[Computational-biology] APPLIED COMPUTATIONAL GENOMICS COURSE

Brian Fristensky frist at cc.umanitoba.ca
Tue May 30 13:31:21 EST 2006


Newsgroups: bionet.biology.computational
Subject: APPLIED COMPUTATIONAL GENOMICS COURSE
Summary: 
Followup-To: 
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Organization: University of Manitoba
Keywords: bioinformatics, computational biology
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                        Genome Canada
              APPLIED COMPUTATIONAL GENOMICS COURSE

September 8-14, 2006, University of Manitoba
Winnipeg, Manitoba, Canada 

(International attendees welcome!)
------------------------------------------------------

Bioinformatics in the post-genomic era requires the analysis of
large and diverse datasets using automated tools. While
many Web-based tools are available to the lab researcher,
the Web is awkward for tasks beyond single-sequence annotation.
Researchers need to become productive in a server-based
Unix environment with its wealth of scripting and automation
tools. Even at an entry-level, this can be an intimidating
endeavor. The Genome Canada Bioinformatics Platform is
empowering researchers by teaching a hands-on course,
with lectures and tutorials presented by a panel of
experts. The course uses  tools and services available
through the Genome Canada Bioinformatics Platform.
Most tools used are open-source, and can be freely
downloaded for use at one's home institution.
Topics include (tentative): 

Becoming a power user 
o   Basic Unix skills on a network-centric desktop 
o   BIRCH: Working with sequence datasets on a comprehensive
bioinformatics
    system 
o   BIRCH: Creating your own in-house bioinformatics system 

Creating automated data pipelines 
o   Perl scripting: Quick automation of data analysis tasks and
utilization
    of web services 
o   BioPerl; Object-oriented Perl; Data warehousing - the SeqHound API 
o   BioMOBY: a transparent software layer that automatically finds and
uses
    web services 

High throughput genome annotation 
o   TimeLogic Decypher  and Paracel Gene Matcher  
o   MAGPIE, BLUEJAY  : Automated genome analysis, annotation and
visualization  
o   OSPREY: High-throughput oligonucleotide design

Canadian Bioinformatics Help Desk 

Secure use of remote bioinformatics systems: 

o   command line: ssh, sftp, scp, tar, gzip
o   remote desktop: VNC 

For more information about this workshop go to:

    http://www.gcbioinformatics.ca/training




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