A Service for Genome Canada Researchers

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Canadian Bioinformatics Help Desk

• A Service for Genome Canada Researchers

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Who Are We?

• We were established in Feb 2003
• We are part of the Bioinformatics Platform for
  Genome Canada
• Our primary raison d'être is to support the
  bioinformatics needs of Genome Canada researchers
• Our team is made up of three full-time
  bioinformatics professionals, with support from
  three affiliate staff

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Personnel
Dr. David Wishart, Director
Ian J. Forsythe, Bioinformatician
Dr. Paul Stothard, Bioinformatician
Dr. Gary Van Domselaar, Bioinformatician
Xiaoli Dong, Programmer Analyst
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Services

• Telephone support
• (780-492-5969)
• Online support
• Software repository
• Research directory
• Biweekly newsletter
• Software advice
• Programming tutorials
• Custom programming

• Custom graphics
• Website development
• Database development
• LIMS development
• Batch processing
• Data mining
• Data handling
• Data archiving

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Website

• Our information-rich website is loaded with
  useful links
• Our searchable directory facilitates
  collaborations
• Our links page provides many important Canadian
  bioinformatics links

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Website
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Research Directory
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Links
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Newsletter

• Biweekly (30 issues to date)
• Over 1500 subscribers
• Bioinformatics Profiles of Canadian
  bioinformatics research groups
• Software Spotlights on the latest in
  bioinformatics software
• What's New in Bioinformatics
• Training workshops and meetings
• Bioinformatics jobs
• Newsletter archive

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Newsletter
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Software Spotlight
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What's New
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Web Servers

• 26 web-based applications for
• Protein structure evaluation and comparison
• Plasmid and genome drawing
• 2D gel analysis
• SNP searching
• Medline text mining
• Bacterial genome databases
• Protein property prediction

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Assess Structure Quality
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Explore Bacterial Genomes
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BacMap Genome Atlas

• Published in the database issue (Jan 1, 2005) of
  Nucleic Acids Research
• Interactive, visual database containing
• Over 260 fully-labeled, zoomable, and searchable
  maps of bacterial genomes
• Gene labels are hyperlinked to detailed textual
  annotations
• Genomes can be queried using BLAST or keyword
  searches

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Manage cDNA Libraries
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Superimpose Protein Structures
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SuperPose Web Server

• Published in the July 2004 Web Server issue of
  Nucleic Acids Research
• Protein superpositions are calculated using a
  modified quaternion approach
• Generates sequence alignments, structure
  alignments, PDB coordinates, RMSD statistics,
  difference distance plots, and interactive images
  of superimposed structures

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Automate Plasmid Annotations
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PlasMapper Web Server

• Published in the July 2004 Web Server issue of
  Nucleic Acids Research
• Draws an annotated plasmid map based on
  user-inputted plasmid DNA sequence
• Supports an extensive array of display options

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Feature Site Database
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Create Circular Genome Maps
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CGView

• Published in Bioinformatics (Oct 2004)
• Written in Java
• Generates high quality, zoomable maps of circular
  genomes
• Accepts multiple input formats (XML,
  tab-delimited, and NCBI ptt)
• Easily integrated into sequence analysis pipelines

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LIMS
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GC Applied Health Projects
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GC Comp III
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• Develop a secure working environment
• Consider using HTTPS(HTTP over SSL)
• Determine the best use of firewalls to protect
  different data types
• Keep patient data confidential (anonomize it and
  export what is needed for research using a unique
  identifier for each patient)

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GelScape

• Web-based
• Gel-viewing
• Annotation system
• 1D/2D gels
• Western blots

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Software Repository

• More than 60 software titles to choose from
• Covering all aspects of bioinformatics and
  general data processing

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Over 60 titles...
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Top 10 Software Downloads

• Introduction to Perl Programming I
• Introduction to Perl Programming II
• Add Summary (to BLAST summary table)
• Codon Usage Calculator
• Molecular Weight/Isoelectric Point Calculator
• ORF Finder
• Annotator (runs local BLAST)
• Blast Client (batch web submission to NCBI)
• Clickable Sequence Features
• Reverse Complementation

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What we can do for you

• Genomic analysis Calculate gene statistics for
  every gene in the genome.
• Data visualization Sequence analysis program
  that provides graphical output over the web.
• Database management Custom relational database
  with web interface.

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What we can do for you

• Web robot Be able to submit thousands of
  sequences to BLAST without running BLAST locally.
• Machine learning Use supervised machine
  learning to make sense of your data.
• Sequence analysis An application that searches
  for a specific consensus sequence and returns all
  matches.

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Request Process

• Send us an email detailing your request,
  info_at_gchelpdesk.ualberta.ca
• Or phone us at 780-492-5969
• We usually reply within 1-2 days with a list of
  possible options
• We tailor the solution to your specific needs

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Testimonials

• "We look forward to telling other
  bioinformaticians about the wonderful stuff you
  guys have done." Bioinformatician, Genome BC
• "You've just made my day! Thanks so much for the
  advice. I can't tell you how much I appreciate
  it." Scientist, Health Canada
• "We are very impressed with the program and I
  know it will make our work much easier. Thank you
  for the great work." Research Assistant,
  Natural Resources Canada

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Contact Us

• Visit our web sitehttp//gchelpdesk.ualberta.ca
• Send us an emailinfo_at_gchelpdesk.ualberta.ca
• Give us a call 780 492-5969
• We are here to serve your bioinformatics needs

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• Bioinformatics
• Support
• Services
• Servers
• Software

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Acknowledgments

• The CBHD, as part of the Integrated and
  Distributed Bioinformatics Platform, is supported
  by Genome Prairie, in part through Genome Canada,
  a not-for-profit corporation which is leading a
  national strategy on genomics with 375 million
  in funding from the Government of Canada.

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Acknowledgments

• The University of Alberta
• My colleagues
• Dr. David Wishart
• Dr. Paul Stothard
• Dr. Gary Van Domselaar
• Xiaoli Dong
• Nelson Young
• Savita Shrivastava