Date: Thu, 18 Mar 2004 18:22:56 -0700
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| CBHD
Newsletter Issue 10 - March 18, 2004  |
CONTENTS:
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http://gchelpdesk.ualberta.ca/news/18mar04/cbhd_news_18mar04.php
| Welcome to the tenth issue of the Canadian Bioinformatics Help Desk (CBHD) Newsletter. Back issues of this newsletter can be viewed at our newsletter archive site (http://gchelpdesk.ualberta.ca/news/news.php). Our circulation base has reached 1080 subscribers. In this issue's Bioinformatics Profile, we feature an article on Bioinformatics.ca. This issue's Spotlight article is a Workshop Spotlight on the upcoming Canadian Proteomics Initiative (CPI) 2004 Workshops. This biweekly newsletter is intended to keep Genome Canada researchers and other Help Desk users informed about new software, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning bioinformatics, genomics, and proteomics. The CBHD newsletter is a mandated service of the Help Desk and we hope to provide enough useful content to keep you interested and informed. If you know of anyone who would be interested in receiving future issues of this newsletter or contributing content to the newsletter, please email us at ian*gchelpdesk.ualberta.ca. To subscribe to this newsletter, click here. To unsubscribe from this newsletter, send an email message to ian _ gchelpdesk.ualberta.ca with the word "unsubscribe" in the subject line or body of the message. |
 1) Bioinformatics Profile |
Resources,
Jobs, and Training for
Bioinformatics Research in CanadaFeature article contributed by Joanne Fox (joanne^bioinformatics.ubc.ca), Stefanie Butland, Scott McMillan, Graeme Campbell, and Francis Ouellette (UBC Bioinformatics Centre, http://bioinformatics.ubc.ca) What is bioinformatics.ca?
bioinformatics.ca (http://bioinformatics.ca) is the home page for the Canadian Bioinformatics Workshop series (see Figure 1). Since its inception in the summer of 1999, bioinformatics.ca has become a valuable resource for Canadian researchers looking for information about current research, available jobs, qualified personnel, bioinformatics tools, and training opportunities in bioinformatics. The bioinformatics.ca web site now receives over 300 visitors daily. All content on bioinformatics.ca is developed and maintained by Francis Ouellette's group at the UBC Bioinformatics Centre (UBiC, http://bioinformatics.ubc.ca). bioinformatics.ca is supported by UBiC and the Canadian Genetic Diseases Network (CGDN, http://www.cgdn.generes.ca/).
Figure 1. Home page of bioinformatics.ca (http://bioinformatics.ca). Online resources for bioinformatics training, jobs, and research in Canada.
Training
Opportunities in Bioinformatics—The Canadian Bioinformatics
Workshop Series
bioinformatics.ca is the home of the Canadian Bioinformatics Workshops (CBW), a series of short courses designed to develop Canadian expertise in bioinformatics. The CBW courses to be held in 2004 include the two week Bioinformatics workshop, completed this February in Vancouver, as well as Developing the Tools (May 3-9, 2004 in Montreal), Proteomics (July 19-24, 2004 in Calgary), and Genomics (August 16-21, 2004 in Vancouver). Interested applicants should check the closing dates for application to these workshops on bioinformatics.ca. Up to date course content including lecture notes, slides, and supplementary information, is now hosted live on bioinformatics.ca. The content for the latest of Bioinformatics workshop can be found at http://www.bioinformatics.ca/workshop_pages/bioinformatics2004_vancouver/ and includes open access to all of the teaching material (PowerPoint and PDF files, useful links, and additional reading). The CBW series and the online course content are extremely valuable educational resources in bioinformatics. bioinformatics.ca also contains information on other training opportunities such as course and program listings for bioinformatics in Canada.
Community
Resources for Bioinformatics in Canada
bioinformatics.ca
offers several resources to connect people involved in the
Canadian bioinformatics community. The People page
(http://www.bioinformatics.ca/people/)
contains a searchable listing
of principal investigators and group leaders who have an interest in
the development of bioinformatics research, resources, and/or
teaching in Canada. This listing includes practitioners as well as
developers of algorithms, databases, or resources for bioinformatics.
