CBHD Newsletter Issue 29 - December 16, 2004	CONTENTS: Bioinformatics Profile Sun Solutions for Computational Biology Software Spotlight SEQUEROME Workshop Spotlight Canadian Bioinformatics Workshop What's New? Latest version of mpiBLAST Released Allen Brain Atlas New Quantian Release Upcoming Events Bioinformatics Training Canadian Bioinformatics Workshop University of Toronto - New Specialist Program in Bioinformatics and Computational Biology Bioinformatics Meetings Software Repository Call for Submissions Deposit Software Bioinformatics Jobs CBHD Registration Free Subscription
Online version of this newsletter: http://gchelpdesk.ualberta.ca/news/16dec04/cbhd_news_16dec04.php

1) Bioinformatics Profile

), a full line of mass storage solutions, as well as novel visualization capabilities. For example, the Tokyo Human Genome Center has 788 UltraSPARC CPUs in SF15K SMPs with 1.7 Tb memory machine; the San Diego Supercomputer Center runs 500+Tb of Sun storage in support of the Distributed Terascale Facility; the Texas Advanced Computing Center runs a distributed visualization network for DTF based on Sun technology.

Figure 2. Sun offers a wide range of Sun Sparc(r) and AMD Opteron based servers which enable Computational Biologists to fit the application to the appropriate architecture: edge computers for "embarrassingly parallel" jobs like BLAST, and SMP for larger simulations, molecular modeling, and large databases.

2) Software Spotlight

• Present a 'Nucleotide sequence to Protein structure' interface to a user who has little or no idea of the possible structural or functional domains contained within his or her ORF.
• Provide more information on 'Hits' for each record in a regular sequence query report.
• Provide user with 'Search Trees' (as opposed to 'Search Histories') to trace back a search pattern. This would enable creation of search templates for carrying out repeated search procedures on a family of sequence/structure data.
• 'Intelligent text summarization' tools that would generate a 'text summary' based on input sequences.
  

Description and analysis...

Click on thumbnail below to view a larger image.



Figure 1. Homepage of SEQUEROME displaying features.

Query pane [left panel]: Each browser session intends to perform without asking too many questions at the outset. The user has to just dump in the sequence in the Query pane, and BLAST the sequence right away using standard parameters. Experienced users can perform further special operations using the 'Advanced' options (Figure 2). Alternatively the user can also perform a variety of other actions including 'sequence manipulation'/ 'analysis'/ 'alignment' using popular existing tools available on the Web. The One-box any-sequence, takes input in any format (FASTA, with or without spaces/numbers...).

This includes searching by specific databases or performing some general sequence manipulations. Results obtained from 'sequence manipulation' e.g. translation, can be further carried on to do additional BLAST searches while preserving the history of the earlier search.



Figure 2. Query pane displaying user defined settings/options.

Results Pane [right panel]: Once the user dumps in the sequence, SEQUEROME queries the input sequence against a variety of databases/tools ('popular public domains' and 'privately hosted services') including BLAST, PDB, REBASE and others, and generates 'user-defined' outputs that are intuitive and easily comprehensible. Once the BLAST report is displayed in the Results pane, the user has the freedom to perform a 'quick analysis' on any of the BLAST hits and proceed to select that sequence for further analysis (Figure 3A). The 'view sequence' link allows direct visualization of the 'sequence match' as highlighted regions (for ease of selection and archival purposes) (Figure 3B). Most of the results from third party services can be viewed directly in the Results pane without opening any additional browser windows. This feature should be a refreshing change for all those tired of operating an impossible number of browser sessions at a time. For protein BLAST results, PDBids are also displayed in appropriate cases so that the structure of the molecule with a match can be viewed directly (with an already downloaded version of a molecular structure viewer e.g. 'Cn3D', 'Rasmol'... (Figure 4).





Figure 3. Results pane with 'quick analysis' (A) and 'view sequence' (B) features.

Search history Pane [bottom panel]: While the user is performing all these operations, the results of each operation are recorded in the Search History pane, enabling easy retrieval and selection of earlier results. For each of the results, the user has a choice of 'print', 'save' or 'mail' options using small buttons on top of each icon (

Figure 4. Sequence-to-Structure interface starting with a DNA sequence.

