QSAR - Canadian Bioinformatics Help Desk Newsletter -- April 1, 2004

Figure 1. The Chinook user interface. Bioinformatics services are discovered and submitted from this interface.

From a service perspective, Chinook allows a service provider to create and advertise a new service by simply editing an XML file and starting a Tomcat server; as long as the new service has a standard output format, no additional programming is required.

Chinook also publishes a mid-level API that has been integrated into the Sockeye Comparative Genome Browser to enable Sockeye to access a wide range of dynamically-updated bioinformatics functionalities. Access to Chinook-hosted services can be integrated into any Perl or Java application via the command-line or through Chinook's default user interface. Ongoing effort is underway to integrate the Chinook API into the OrthoSeq project at the Wasserman Lab in Vancouver (CMMT). If you have a software project that would benefit from integrating diverse bioinformatics services, e-mail chinook-#-bcgsc.bc.ca.

Figure 2. Chinook in Sockeye. Job results from an alignment analysis submitted through Chinook are formatted and displayed in 3D in Sockeye.

While Chinook is fully-functional, further development is ongoing to ensure its ease of use. Mailing lists and further project information can be found at http://smweb.bcgsc.bc.ca/chinook.htm. A web-start accessible Chinook client is available from the Chinook homepage. For source distributions, please contact smontgom]_[bcgsc.bc.ca directly. An anonymous CVS and downloadable distributions will be available soon from the website. Chinook is open-source and has recently been selected to win an award for the BCNET Coolest Application contest (presented at the BCNET Advanced Networks Conference).

Chinook currently supports: LAGAN, mLAGAN, ClustalW, Smith-Waterman, T-Coffee, DIALIGN, Orca, Promoterwise, Teiresias, Lawrence Gibbs Sampler, Elph, and NCC. More algorithms are being added weekly. (Global access is prevented to some of these applications where licensing restrictions prevent redistribution).

2) What's New?

31 Mar 2004	Rat Genome Sequenced - The Rat Genome Sequencing Project Consortium announced that it has completed "a high-quality, draft sequence" of the genome of the Brown Norway strain of the laboratory rat (Rattus norvegicus). This work was published in the April 1 issue of Nature.  Source: NIH News Advisory
24 Mar 2004	Large Scale Sequencing Database - The International Sequencing Consortium (ISC) has launched a large scale sequencing database. Using this free, online resource, scientists and members of the public can now access information about the status of their favorite genomic sequencing projects by visiting ISC's home page, intlgenome.org. ISC's database allows users to sort various sequencing project information by organism, sequencing group, or funding agency.  Source: NIH News Advisory
23 Mar 2004	$60M to Genome Canada - The Government of Canada recently announced the next federal budget. Genome Canada will receive $60M. Dr. Martin Godbout, President & CEO of Genome Canada, offered these comments about the Government's new budget, "The Canadian Government is sending a clear message: that Canada is and will continue to be an international player in the field of genomics and proteomics research."  Source: Genome Canada Press Release
10 Mar 2004	Java APIs for Bioinformatics - Stephen Montgomery, a graduate student at Canada's Michael Smith Genome Sciences Centre in Vancouver, BC, recently wrote this O'Reilly ONJava.com article about Java APIs for bioinformatics. This article includes sections on: BioJava, caBio (Cancer Bioinformatics Infrastructure Objects), ENSJ (Java implementation of the EnsEMBL driver and data adaptors), Phylogenetic Analysis Library (PAL), and other miscellaneous Java APIs for bioinformatics. Last year, Stephen wrote another ONJava.com article entitled Java for Bioinformatics. Here is another Stephen Montgomery article on Java vs. Perl for Bioinformatics? Source: O'Reilly ONJava.com

3) Upcoming Events

BIOINFORMATICS TRAINING

CBRi Interdisciplinary Workshop: Bioinformatics for Proteomics - The Canadian Bioinformatics Resource for Industry (CBRi) presents a two-day course entitled "Interdisciplinary Workshop: Bioinformatics for Proteomics" to be held in Burnaby, BC, on April 15-16, 2004, at 9 AM - 6 PM. This hands-on course will provide participants the ability to use bioinformatics software for proteomic analysis and the study of protein structure. Space is limited, so register early! To view the flyer for this course, that includes a registration form, click here. For more information, please visit http://www.vitesse.ca/programs/bioinfo_proteomics.asp

Applied Computational Genomics Course - The next ACGC will be held in Winnipeg, Manitoba, on June 12-20, 2004. Early bird registrations must be received before May 1, 2004. For more information, see an earlier Bioinformatics Profile article or visit the course web page. To register now, please visit the registration page.