Principal investigators and group leaders from academia, government
labs and industry in the bioinformatics field, are encouraged to
contact curators a bioinformatics.ca
to be added to this listing.
bioinformatics.ca has a very popular Jobs page (http://www.bioinformatics.ca/jobs/) which is regularly profiled in the Canadian Bioinformatics Help Desk Newsletter. The Jobs page advertises Canadian academic, government and industry positions, as well as international post-doctoral fellowships, graduate schooling, and co-op programs. In keeping with the bioinformatics.ca mission of promoting a strong Canadian bioinformatics community, professional/occupational postings are limited to those within Canada. Reflecting the popularity of this page, the Jobs page on bioinformatics.ca is one of the top hits of a Google search for "bioinformatics jobs". The Jobs page is a valuable resource for Canadian researchers and companies who would like increased exposure for attracting highly qualified personnel. Employers can post opportunities by creating an account on the Jobs page. The content on the Jobs page is also available for syndication so that you can have the bioinformatics.ca job postings on your homepage. The Jobs page also includes a new feature called the Jobs Alert Mailing List where you can subscribe to receive information by email about new job postings.
The Bio Weblog (http://bioinformatics.ca/weblogs/) is a new way of sharing tidbits of interesting bioinformatics related news items on the web. Weblogs are a shared on-line journal where many people can post items for others to read. The bioinformatics.ca Bio Weblogs are written by researchers at UBiC, cover current topics in bioinformatics, and are read by researchers worldwide. Direct feeds of the Bio Weblogs are available for syndication and are distributed to many sources including automated news readers. The Bio Weblog also offers a unique way that we can highlight Canadian bioinformatics news and research. You can also obtain the syndicated feed for the Bio Weblog (see Bio Weblog page for instructions) to keep up-to-date with new bioinformatics.ca Bio Weblogs. If you have an idea for an item that should be featured in the Bio Weblog (or would like to become a Bio Weblogger), you can contact curators^bioinformatics.ca.
Resources
for Bioinformatics Research
The Links Directory facilitates finding bioinformatics resources relevant to your research. The Links Directory contains a searchable directory of selected bioinformatics links, molecular resources, tools, and databases (see Figure 2).
Figure 2. Top Level Listings of the Links Directory on bioinformatics.ca (http://bioinformatics.ca/links_directory). Links are organized from a biologist's perspective, helping researchers find relevant links quickly. The Links Directory is actively maintained by researchers at UBiC and by the bioinformatics community.
With the interdisciplinary and collaborative nature of many modern bioinformatics research projects, the strength of the bioinformatics community in Canada will emerge as an advantage. The team of bioinformaticians developing and maintaining bioinformatics.ca plans to strongly encourage and facilitate communication between and about researchers involved in developing and using bioinformatics resources in Canada. You can contribute to bioinformatics.ca: By posting jobs on the Jobs page, by suggesting links for the Links Directory, by suggesting interesting Bio Weblog features, by sending us information on bioinformatics courses offered at your institution, and by suggesting people who should be included on the People page. Please send your suggestions to curators::bioinformatics.ca. With your input and efforts from the curators team, bioinformatics.ca will remain a valuable resource for bioinformatics researchers in Canada.
 2) Workshop Spotlight
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Canadian Proteomics
Initiative 2004 Workshops Feature article contributed by Lorin Charlton (lorin.charlton_._pence.ca)
The Canadian Proteomics Initiative (CPI), to be held on May 14-16 in Montreal, provides a general forum for disseminating the latest developments in proteomics and protein chemistry. As part of it's educational mandate, CPI offers three post-conference workshops on May 17 and 18. Registration is limited to 20 students per workshop. For more information, please visit the PENCE web site (http://www.pence.ca/CPI/index.php?tutorials).
1. The Bioinformatics for Proteomics Workshop
The Bioinformatics for Proteomics Workshop offers a wide variety of topics and subjects including: sequence alignment, protein feature identification, sequence analysis, math and statistics for bioinformatics, visualization and homology modeling, threading, structure assessment, and proteome annotation. Different types of software packages and web programs will also be introduced. To see the full schedule for this workshop, please visit http://www.pence.ualberta.ca/CPI/index.php?bioinfo_schedule
2. The Protein-Protein Interactions Workshop
The Protein-Protein Interactions workshop consists of 4 half-day sessions, including enzyme complementation, tandem affinity purification, BiaCore analysis, and bioinformatic analysis.
3. The Practical Proteomics Workshop
The Practical Proteomics workshop provides a theoretical background in modern proteomics techniques, including the separation of protein mixtures by 2D gel electrophoresis, in-gel digestion, mass spectrometric analysis by peptide mass fingerprinting and peptide sequencing, and database searches for protein identification. To see the schedule for this workshop, please visit http://www.pence.ualberta.ca/CPI/index.php?proteom_schedule
For more information on any of these tutorials, please email Lorin Charlton (lorin.charlton(!)pence.ca). To register for a tutorial, please visit http://www.pence.ualberta.ca/CPI/tutorialregist.htm
3) What's New?