Endnote

Acknowledgements

SEQUEROME has been supported in part by funds from the MURI Grant: DAAD19-00-1-0165 and NSF Grant: CCR 0098271.

For links to this and other web-based bioinformatics programs, please visit the Canadian Bioinformatics Help Desk (CBHD) Web Servers page at http://gchelpdesk.ualberta.ca/servers/.

3) Workshop Spotlight

• Install and use in-house information reference systems.
• Access EnsEMBL using Perl API
• Understand microarray data for gene expression.
• Analyze Single Nucleotide Polymorphisms (SNPs) and genotype data.
• Detect and analyze gene structures from eukaryotic genomes.
  

• Visualize protein structures and make high quality images for publication
• Understand techniques used in high throughput proteomics
• Understand data resulting from proteomics
• Use public domain tools for modeling three-dimensional structures
• Understand concepts and methods involved in threading analyses.
  

Please note: If you know of a bioinformatics workshop that you would like us to feature in future issues of this newsletter, please email Ian Forsythe (ian@gchelpdesk.ualberta.ca).

4) What's New?

14 Dec 2004	Latest version of mpiBLAST Released - mpiBLAST 1.3.0 has just been released and includes several major design improvements in the areas of reliability, performance and accuracy. According to the mpiBLAST home page (http://mpiblast.lanl.gov/), "mpiBLAST is a freely available open source parallelization of NCBI BLAST." For large databases, this software provides a dramatic decrease in the time it takes to complete a BLAST search. This version uses the latest NCBI Toolbox and reports e-value scores that are identical to those reported by NCBI.  Source: Bioinformatics.Org
13 Dec 2004	Allen Brain Atlas - The Allen Institute for Brain Science (AIBS) made its first public release of its gene expression data on nearly 2,000 genes from mouse brain. Genentech's Mark Tessier-Lavigne, chairman of the Allen Institute's scientific advisory board, described it as the "Google for gene activity patterns in the brain." The Atlas expression data for 2,000 mouse genes is fully searchable. In the future, there will data on 10,000 to 15,000 genes. To access this data, please visit the Allen Brain Atlas website (http://www.brainatlas.org/).  Source: Bio-IT World
8 Dec 2004	New Quantian Release - Quantian 0.6.9.2 has just been released and features many useful bioinformatics applications. As stated on the project homepage (http://dirk.eddelbuettel.com/quantian/), "Quantian is a remastering of Knoppix, the self-configuring and directly bootable CD-ROM/DVD that turns any PC or laptop (provided it can boot from CD-ROM/DVD) into a full-featured Linux workstation." Some of the bioinformatics applications included with this distribution are: as outlined on Bioinformatics.Org's web page (http://bioinformatics.org/forums/forum.php?forum_id=2967), "a complete installation of BioConductor as well as BioPerl, EMBOSS, FastDNAML, FastLink, Garlic, NCBI, Loki, ReadSeq, Vibrant, and hundreds of other scientific applications and visualization tools."  Source: Bioinformatics.Org

 

5) Upcoming Events

Bioinformatics Training

Canadian Bioinformatics Workshop - The Bioinformatics Workshop will take place on February 14-26, 2005, in Vancouver, British Columbia (application deadline: December 17, 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. For further details about all Canadian Bioinformatics Workshops, see the above Workshop Spotlight article.

University of Toronto mounts 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, please visit http://biochemistry.utoronto.ca/bcb/

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 (BioneQ) will be offering one workshop in the Spring of 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
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/.
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, please visit http://www.iscb.org/events/event_data.php?207.
13-16 Apr 2005	The International Conference on Microbial Genomes will take place 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."

 

6) 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@gchelpdesk.ualberta.ca). To deposit software now, please visit http://www.gchelpdesk.ualberta.ca/repository/SubmitRealSoftware.php
 

7) 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).

 

 
 

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Job Title	Location	Date Posted
Assistant or Associate Professor	Montréal, PQ	December 6, 2004
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

 

Source: http://www.bioinformatics.ca/jobs (except for the Tier 1 Canada Research Chair and Blueprint positions)

8) 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.

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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 

 

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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.