Canadian Bioinformatics Workshops - In 2004, the CBW will be offering two remaining bioinformatics workshops on: 1. Proteomics (Deadline: May 22, 2004), and 2. Genomics (Deadline: June 19, 2004). These courses may count toward a Certificate in Bioinformatics. For further details, please visit http://www.bioinformatics.ca/workshops.php

BioneQ's Courses and Workshops - BioPerl Bootcamp will be held on June 21-25, 2004. BioneQ offers a variety of courses and workshops in bioinformatics. Here are some of the other courses and workshops that they offer: LIMS Workshop, EST Clustering Workshop, Workshop on Analysis of Expression Data, BASE Demo Installation, and Biojava Bootcamp. For further details, please visit their web site at http://www.bioneq.qc.ca

Training Program in Bioinformatics for Health Research - A bioinformatics training program, leading to a post-graduate diploma, M.Sc., or Ph.D., is offered through a partnership between the BC Cancer Agency, Simon Fraser University and the University of British Columbia. For more information, visit http://bioinformatics.bcgsc.ca

Cold Spring Harbor Laboratory (CSHL) is offering special 2 day courses and fall courses. The deadline for the fall courses is July 15, 2004. For more information, please visit http://meetings.cshl.org/2004/2004courses.htm


BIOINFORMATICS MEETINGS

12-16 May 2004	2004 CSHL Meeting on The Biology of the Genomes - This meeting will take place in Cold Spring Harbor on May 12-16, 2004. For further details, please visit http://meetings.cshl.org/2004/2004genome.htm
14-16 May 2004	CPI 2004, Montreal, Canada - The Fourth International Conference of the Canadian Proteomics Initiative (CPI) will be held in Montreal, Canada, on May 14-16, 2004. The CPI 2004 tutorials will take place on May 17-18, 2004. Registration closes on April 13, 2004. For more information, visit http://www.pence.ualberta.ca/CPI/index.php?home
20-22 May 2004	Biotech China 2004 - "Biotech China 2004 is an international, multidisciplinary conference designed to offer critical perspectives on the current status and future of cutting-edge genomic technologies such as RNAi, systems biology, functional genomics, proteomics and microarray." For more information, please visit http://www.biotechcn.com/
28-30 June 2004	JOBIM 2004 - The Fifth International Conference on Biology, Computer Science and Mathematics (Journées Ouvertes de Biologie, Informatique et Mathématiques) will take place in Montreal, Quebec, at the Mont Royal Centre, on June 28-30, 2004. This annual meeting is for bioinformaticians, biologists, mathematicians, computer scientists, physicists, and others who are interested in the analysis, comparison, and use of genomics and post-genomics data. For further details, please visit the conference home page http://www.congresbcu.com/jobim2004/en/default_eng.htm
31 Jul-4 Aug 2004	ISMB/ECCB 2004 - "In 2004—for the first time ever—Intelligent Systems for Molecular Biology (ISMB) will be held jointly with the European Conference on Computational Biology (ECCB), in conjunction with Genes, Proteins and Computers VIII" on July 31-August 4, 2004, in Glasgow, UK. Registration opens March 1, 2004. The poster submission deadline is April 19, 2004. For a list of key dates, please visit http://www.iscb.org/ismbeccb2004/keydates.html. For further details, please visit http://www.iscb.org/ismbeccb2004/
16-19 Aug 2004	CSB2004 - "The 3rd annual Computational Systems Bioinformatics conference, CSB2004, is being organized once again by the IEEE Computer Society Technical Committee on Bioinformatics under the theme—Systems Bioinformatics." This conference will be held in Stanford, California, USA. The poster submission deadline is May 17, 2004. Pre-conference tutorials will be held on August 16, 2004. Post-conference half-day workshops will be held on August 20, 2004. For more information, please visit the conference web page: http://conferences.computer.org/bioinformatics/
23-27 Aug 2004	ECAI 2004 - The 16th European Conference on Artificial Intelligence (ECAI) will be held in Valencia, Spain, on August 24-27, 2004. On August 23, 2004, there will be a workshop entitled, "Data Mining in Functional Genomics and Proteomics: Current Trends and Future Directions" (http://www.softwareresearch.ca/ecai-bio/index.html). For further details, please visit the conference web site at http://www.dsic.upv.es/ecai2004/

