Extreme Bioinformatics Stephen Montgomery Genetics Graduate Program, UBC Supervisor: Steven Jones

Bioinformatics – Simple Concepts The application of computer science and engineering techniques to biological analysis. The creation of repeatable, reusable, intelligent software

Bioinformatics - Goals Drive biological analysis  Predict function  Deliver results Script-based developmentSystems-based development

Bioinformatics - Problems Audience (Language) Relevance Delivery Usable, Repeatable techniques BioinformaticianBiologist In silicoIn vivo

Bioinformatics - Challenges Create standards for practice  Identification of proven techniques  Simple methods to access techniques  Intuitive design  Repeatable  Adaptability  Presentable results Transitional technology

GENEREG CMSGSC Sockeye Chinook

Sockeye Integrated platform for comparative genomics Montgomery S.B., Astakhova T., Bilenky M., Birney E., Hassel M., Melsopp C., Rak M., Robertson A.G., Sleumer M, Fu T., Siddiqui A. S., and Jones S.J.M., Sockeye: A 3D Environment for Comparative Genomics (accepted to Genome Research, 2003)

Sockeye

Sockeye - EnsEMBL Hubbard T. et al The Ensembl genome database project Nucleic Acids Research Vol. 30, No

Sockeye - Viewing Data

Sockeye – Annotation

Sockeye - Sequence

Sockeye - Regulation

Sockeye - Problems

Sockeye – Problems

Sockeye – Integration issues How to deliver state-of-the-art bioinformatics analysis to a broad spectrum of users How to be responsive and adaptable to algorithm development How to increase collaboration and shift responsibility and accountability to software developers.

Chinook A peer to peer bioinformatics analysis server.

Chinook - Design Easy to add new algorithms Easy to discover classes of algorithms Decentralized network Easy to run client application (either as plug-in or standalone) 3 rd party referencing Allow for dynamic algorithm updates Work across dynamic network

Chinook – Client perspective

Chinook – Loading…

Chinook – Service Discovery

Chinook – 3 rd party referencing

Chinook – Parameter Entry

Chinook – Job Submission

Chinook – Final Results

Chinook – Adding Services

Chinook – More info

Conclusions - Future Novel transitional technology is required to deliver bioinformatics to a broad category of users. Extreme bioinformatics = Adaptability, Extendibility, Repeatability, and Usability. Future Work 2004 – Applications to Regulatory Variation Detection.

Credit Sockeye  Tamara Astakhova  Misha Bilenky  Maik Hassel  James Kennedy  Keven Lin  Gordon Robertson  Monica Sleumer  Eddy Tsang Sockeye Management  Tony Fu  Asim Siddiqui  Steven Jones Chinook  Maik Hassel  James Kennedy Chinook Management  Tony Fu  Asim Siddiqui  Steven Jones Chinook Other  Jonathan Lim (CMMT)  Wyeth Wasserman (CMMT) Special Thanks  Yaron Butterfield  Christine Dahl  Martin Krzywinski  All the support from my numerous other fellow co-workers  Genome Canada THANKS!!!!!