CBHD Newsletter Issue 9 - March 4, 2004 |
CONTENTS:
|
Welcome to the ninth issue of the Canadian Bioinformatics Help Desk (CBHD) Newsletter. Back issues of our newsletter can be viewed at our newsletter archive site (http://gchelpdesk.ualberta.ca/news/news.php). Our circulation base has reached 1070 subscribers. In this issue's Bioinformatics Profile, we feature an article on Faster, Higher, Stronger Sequence Database Searches—homology detection with higher scores and stronger evidence. In our Commercial Software Spotlight we feature Phoretix 1D, a 1D gel image analysis tool, distributed in Canada by United Bioinformatica Inc. 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(a)gchelpdesk.ualberta.ca with the word "unsubscribe" in the subject line or body of the message. |
1) Bioinformatics Profile |
Sequence types | Search Method | Machine |
DNA/protein | BLAST/PSI-BLAST | BlastMachine |
TeraBLAST | Decypher | |
ESTs vs. genomic | GeneBLAST | Decypher |
Smith-Waterman, semi-global | GeneMatcher | |
ESTs vs. protein | S-W Frame | GeneMatcher |
DNA/protein vs. HMMs | HMM Search | Decypher |
ESTs vs. HMMs | HMM Frame Search | Decypher |
HMMs vs. genomic | GeneWise | Genematcher |
2) Software Spotlight |
In the rapidly
changing world of molecular biology high throughput analysis is a fact
of life. As a result there is a need for a powerful,
comprehensive, and user friendly gel analysis software. The
answer
to this requirement is Phoretix 1D Advanced, by Nonlinear Dynamics.
Phoretix 1D is a complete 1D gel analysis package capable of analyzing
any gel (DNA or protein) separated in a single dimension including
PCR-based procedures (AFLP and RAPD), RFLP, SSCP, immunoblots, protein
purification, and the analysis of post-translational
modifications. Phoretix 1D is a highly automated, user friendly,
accurate software
package that provides the user with endless list of analysis
applications.
This software is capable of:
Phoretix 1D is also
available in a professional package (Phoretix 1D Pro) that couples the
power of Phoretix 1D with a database that allows the user to create
multiple libraries enabling the analysis of large cross-gel studies and
projects.
If you are
involved in any 1D gel-based projects and require an accurate,
reliable
and user friendly tool for the analysis and management of your data
then
Phoretix 1D Advanced or Professional should be your package of
choice. For further information, trials, etc., please contact the
Canadian distributor, UBI, at 866 202
2100, or by email at info^^ubi.ca
3)
What's New? |
01 Mar 2004 | Proteome Analyst
Subcellular
Localization Paper - Dr.
David Wishart, Director of the CBHD, along with other researchers in
the Department of Computing Science at the University of Alberta,
recently co-authored a paper that appeared in the March 1 issue of Bioinformatics [ABSTRACT]
[PDF].
If you missed our Bioinformatics Profile article on the Proteome Analyst
Subcellular Localization Prediction Server, please visit http://gchelpdesk.ualberta.ca/news/22jan04/cbhd_news_22jan04.php#profile |
01 Mar 2004 | Chicken Genome
Assembled - The
first draft of the chicken genome sequence has been deposited into free
public databases around the world. This assembly of genomic sequence
data from the Red Jungle Fowl (Gallus
gallus), ancestor of domestic chickens, represents the first
avian genome to be sequenced. To read the NIH News Advisory, please
visit http://www.nhgri.nih.gov/11510730 |
25 Feb 2004 | 2004 Benjamin
Franklin Award in Bioinformatics - The
Bioinformatics Organization, Inc. (Bioinformatics.Org) will present the
2004 Benjamin Franklin Award in Bioinformatics to Lincoln D. Stein of
Cold Spring Harbor Laboratory for his "creation
of a great number of open-source bioinformatics programs and for
championing open-source principals in many venues..." For the
Bioinformatics.Org press release, please visit http://bioinformatics.org/forums/forum.php?forum_id=2516 |
19 Feb 2004 | Genome War -
James Shreeve has written a new book, The
Genome War: How Craig Venter tried to capture the code
of life and
save the world, chronicling the ins and outs of daily life at
Celera
Genomics during the race to sequence the human genome. For a good
introduction to this book, check out Kevin Davies' recent Around the
Bases feature article from BioIT World. |
18 Feb 2004 | Search for Complex
Genes -
This Bio-IT World article describes some of the "tricks of the trade",
old and new, that are being used by researchers to track down "genes
for complex diseases" (http://www.bio-itworld.com/archive/021804/genes.html). |
18 Feb 2004 | Continued Need for
Bioinformatics -
Analysts at Navigant Consulting believe that the need for
bioinformatics analytical software in the Pharmaceutical and
Biotechnology sectors will not go away over the next five years. Source: http://businesswire.com |
16 Feb 2004 | Bioinformatics
Software in Academia - There
is an abundance of bioinformatics software in academia. However, in
some cases, some projects have never been completed or they contain
outdated code. One dilemma that many academics face—resurrect the
legacy code, start from scratch, or abandon it altogether. Here is an
interesting article from The Scientist on this subject (http://www.the-scientist.com/yr2004/feb/prof2_040216.html). |
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." The deadline for acceptance of
oral presentations has been extended to March 10, 2004.
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 |
6) Bioinformatics Jobs |
Job Title | Location | Date Posted |
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 |
BIOINFORMATICS
SOFTWARE SPECIALIST |
Montreal
(Saint-Laurent), PQ |
February 19, 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 additional
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 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:
Bioinformatician
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.caThe
CBHD is sponsored by:
This archive was generated by hypermail 2.2.0 : 2005-11-24 - 10:21 GMT