17 Mar 2004
LION bioscience and
EBI Renew and Expand Their Ties - Bioinformaticians worldwide
will benefit from the expanded relationship between LION bioscience and
the EMBL-European Bioinformatics Institute (EBI). According to a March
17 Business Wire news release, "The SRS server at EBI will be set up to
be the public reference server worldwide." Source: Business
Wire
15 Mar 2004
Corn
Genome Mapping Five Years Ahead of Schedule - Monsanto Co.,
Pioneer
Hi-Bred International Inc. and Ceres Inc. will combine forces to map
the corn genome by as early as 2007. Source: Reuters
01
Mar 2004
Machine Learning
Algorithm Available Online - Researchers at Columbia
University and the University of Washington have recently published a
paper in Bioinformatics about a support vector machine (SVM) learning
algorithm that they have made available to the public via a web
interface. As the authors wrote in the Bioinformatics article, "This
interface allows novice or occasional users to apply a sophisticated
machine learning algorithm easily to their data." Source: Bioinformatics
10 Nov 2003
Bioinformatics
Toolbox for MATLAB - The
MathWorks Inc. announced the release of a new bioinformatics toolbox
built on MATLAB. According to the MathWorks press release, "The product facilitates
the analysis of complex bioinformatics data, from genomic sequences to
microarray data analysis, and speeds up the development and deployment
of algorithms." For more
information on this product, please visit The MathWorks product page (http://www.mathworks.com/products/bioinfo/).
Source:
The
MathWorks press release
BIOINFORMATICS TRAINING
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 last issue's Bioinformatics
Profile
article or visit the course
web 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 a special 2 day course,
summer, and fall courses. The deadlines for summer and fall
courses are March 15, 2004
and July
15, 2004,
respectively. 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. The
deadline for abstracts is March
15, 2004. Registration closes
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/
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/
16-20 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
deadline for the submission of papers is March 22, 2004.
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 Aug 2004
ECAI 2004 -
The 16th European Conference on
Artificial Intelligence (ECAI) will be held in Valencia, Spain. 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).
The deadline
for
the submission of papers is March 31, 2004.
For further details,
please visit the conference web site at http://www.dsic.upv.es/ecai2004/
5)
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
6)
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).
| Job Title | Location | Date Posted |
| Bioinformaticians [doc] |
Sherbrooke, PQ |
March 18, 2004 |
| Bioinformatician | Toronto, ON |
March 11, 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 |
| Database
Administrator; Chemistry
Database Curators [details] |
Toronto, ON | February 26, 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 |
Toronto, ON |
February 5,
2004 |
| Postdoctoral
position in statistical and evolutionary bioinformatics/phylogenetics |
Halifax, NS | February
4, 2004 |
| Curators |
Montreal,
PQ |
January 30, 2004 |
| Application
Scientists (Part Time) |
Calgary,
AB |
January
26, 2004 |
| Gene
Expression Research Associate (plus numerous other
positions
at the Genome Sciences Centre) |
Vancouver, BC | January
26, 2004 |
| Computational
Biology
position (Assistant/Associate Professor tenure track) |
Hamilton, ON | January 24, 2004 |
| Future
positions: Bioinformatics, molecular microbiology, and genomics |
Burnaby,
BC |
Starting
in 2004-2005 |
Source: http://www.bioinformatics.ca/jobs except for the Bioinformaticians (Sherbrooke), Data Administrator, Chemistry Database Curators, Computational Biology tenure track, and future positions
 7) 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).
Free Subscription
To start your free subscription to this newsletter, send an email message to ian===gchelpdesk.ualberta.ca with the word "subscribe" in the subject line or body of the message. Please forward this newsletter to any interested colleagues or collaborators. We appreciate your comments; send your comments and feedback about this newsletter to ian(_)gchelpdesk.ualberta.ca
|
Ian J.
Forsythe, MSc
Phone: (780)
492-5969Bioinformatician Canadian Bioinformatics Help Desk University of Alberta Department of Biological Sciences, CW 405 Edmonton, AB Canada T6G 2E9 Fax: (780) 492-9234 Email: ian_+_gchelpdesk.ualberta.ca Website: http://gchelpdesk.ualberta.ca |
The
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