QSAR - Canadian Bioinformatics Help Desk Newsletter -- December 2, 2004

From: ian] <ian]|[redpoll.pharmacy.ualberta.ca>
Date: Fri, 3 Dec 2004 16:50:04 -0700





  Canadian Bioinformatics Help Desk Newsletter -- December 2,
2004
  
  
  
  
  
  
  
  
  


Help Desk News Banner Bioinformatics Platform: A GenomePrairie Project
CBHD Newsletter
Issue 28 - December 2, 2004
CBHD Splash Image

       CONTENTS:
Online version of this newsletter:
http://gchelpdesk.ualberta.ca/news/02dec04/cbhd_news_02dec04.php

Welcome to the twenty-eighth issue of the Canadian Bioinformatics Help Desk (CBHD) Newsletter. Back issues of this newsletter can be viewed from our newsletter archive (http://gchelpdesk.ualberta.ca/news/news.php). Our circulation base has recently exceeded 1400 subscribers. In this issue we feature a Software Spotlight article on the release of Chinook version 1.0 from Canada's Michael Smith Genome Sciences Centre. 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, contributing content to the newsletter, submitting useful scripts or applications to the Help Desk Software Repository, or bringing new bioinformatics web servers to our attention, 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 or body of your message.

Software Spotlight Icon1) Software Spotlight

Feature article contributed by Stephen Montgomery, Canada's Michael Smith Genome Sciences Centre

Chinook Icon
Chinook 1.0 Released

Chinook Contributors: Stephen Montgomery, Tony Fu, Jun Guan, Keven Lin, Steven Jones

Chinook is a peer-to-peer software system for bioinformatics analysis developed at the BC Genome Sciences Centre. It has recently reached v1.0 status. Using Java, Chinook allows bioinformaticians to turn their command line scripts and utilities into Web Services that are advertised over the Internet. Users of Chinook have the ability to access these tools from either a Java user interface (figure 1) or through a Perl-based API.

There are over 25 bioinformatics utilities that have been integrated into Chinook to date, including tools for alignment, PCR prediction, gene regulation analysis, and assembly. These tools are currently distributed through 3 servers in the Vancouver area, with more servers coming online around Canada and world-wide in the next few weeks. Furthermore, we are actively helping set-up servers and services for bioinformaticians with computers and/or novel tools that they want to share, please contact us at chinook#,#bcgsc.bc.ca. This involves dedicating a computer for incoming analyses over the Internet (pretty much in the same way that a CGI script runs on a web server).

Click on the thumbnail below to view a larger image.

Chinook User Interface Thumbnail

Figure 1. Chinook User Interface: From here users can find services, visit tool-maker websites, and submit analyses.

New features include:
  1. A human-friendly interface (Visual indicators to help job submission)
  2. The ability to save and reload submitted jobs (Chinook doesn't always need to be running)
  3. Support for JASPAR database and TFBS Matrices
  4. Integrated Bug/Feature Submission
  5. Java 1.5 compatible
  6. New programming model for defining bioinformatics objects (Using dynamic class-loading)
  7. More Perl functionality and test scripts
  8. Advanced report monitoring features, see the STDOUT and STDERR from the server
  9. Extensively customizable file upload/download utilities via the BCGSC's FileWire
  10. Over 100 pages of user and developer documentation
  11. CVS hosted by java.net
Visit Chinook at http://www.bcgsc.bc.ca/chinook for source download (CVS), web start, and documentation today!

A previous article on Chinook appeared in the April 1, 2004 issue of the CBHD Newsletter. Chinook won the
"Best Overall Application Award" in BCNET's 2004 Coolest Applications Contest.


Please note:
If you have any bioinformatics software that you would like us to feature in future issues of this newsletter, please email Ian Forsythe (ian ~~ gchelpdesk.ualberta.ca).


new icon2) What's New?
 


