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Canadian Bioinformatics Resources: A Distributed Computational Biology Resource

A comprehensive, distributed computational biology resource with nodes across Canada, accessed through the Web and computer terminals via CA*Net3 Distributed Networking.

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Canadian Bioinformatics Resources: A Distributed Computational Biology Resource

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  1. The Canadian Bioinformatics Resources – An Overview

  2. What are we? • A distributed computational biology resource with nodes across the country, accessed through the Web and computer terminals via CA*Net3

  3. Distributed

  4. Networking History • Started with 56Kbps lines for the institutes • Collaborated with CANARIE as a test-bed application for the new CA*net II (OC3 ATM lines @ 155Mbps), with Nova Scotia being the first site in the world connected to a national advanced network

  5. Networking Present • In 1998 CANARIE was mandated to create the first national optical Internet network • CA*net 3 uses wavelength multiplexing over fiber to each province’s gigabit point of presence (GigaPoP) Cisco 12008 router • Nova Scotia was the first province connected to CA*net 3, and our CBR servers now run Gigabit Ethernet

  6. Networking Future • By the end of 2000 all CBR servers should be on the gigabit backbone • Currently CA*net 3 runs two OC48 (2.5Gbps) wave lengths, preparing to increase to eight OC192s (total 80Gbps)

  7. Network Associations • EMBNet: Canadian national node • APBioNet: founding member • Canadian Bioinformatics Workshops Partner

  8. Who uses it? • Internal NRC users and their industrial collaborators use CBR-I terminal access. • Members of not-for-profit, research organizations use CBR-II. Basic Web access is free, terminal and SeqWeb access come with the $195 registration. $195 I vs. II Internal/External

  9. What is it used for? Computational Resources • Large redundant disk storage, automated updates • Retrieval of known DNA/Protein sequences • High speed parallel processing, interface features • Alignment of new sequence to the database sequences (Blast, FastA) • System Stability • Intensive computation, tool integration (ClustalW & WebPhylip)

  10. What is it used for? Analysis Software • Analysis tool suites (GCG) • Investigate sequences using wide range of tools • Platform specific software access (Sun, SGI, DEC, Linux) • Protein identification and characterization • Finding novel functions, structures (Expasy, HyperChem)

  11. What is it used for? Tool Development • Installation of server programs and infrastructure for tool development • Sharing of users’ programs and expertise • Sample projects using CBR resources: MAGPIE, Bluejay, Proteomics

  12. MAGPIE • Intelligent automated DNA analysis using queued requests for local and Internet-accessed programs • Web based reporting with private/public data views • Automated public database submission based on human confirmation of MAGPIE analysis

  13. MAGPIE: Project Overview

  14. MAGPIE: DNA/Gene Summary

  15. MAGPIE: More DNA Info

  16. MAGPIE: Evaluated Evidence

  17. MAGPIE: Human Annotation

  18. Bluejay • Java-based visualization of data in XML format using abstract graphics libraries • Adding XML to CBR services will make advanced queries and tool integration easier while staying compatible with old browsers • Proxy server (in mod_perl) for transparent access to non-XML data sources on the Web

  19. Bluejay Proxy Server Proxy (mod_perl under Apache) Client Server GET /path/to/file URI request from browser URI request from user Intervention by request handler GET http://.../path/to/file Accept: text/xml, ... URI request from content handler GET /path/to/file Content-type: ... Content-type: text/... URI content translation in content handler URI content display Content-type: text/xml

  20. Bluejay

  21. Proteomics • Web front-end to a relational database storing 2-D gel experiment information • Facilities to upload images and experiment spot linking/annotation information from client, then display the annotated image data dynamically according to user preferences • Integrated PI/MW estimations to search for known proteins that a spot might represent

  22. Proteomics

  23. How much is CBR being used? • 14,000 external homepage hits since Aug ’99 • 550,000 pages served since Feb. ’99

  24. Examples Users • Internally, a MAGPIE project of a pathogen Candida albicans) being used by BRI, requiring tens of thousands of database searches • Externally, The Pox Virus Resource (UVic) is using CBR-II processors and databases to keep analysis up to date

  25. Why use us instead of others? • High speed Internet connectivity • Command line/X Windows access • “One-stop” analysis • User support • Less infrastructure on the client end

  26. Coming up • Small & medium enterprise services • Always more Web services • Genematcher

  27. Who are we? Christoph Sensen Project Leader Rob Hutten UNIX Sys Admin Heather Penney Admin/Graphics Sheldon Briand Application/DB Support User support Heidi Bishop

  28. Ω

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