8/20/2015 3:14:27 AM The Canadian Bioinformatics Resources – An Overview

8/20/2015 3:14:27 AM What are we?  A distributed computational biology resource with nodes across the country, accessed through the Web and computer terminals via CA*Net3

8/20/2015 3:14:27 AM Distributed

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 155Mbps), with Nova Scotia being the first site in the world connected to a national advanced network

8/20/2015 3:14:27 AM 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 router  Nova Scotia was the first province connected to CA*net 3, and our CBR servers now run Gigabit Ethernet

8/20/2015 3:14:27 AM 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)

8/20/2015 3:14:27 AM Network Associations  EMBNet: Canadian national node  APBioNet: founding member  Canadian Bioinformatics Workshops Partner

8/20/2015 3:14:27 AM 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. I vs. II Internal/External $195

8/20/2015 3:14:27 AM  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) What is it used for? Computational Resources

8/20/2015 3:14:27 AM What is it used for?  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) Analysis Software

8/20/2015 3:14:27 AM What is it used for?  Installation of server programs and infrastructure for tool development  Sharing of users’ programs and expertise  Sample projects using CBR resources: MAGPIE, Bluejay, Proteomics Tool Development

8/20/2015 3:14:27 AM 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

8/20/2015 3:14:27 AM MAGPIE: Project Overview

8/20/2015 3:14:27 AM MAGPIE: DNA/Gene Summary

8/20/2015 3:14:27 AM MAGPIE: More DNA Info

8/20/2015 3:14:27 AM MAGPIE: Evaluated Evidence

8/20/2015 3:14:27 AM MAGPIE: Human Annotation

8/20/2015 3:14:27 AM 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

8/20/2015 3:14:27 AM Bluejay Proxy Server URI request from user URI content display URI request from content handler URI request from browser Client Proxy (mod_perl under Apache) Server Intervention by request handler URI content translation in content handler GET GET /path/to/file Content-type: text/xml Content-type: text/... GET /path/to/file Content-type:... Accept: text/xml,...

8/20/2015 3:14:27 AM Bluejay

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

8/20/2015 3:14:27 AM Proteomics

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

8/20/2015 3:14:27 AM 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

8/20/2015 3:14:27 AM 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

8/20/2015 3:14:27 AM Coming up  Small & medium enterprise services  Always more Web services  Genematcher

8/20/2015 3:14:27 AM Who are we? User support Heidi Bishop Heather Penney Admin/Graphics Rob Hutten UNIX Sys Admin Christoph Sensen Project Leader Sheldon Briand Application/DB Support

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