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The Canadian Bioinformatics The Canadian Bioinformatics Resources – An OverviewResources – An Overview

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What are we?What are we?

A distributed computational biology resource with nodes across the country, accessed through the Web and computer terminals via CA*Net3

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DistributedDistributed

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Networking HistoryNetworking 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

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Networking PresentNetworking 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

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Networking FutureNetworking 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)

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Network AssociationsNetwork Associations

EMBNet: Canadian national node

APBioNet: founding member

Canadian Bioinformatics Workshops Partner

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Who uses it?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. IIInternal/External

$195

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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?What is it used for?Computational Resources

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What is it used for?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

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What is it used for?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

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MAGPIEMAGPIE

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

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MAGPIE: Project OverviewMAGPIE: Project Overview

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MAGPIE: DNA/Gene SummaryMAGPIE: DNA/Gene Summary

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MAGPIE: More DNA InfoMAGPIE: More DNA Info

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MAGPIE: Evaluated Evidence MAGPIE: Evaluated Evidence

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MAGPIE: Human AnnotationMAGPIE: Human Annotation

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BluejayBluejay

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

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Bluejay Proxy ServerBluejay Proxy Server

URI requestfrom user

URI content display

URI requestfrom content handler

URI requestfrom browser

Client Proxy(mod_perl under Apache)

Server

Intervention byrequest handler

URI content translation in content handler

GET http://.../path/to/file

GET /path/to/file

Content-type: text/xml

Content-type: text/...

GET /path/to/file

Content-type: ...

Accept: text/xml, ...

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BluejayBluejay

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ProteomicsProteomics

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

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ProteomicsProteomics

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

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HitsCanada

48%

Unknown21%

.com9%

Others15%.edu

7%

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Examples UsersExamples 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

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Why use us instead of others?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

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Coming upComing up

Small & medium enterprise services Always more Web services Genematcher

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Who are we?Who are we?

User supportHeidi Bishop

Heather PenneyAdmin/Graphics

Rob HuttenUNIX Sys Admin

Christoph SensenProject Leader

Sheldon BriandApplication/DB Support

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