Canadian Bioinformatics Help Desk Newsletter -- March 3, 2005

2) What's New?

3 Mar 2005	NCBI Coffee Break Tutorials - For researchers looking to become more familiar with the National Center for Biotechnology Information's (NCBI) tools, look no further than the NCBI Coffee Break Tutorials. This site is packed with some very informative tutorials that have one thing in common; they all involve NCBI's tools (PubMed, GEO, BLAST, LocusLink, SNPs database, Entrez, UniGene, etc). My favourite tutorials are the ones with Flash animations; these include: the GEO tutorial, the LocusLink tutorial, and the SNPs database tutorial. Make the NCBI Coffee Break tutorials a part of your next coffee break!
1 Mar 2005	Oncogenomics Normal Tissue Database - Researchers at the National Cancer Institute (NCI), part of the National Institutes of Health (NIH), have created the largest open-source database for normal tissue from human organs. This new database will serve as an important resource for the research community. Scientists that are looking at up- and down-regulation of various genes in diseased tissues will now be able to use the gene expression levels from this database as reference points for normal tissue. Featured in this database are expression profiles for 18,927 unique genes. This database has been published in the March 2005 issue of Genome Research. To access the database, visit http://ntddb.abcc.ncifcrf.gov/cgi-bin/nltissue.pl. To visit the new NCI web site, go to http://home.ccr.cancer.gov/oncology/oncogenomics/. Source: NIH News Release
22 Feb 2005	Blueprint Releases Latest Version of BIND - The Blueprint Initiative, led by Dr. Christopher Hogue of the Samuel Lunenfeld Research Institute of Toronto's Mount Sinai Hospital, released version 3.7 of its Biomolecular Interaction Network Database (BIND) that includes better browsing and searching features. According to the Blueprint press release, this latest version of BIND includes: "Tabbed search results, which are divided into interaction, complex, and pathway categories; OntoGlyph summaries, which provide researchers with a rapid view of what functional, binding, and subcellular localization features are associated with their query molecule; OntoGlyph search filtering, which allows researchers to focus their attention on molecules that fit within specific categories; Small-molecule browse upgrades that display key small molecule information such as LD50, logP values, and melting and boiling points; Taxonomy identifier searches, which allow researchers to focus their attention on molecules within a specific taxon; and BIND downloads interface, which makes it easier for users to access and download files from the BIND FTP site." Source: Blueprint Press Release

3) Upcoming Events

Bioinformatics Training

Canadian Bioinformatics Help Desk Seminar and Workshop - The Canadian Bioinformatics Help Desk will be presenting a brief seminar entitled "Bioinformatics Tools and Resources for the Life Science Researcher" at 2:00 p.m. on Friday, March 11, in 2F1.04 Walter Mackenzie Health Sciences Centre (Classroom D), 2nd floor, 8440-112 Street, University of Alberta. In this seminar, we will describe some of the bioinformatics tools and resources available to Canadian researchers through the Bioinformatics Platform for Genome Canada. Please join us for refreshments from 2:00 to 2:15 p.m. Following the seminar, there will be a free bioinformatics workshop from 3:00 to 5:30 p.m. in 2F1.02 Walter Mackenzie Health Sciences Centre Computer Lab, University of Alberta, limited to the first 19 registrants, that will explore in greater detail some of the bioinformatics tools and resources available to researchers in Canada. To reserve your spot in this workshop, please send an e-mail to Ian Forsythe at if@ualberta.ca with your name, title, department, and telephone number. For more information about the seminar, visit http://gchelpdesk.ualberta.ca/cbhd_workshop_ua_med/SeminarAnnouncement.pdf. For more information about the workshop, visit http://gchelpdesk.ualberta.ca/cbhd_workshop_ua_med/.

Applied Computational Genomics Course (ACGC) -The next Applied Computational Genomics Course (ACGC) will be held at the University of Calgary, in Calgary, Alberta, from Saturday, April 30th to Sunday, May 8th, 2005. For further details, please see the course announcement (http://gchelpdesk.ualberta.ca/training/acgc/ACGC_Calgary_Spring2005.php) or visit the course web page (http://www.gcbioinformatics.ca/ACGCSpring05.htm). Register by March 25, 2005, for a lower workshop rate!

Canadian Bioinformatics Workshops—Genomics - The Genomics Workshop will take place on May 2-7, 2005, in Calgary, Alberta (application deadline: passed). The workshop flyer is available here as a pdf. For other upcoming workshops, please visit http://www.bioinformatics.ca/workshops.php. Lecture notes for all four workshops (Bioinformatics, Developing the Tools, Proteomics, and Genomics) are freely available at http://www.bioinformatics.ca/workshops.php under a Creative Commons License. For further details about all Canadian Bioinformatics 2005 Workshops, see our Workshop Spotlight article from the December 16, 2004 issue of the newsletter.

