the canadian bioinformatics resources – an overview
DESCRIPTION
The Canadian Bioinformatics Resources – An Overview. What are we?. A distributed computational biology resource with nodes across the country, accessed through the Web and computer terminals via CA*Net3. Distributed. Networking History. Started with 56Kbps lines for the institutes - PowerPoint PPT PresentationTRANSCRIPT
04/22/23 02:03 PM
The Canadian Bioinformatics The Canadian Bioinformatics Resources – An OverviewResources – An Overview
04/22/23 02:03 PM
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
04/22/23 02:03 PM
DistributedDistributed
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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)
04/22/23 02:03 PM
Network AssociationsNetwork Associations
EMBNet: Canadian national node
APBioNet: founding member
Canadian Bioinformatics Workshops Partner
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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
04/22/23 02:03 PM
MAGPIE: Project OverviewMAGPIE: Project Overview
04/22/23 02:03 PM
MAGPIE: DNA/Gene SummaryMAGPIE: DNA/Gene Summary
04/22/23 02:03 PM
MAGPIE: More DNA InfoMAGPIE: More DNA Info
04/22/23 02:03 PM
MAGPIE: Evaluated Evidence MAGPIE: Evaluated Evidence
04/22/23 02:03 PM
MAGPIE: Human AnnotationMAGPIE: Human Annotation
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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, ...
04/22/23 02:03 PM
BluejayBluejay
04/22/23 02:03 PM
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
04/22/23 02:03 PM
ProteomicsProteomics
04/22/23 02:03 PM
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
020000400006000080000
100000
Feb-
99Ma
r-99
Apr-
99Ma
y-99
Jun-
99Ju
l-99
Aug-
99Se
p-99
Oct-9
9No
v-99
Dec-
99Ja
n-00
Feb-
00Ma
r-00
Apr-
00Ma
y-00
Hits Canada48%
Unknown21%
.com9%
Others15%.edu
7%
04/22/23 02:03 PM
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
04/22/23 02:03 PM
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
04/22/23 02:03 PM
Coming upComing up
Small & medium enterprise services Always more Web services Genematcher
04/22/23 02:03 PM
Who are we?Who are we?
User supportHeidi Bishop
Heather PenneyAdmin/Graphics
Rob HuttenUNIX Sys Admin
Christoph SensenProject Leader
Sheldon BriandApplication/DB Support
04/22/23 02:03 PM
ΩΩ