Chinook: A collaborative system for bioinformatics analysis. RIP The Genome Sciences Centre Stephen Montgomery.

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Presentation transcript:

Chinook: A collaborative system for bioinformatics analysis. RIP The Genome Sciences Centre Stephen Montgomery

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

Each community has its own culture

An interaction map of biologists and bioinformaticians

Things get more complicated…  Organizational boundaries (EnsEMBL vs. UCSC)  Access to different resources (computational, monetary)  Time (where to start, what to use…)  Different tools and user interfaces  Overlap in integrative efforts (suite building)  Communication efficacy (who you know…)  Installation requirements  Reliability and repeatability  Attribution issues

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

A community-based approach to bioinformatics analysis

Chinook overview 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  Address problems relevant to bioinformatics Attribution Data management Resource distribution

Discovering and Running jobs

Monitoring jobs

Server Information Panel Static Service Entry Panel Filter Pane

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

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

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

Future Plans

Acknowledgements GENOME SCIENCES CENTRE Steve Jones Tony Fu Jun Guan Keven Lin Asim Siddiqui Genereg 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