BioneQ Workshop - The Quebec Bioinformatics Network (BioneQ) will be offering a Bioethics in Bioinformatics workshop on Thursday, March 24, 2005, from 9:30 a.m. to 5:00 p.m., in room 1035, Pav. Joseph-Armand Bombardier, Université de Montréal. For more information on previous workshops offered by BioneQ, visit the BioneQ home page at http://bioneq.qc.ca/.

Computational and Statistical Aspects of Microarray Analysis (Third Edition) - This five day course will be held on June 19-25, 2005, in Bressanone-Brixen, Italy and will focus on microarray experiments, covering statistical topics such as preprocessing, normalization, quality assessment, gene identification, machine learning and inference for graphs and networks. Applications of these methods to proteomics and other high throughput technologies will also be covered. Participants should have some minimal background in biological, statistical and computational aspects of microarrays, or other high-throughput data. Participants interested in hands-on, interactive activities should consider signing up for the lecture and laboratory series (space is very limited). These require a basic knowledge of the R or S language. An introductory R course will be given. The maximum number of participants is 100 for the morning lectures and 30 for the laboratory sessions. For further details, visit the course website: http://www.economia.unimi.it/marray/2005/

Bioinformatics Degree Programs

University of Toronto Introduces a New Specialist Program in Bioinformatics and Computational Biology - Bioinformatics and Computational Biology at the University of Toronto is a full, four year Specialist Program of Study, that is balanced between its foundational disciplines while covering advanced topics in both the theoretical and the life sciences. The program draws on the University of Toronto's state-of-the-art facilities across the Departments of Biochemistry, Computer Science, Botany and Zoology; as well, it is firmly embedded in a comprehensive landscape of world-leading graduate and postgraduate research in one of the University's priority areas. The Program aims to train the generalist, who will become creative at the intersection of two fields, rather than pursue their subspecialization. Accordingly introductory and advanced courses in mathematics, statistics and machine learning, computer science, molecular biology and genetics are included in the program, as well as specialized bioinformatics courses. Graduates will be well prepared to pursue graduate studies in any of the participating departments, or to apply their skills in research-oriented industry positions. For more information, visit http://biochemistry.utoronto.ca/bcb/

B.Sc., M.Sc. and Ph.D. Programs in Bioinformatics at the Université de Montréal - The Université de Montréal is offering undergraduate (B.Sc.) and graduate degrees (M.Sc. and Ph.D.) in Bioinformatics. For further details, visit http://www.bioinfo.umontreal.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.

Bioinformatics Meetings

	ISCB-Sponsored Conferences - There are many bioinformatics and computational biology related conferences that are sponsored by The International Society for Computational Biology. For a listing of ISCB-sponsored conferences, please visit http://www.iscb.org/events/event_board.php
28 Mar-1 Apr 2005	Structure-Based Drug Design & Virtual Screening - This conference, hosted by the Cambridge Healthtech Institute, will be held in Boston, Massachusetts from March 28 to April 1, 2005. For further details, visit http://www.iscb.org/events/event_data.php?207.
13-16 Apr 2005	The International Conference on Microbial Genomes will take place on April 13-16, 2005, in Halifax, Nova Scotia. As per the conference website (http://www.tigr.org/conf/mg2005/index2.htm), "Session topics will include metagenomics, population processes, comparative genomics, fungal genomics, genome evolution and environmental genomics."
18-21 Apr 2005	HUGO's 10th Human Genome Meeting will take place in Kyoto, Japan, on April 18-21, 2005. For more details, visit http://hgm2005.hgu.mrc.ac.uk/.
13-14 May 2005	The Fifth International Conference of the Canadian Proteomics Initiative (CPI) will take place on May 13-14, 2005, in Toronto, Ontario. This conference brings together experts in all areas of proteomics. According to the conference website, the areas of expertise include: "functional proteomics, structural proteomics, protein display, protein expression, protein chemistry and protein interactions". For more information, visit the conference website (http://www.pence.ca/CPI/). Please note that early bird registration has been extended to March 15, 2005 (http://www.pence.ca/CPI/index.php?registration).
23-24 June 2005	The 6th Annual Bioinformatics Open Source Conference (BOSC'2005) will take place on June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. For more information, visit http://open-bio.org/bosc2005/. Source: BOSC 2005 Web Site
25-29 June 2005	ISMB 2005 will take place on June 25-29, 2005, in Detroit, Michigan. ISMB (Intelligent Systems for Molecular Biology) is the "world's largest and oldest Bioinformatics Conference". For additional information, visit http://www.iscb.org/ismb2005/
11-14 Sep 2005	PBC'05, Workshop on Parallel Bio-Computing - This workshop will take place on September 11-14, 2005, in Poznan, Poland, in conjunction with the Sixth International Conference on Parallel Processing and Applied Mathematics PPAM 2005 (http://ppam.pcz.pl). Topics of interest include: Bioinformatic databases; computational genomics and proteomics; DNA assembly, clustering, and mapping; parallel algorithms for biological analysis; parallel architectures for biological applications; system tools that support large scale high-performance bio-computing; molecular sequence analysis; phylogeny reconstruction algorithms; protein structure prediction and modeling. Papers can be submitted online by visiting http://icis.pcz.pl/~zola/pbc05/submit/. Source: Bioinformatics.Org