4) Help Desk Software Repository

The Help Desk software repository is where researchers may upload or download bioinformatics programs of interest. Currently the repository has 51 programs. These are freeware packages that are available for anyone to download and install on their own computer. Many of the programs in the Help Desk repository have been thoroughly tested and a number have been published as research articles. Please take advantage of this resource. Downloads are encouraged and submissions are always welcome. The repository can be found at: http://gchelpdesk.ualberta.ca/repository/

Attention all programmers—we encourage you to submit your favourite bioinformatics software to the Help Desk Software Repository.

Please email Ian Forsythe (ian:-:gchelpdesk.ualberta.ca) if you would like to deposit software into the software repository. To deposit software now, please visit http://www.gchelpdesk.ualberta.ca/repository/SubmitRealSoftware.php

fetch_swissprot_using_id.pl —Our latest addition to the Software Repository

Paul Stothard, CBHD Bioinformatician, recently added this new Perl script to the Software Repository. The script accepts a list of Swiss-Prot IDs and automatically fetches the corresponding sequences and sequence titles from ExPASy. For further details, please visit http://gchelpdesk.ualberta.ca/repository/VersionDetails.php?fileId=53&submissionId=38

5) Bioinformatics Jobs

This is a resource for advertising positions in bioinformatics and computational biology. If you have a job you would like posted in this newsletter please email curators a bioinformatics.ca directly. Job postings will be carried for a maximum of 4 issues (8 weeks) unless the position is filled prior to that date.


Genome Canada is advertising several positions. Check out their career brochure (http://www.genomecanada.ca/GCmedia/CareerOpportunities.pdf) and their latest job postings (http://www.genomecanada.ca/GCcarriere/index.asp?l=e).

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Job Title	Location	Date Posted
Numerous positions at the Genome Sciences Centre	Vancouver, BC	March 31, 2004
Microbiology Co-op	Ottawa, ON	March 24, 2004
Bioinformaticians [doc] [pdf]	Sherbrooke, PQ	March 18, 2004
Tenure Stream Assistant Professor	Toronto, ON	March 3, 2004
SHARCNet Chair in Bioinformatics	London, ON	March 2, 2004
NSERC Industrial Research Chair in Biomedical Mass Spectrometry	Winnipeg, MB	March 2, 2004
Position in functional genomics	Quebec, PQ	February 26, 2004
Postdoctoral position	Montreal/Quebec City, PQ	February 23, 2004
BIOINFORMATICS ANALYST	Montreal (St-Laurent), PQ	February 23, 2004
DNA Sequence Finisher, RAII	Vancouver, BC	February 16, 2004
Molecular Database Curators and other positions at Blueprint	Toronto, ON	February 5, 2004
Postdoctoral position in statistical and evolutionary bioinformatics/phylogenetics	Halifax, NS	February 4, 2004
Future positions: Bioinformatics, molecular microbiology, and genomics	Burnaby, BC	Starting in 2004-2005

Source: http://www.bioinformatics.ca/jobs except for the Genome Sciences Centre positions, Bioinformaticians positions (Sherbrooke), other positions at Blueprint, and future positions

6) CBHD Registration

WHY REGISTER?

Registering with the Canadian Bioinformatics Help Desk benefits both you and us.

Benefits include:

• Add your contact information to our Directory of Canadian Researchers, facilitating communication and collaboration with other Canadian researchers.
• Receive updates about bioinformatics software, news, events, conferences, and training sessions via our biweekly newsletter.
• Deposit software into our Bioinformatics Software Repository.
• Visit our registration web page to register now (http://www.gchelpdesk.ualberta.ca/user/register.php).

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Ian J. Forsythe, MSc Bioinformatician Canadian Bioinformatics Help Desk University of Alberta Department of Biological Sciences, CW 405 Edmonton, AB Canada T6G 2E9 Phone: (780) 492-5969 Fax: (780) 492-9234 Email: ian^^gchelpdesk.ualberta.ca Website: http://gchelpdesk.ualberta.ca

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