to different resources  Computational / Monetary / Personnel Finite time available A different social network Professional obligations  Each group Organizational boundaries Toolkit (suites and scripts) Method of providing tools (OS, Internet, Interfaces)

6. An improved interaction map of biologists and bioinformaticians Improved Communication Access to communities Access to resources Retain sub-organization

7. A community-based approach to bioinformatics analysis Use the principles of peer-to-peer technology  Allow biologists to easily discover and run bioinformatics tools  Create a dynamic, reliable network for analysis  Reduce overlapping integration efforts  Improve communication within/outside organizations  Address problems relevant to bioinformatics Attribution Data management Resource distribution

8. discover and run jobs here or through bioperl

10. Running Chinook Use Ant  ant p2p-start  ant server-start From an IDE From an Installer

11. Algorithms integrated into Chinook ClustalW Genscan Conreal Sim4 DIALIGN MSCAN LAGAN ANN-Spec Mauve Recursive Gibbs Motif Sampler ORCA MEME Shuffle-LAGAN Motifsampler T-Coffee RSAT oligo analysis Promoterwise STUBB Primer3 Teiresias Eponine wConsensus ELPH

12. Projects involving Chinook OrthoSEQ plans to provides analysis through the Chinook/Bioperl Perl API. Sockeye uses Chinook to deliver state-of-the-art alignment, PCR prediction, and regulatory analysis Pegasys plans to provide pipeline management to subset of services advertised by Chinook. Bio-Linux planning to integrate a subset of their algorithms.

13. Use cases of Chinook Grid/Cluster computing. Internally connect teams / individuals. Collaborate with remote individuals. Provide an API layer to your algorithms. Insert bioinformatics analysis into applications. Show off your tools.

14. Chinook Architecture

16. Chinook Configuration Add new services Set Server Mode Open ports Customize Advertisements Run

17. Adding services (XML-Based)

18. Adding services (GUI-based)

19. Chinook Server Modes RMI vs. Web services Web Services  Runs over Tomcat and Axis (SOAP engine)  Harder to set-up, More management features  Language independent RMI  Uses the RMI registry (included in JDK/JRE)  Easier to set-up  Only allows Java to Java communication

20. How the P2P works JXTA Advertisements

21. Customizing your advertisements Edit the advertisements/ directory in your Chinook installation to include your endpoint location. Not localhost

22. Run

23. CMMT-DEMO

24. Future Plans

25. Acknowledgements GENOME SCIENCES CENTRE Steve Jones Tony Fu Jun Guan Keven Lin Asim Siddiqui Genereg team @ GSC Mark Mayo Bernard Li CENTRE FOR MOLECULAR MEDICINE AND THERAPEUTICS Wyeth Wasserman Jonathan Lim UBC BIOINFORMATICS CENTRE Francis Ouellette Graham McVicker Sohrab Shah Funding: MSFHR, Genome Canada VISIT http://smweb.bcgsc.bc.ca OR http://www.bcgsc.bc.ca/chinookhttp://smweb.bcgsc.bc.cahttp://www.bcgsc.bc.ca/chinook