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 64 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 free resource. Downloads are encouraged and submissions are always welcome. Please visit our software repository at http://gchelpdesk.ualberta.ca/repository/ and our recently created web servers page at http://gchelpdesk.ualberta.ca/servers

Attention all programmers — we encourage you to submit your favourite bioinformatics software or web server to the Help Desk.

If you would like to deposit software into the software repository or bring any bioinformatics web servers to our attention, please email Ian Forsythe (ianf@cs.ualberta.ca). To deposit software now, please visit http://www.gchelpdesk.ualberta.ca/repository/SubmitRealSoftware.php

Recent Addition to the Software Repository — remove_x.pl

This Perl script reads multiple sequence files in FASTA format from a file and removes X's and x's from the sequences. Any sequences less than $MIN_SIZE bases are not written out. The resulting files are written to an output file. There are two command line options: -i input file -o output file Example usage: perl remove_x.pl -i my_sequences.txt -o my_output.txt. This script was written by Paul Stothard, Canadian Bioinformatics Help Desk Bioinformatician. To view the repository entry for this script, please visit http://gchelpdesk.ualberta.ca/repository/VersionDetails.php?fileId=67&submissionId=49.

5) Bioinformatics Jobs

This is a resource for advertising positions in bioinformatics or computational biology. If you have a job you would like posted in this newsletter, please send an email to curators@bioinformatics.ca. 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
Bioinformatics Support Officer	Montréal, PQ	February 28, 2005
Bioinformatics Programmer	Victoria, BC	February 22, 2005
Java Developer	Montréal, PQ	February 21, 2005
Bioinformatics (Faculty Position)	Montreal, PQ	February 15, 2005
Software Developers (2)	Calgary, AB	February 4, 2005
Canada Research Chair in Bioinformatics	Ottawa, ON	January 30, 2005
Database Programmer	Vancouver, BC	January 25, 2005
Bioinformatics Analyst	Montreal (St-Laurent), PQ	January 24, 2005
Postdoctoral Fellows in Bioinformatics and Network Biology	Montreal, PQ	January 18, 2005
Assistant Professor	Ottawa, ON	January 17, 2005
Molecular Database Curators at Blueprint Asia	Toronto, ON	January 6, 2005
Biostatistician - Fungal Genomics Project	Montreal, PQ	January 5, 2005

Source: http://www.bioinformatics.ca/jobs (except for the Blueprint Asia position)

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, training sessions, and degree programs via our biweekly newsletter.
Deposit software into our Bioinformatics Software Repository.
Visit our registration web page to register now.

Free Subscription

To start your free subscription to this newsletter, send an email message to ianf@cs.ualberta.ca with the word "subscribe" in the subject or body of your message. Please forward this newsletter to any interested colleagues or collaborators. Please send your comments and feedback about this newsletter to ianf@cs.ualberta.ca

Ian J. Forsythe, M.Sc.
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: ianf@cs.ualberta.ca
Website: http://gchelpdesk.ualberta.ca

The Canadian Bioinformatics Help Desk, 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.


CBHD Newsletter Issue 34 - March 3, 2005	CONTENTS: Software Spotlight Gearing up for Bioinformatics What's New? NCBI Coffee Break Tutorials Oncogenomics Normal Tissue Database Blueprint Releases Latest Version of BIND Upcoming Events Bioinformatics Training CBHD Seminar and Workshop Applied Computational Genomics Course (ACGC) Canadian Bioinformatics Workshops—Genomics Bioinformatics Degree Programs Bioinformatics Meetings CPI 2005 ISMB 2005 Software Repository Call for Submissions Deposit Software Recent Addition — remove_x.pl Bioinformatics Jobs CBHD Registration Free Subscription
Online version of this newsletter: http://gchelpdesk.ualberta.ca/news/03mar05/cbhd_news_03mar05.php