1 Dec 2004 New BIND Datasets - Scientists at the Blueprint Initiative have added 996 interaction records from a Saccharomyces cerevisiae Protein-RNA dataset to the BIND database. A new protein-DNA dataset from a recent study on methyl-CpG binding proteins has been imported into BIND. Submit your own interaction datasets to BIND through the BIND website (high throughput or individual interactions).  Source: Blueprint.org

8 Nov 2004 PathwayAssist™ 3.0 Release - Ariadne Genomics, Inc. announced the latest release of PathwayAssist™, "desktop software for the visualization and analysis of biological pathways." As stated on their web page, "The new software includes a database of 500,000+ molecular interactions for pathway data mining, significantly improved visualization tools, and wizards for data import and export. The PathwayAssist™ 3.0 software from Ariadne Genomics' PathwayStudio™ Suite of products is a state-of-the-art tool for building, analysis, expansion and navigation of biological pathways, gene regulation networks and protein interaction maps."  Source: Ariadne Genomics Press Release

 
Event Icon3) Upcoming Events
Bioinformatics Training

CBRi Bioinformatics Tools in Drug Discovery Workshop Dr. David Wishart will be teaching a Bioinformatics Tools in Drug Discovery workshop on December 9-10, at the CBRi Facility on the BCIT-Burnaby Campus, in Burnaby, British Columbia. This hands-on workshop will introduce students to the principles and practices of bioinformatics in drug discovery. For further details, please see the workshop flyer: http://gchelpdesk.ualberta.ca/vitesse/BioinfoToolsDec04.php.

Canadian Bioinformatics Workshop - The Bioinformatics Workshop will take place on February 14-26, 2005, in Vancouver, British Columbia (application deadline: December 13, 2004). 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.

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, please visit the course website: http://www.economia.unimi.it/marray/2005/

M.Sc. and Ph.D. Programs in Bioinformatics at the Université de Montréal - The Université de Montréal is offering graduate degrees (M.Sc. and Ph.D.) in Bioinformatics. For further details, please visit the M.Sc. or Ph.D. program web pages.

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.

Spring 2005 BioneQ Workshop - The Quebec Bioinformatics Network will be offering one workshop in the Spring 2005 in Montreal: Bioethics in Bioinformatics. For more information on previous workshops offered by BioneQ, please visit the BioneQ home page at http://bioneq.qc.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

10-12 Dec 2004 Rocky '04 - The second annual Rocky Mountain Regional Bioinformatics Conference will be held in Aspen, Colorado on December 10-12, 2004. For further details, please visit http://www.iscb.org/events/event_data.php?200

16-19 Dec 2004 International Conference on Bioinformatics and its Applications (ICBA '04) - This conference will be held in Fort Lauderdale, Florida, on December 16-19, 2004. The main focus of this conference will be "major developments, problems, and trends and applications in Bioinformatics." For more information, please visit http://www.iscb.org/events/event_data.php?144

4-8 Jan 2005 Pacific Symposium on Biocomputing 2005 - This ISCB-sponsored event will be held on the Kohala Coast on the Island of Hawaii on January 4-8, 2005. According to the ISCB announcement, this conference will feature presentations on "databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology." For further details, please visit http://www.iscb.org/events/event_data.php?183

10-13 Jan 2005 CHI's Pep Talk - "The Protein Information Week" will take place in San Diego, California, on January 10-13, 2005. "Proteomics in a Six-Pack" includes proteomics conferences on: Protein Arrays, Protein Expression, Protein Folding Disorders, Protein Process Development, Human Proteome, and Protein Therapeutics. For further details, please visit http://www.chi-peptalk.com/.


software CD4) Help Desk Software Repository
The Help Desk software repository is where researchers may upload or download bioinformatics programs of interest. Currently the repository has 61 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 (ian[a]gchelpdesk.ualberta.ca). To deposit software now, please visit http://www.gchelpdesk.ualberta.ca/repository/SubmitRealSoftware.php
 

jobs image5) 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 Home Page
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
Tier 1 Canada Research Chair - Proteomics / Bioinformatics Vancouver, BC
December 3, 2004
Canada Research Chair in Bioinformatics Ottawa, ON
December 2, 2004
Post-doctoral Associate
Toronto, ON November 18, 2004
BIOINFORMATICS FACULTY POSITION
Burnaby, BC
November 5, 2004
Several positions at Blueprint
Toronto, ON
October 7, 2004
Bioinformatics/Systems Biology
Hamilton, ON October 5, 2004
 
Source: http://www.bioinformatics.ca/jobs (except for the Tier 1 Canada Research Chair and Blueprint positions)


registration6) CBHD Registration

Why Register?

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

Benefits include: 


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 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 ian-#-gchelpdesk.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: ian * gchelpdesk.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.
Genome Prairie Home Page Genome Canada Home Page

 

 
Received on 2001-09-06 - 20:37 GMT

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