Canadian Bioinformatics Help Desk Newsletter -- March 7, 2006

The Canadian Bioinformatics Help Desk, as part of the Integrated and Distributed Bioinformatics Platform for Genome Canada, is supported by Genome Alberta, Genome Canada and other co-funding partners. Genome Canada is a not-for-profit corporation that is leading Canada's national strategy on genomics with $600 million in funding from the federal government.

Background

The DrugBank database is a unique bioinformatics and cheminformatics resource for in silico drug discovery and exploration. DrugBank combines detailed drug information (i.e. chemical, pharmacological, pharmaceutical) with comprehensive drug target information (i.e. sequence, structure, pathway). The database contains nearly 4300 drug entries including more than 1000 FDA-approved small molecule drugs, 113 FDA-approved biotechnology drugs (protein- and peptide-based therapeutics), 62 nutraceuticals, over 3000 experimental drugs, and links to more than 6000 protein sequences (i.e. drug targets). The individual drug entries, or DrugCards, contain more than 80 data fields, half of which describe the drug and chemical data and the other half of which describe the drug target or protein data. Many of these data fields provide hyperlinks to external websites (GenBank, Swiss-Prot, PDB, Pfam, PubChem, ChEBI, KEGG, etc.) and a variety of structure viewing applets (Figure 1).

3D Structure of Ibuprofen

Figure 1. The 3D structure of Ibuprofen using one of DrugBank's structure viewing applets.

Many Ways to Explore DrugBank

The information contained within DrugBank can be easily accessed using eight convenient buttons (Home, Browse, PharmaBrowse, ChemQuery, Text Query, SeqSearch, Data Extractor, and Download) located within the navigation panel at the top of every DrugBank web page. Users may perform a simple text query that will search the entire textual component of the database. Alternatively, users can freely browse the database using the Browse button. The browse method provides users with a tabular synopsis of DrugBank's content (Figure 2). As part of the Browse feature, users can re-sort the contents of DrugBank by accession code, generic name, molecular weight, CAS number, drug category, or indication. By clicking on a DrugCard, the user is presented with the full data content for the corresponding drug (Figure 3). The PharmaBrowse button allows users to browse through drugs as grouped by their indication. This feature is designed for those who think of drugs as clusters of indications or drug classes and is particularly useful for pinpointing potential drug leads. The PharmaBrowse feature provides navigation hyperlinks to over 70 drug classes. The ChemQuery button allows users to sketch a chemical structure, using ACD's chemical sketching applet, or enter a SMILES string of a possible lead compound. The user submits this information to DrugBank's structure similarity search tool and looks for chemicals similar or identical to the query compound (Figure 4). The Text Query button supports sophisticated text searches, allowing for partial word matches, case-sensitive matches, misspellings, etc. The SeqSearch button allows users to conduct sequence similarity searches using BLASTN or BLASTP against DrugBank's 15,000 sequences. DrugBank supports both single and multiple BLASTP queries. Thus, whole proteome BLAST queries can be performed. The DataExtractor button provides an easy-to-use, yet powerful, relational query search tool that allows users to intuitively construct Structured Query Language (SQL)-like queries without having to know SQL (Figure 5). For example, using the DataExtractor, a user could easily construct the following query: 'find all drugs that have a melting point range of 80 to 169 degrees Celsius, a LogP range of 0 to 2, whose indication is pain'. This feature allows users to "extract" very specific information from DrugBank and display it as a table with hyperlinks using their web browser. With the Download button, users can also freely download selected text components and sequence data from DrugBank and track the latest DrugBank statistics.

Click on the thumbnail below to view a larger version of the image

Figure 2. DrugBank's Browser mode provides a tabular synopsis of the database's content.

Click on the thumbnail below to view a larger version of the image

Figure 3. DrugCards contain over 80 data fields and include hyperlinks to many useful, external websites (GenBank, Swiss-Prot, PDB, Pfam, PubChem, ChEBI, KEGG, etc).

Click on the thumbnail below to view a larger version of the image

Figure 4. With the ChemQuery feature, users can search for chemicals with a structure that is similar or identical to the query compound.

Click on the thumbnail below to view a larger version of the image

Figure 5. The Data Extractor allows users to create powerful relational database queries using a simple graphical user interface and "extract" tables of information that fit their specific search criteria.

To access DrugBank online, visit http://redpoll.pharmacy.ualberta.ca/drugbank/.

Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72. [PubMed] [PDF]

Complete explanation of all the DrugCard fields and DrugBank data sources: http://redpoll.pharmacy.ualberta.ca/drugbank/cgi-bin/drugcard_field_expl.cgi

This project is supported by Genome Alberta and Genome Canada, a not-for-profit organization that is leading Canada's national genomics strategy with $600 million in funding from the federal government.

Please note: If you are part of a bioinformatics research group, know of any bioinformatics software, hardware, meetings, workshops, training sessions, degree programs or web servers that we should feature in future issues of this newsletter, please email Ian Forsythe (ianf@cs.ualberta.ca).

2) Hardware Spotlight

Feature article contributed by Stefan Unger, Business Development Manager Life Sciences, Sun Microsystems, Inc.

Sun Microsystems Announces the Discovery Cluster for the Life Sciences

Exceptional Price/Performance in a Pre-Assembled Rack

Sun Microsystems^TM announces the "Discovery Cluster for the Life Sciences". The Discovery Cluster is a pre-assembled, base-level configuration of a Sun Grid Rack System (SGRS) with components selected especially for the Life Science HPC market.

The Discovery Cluster is Sun's solution approach to the compute needs for the drug discovery process. It is based on the Sun Fire^TM X2100 64-bit x64 server, powered by the AMD Opteron^TM dual core processor. The X2100 delivers up to one-and-a-half times the performance, and uses about one-third of the power of competing systems, yet costs a fraction of their price. Bioinformatics and molecular modeling benchmarks confirm the exceptional price/performance advantages of the Sun Fire X2100 over Intel Xeon based clusters. These highly reliable and energy efficient X2100 servers are also the fastest enterprise x64 servers in their class.

At under $94,000 (US list price) per fully populated, pre-assembled rack, the Discovery Cluster provides 1 TeraFlop of theoretical peak performances in three racks for under $282,000. In addition, the power, cooling and management requirements are substantially less than Intel Xeon based clusters. Academic pricing is available.

The Discovery Cluster comes pre-assembled, with hardware, cabling, Solaris^TM 10 and Sun Grid Engine software. Multiple operating systems (Solaris 10 x64, Linux (Red Hat, Suse), and Windows) are supported. Many alternative configurations are available, such as memory, IB switches, more local disk, and Sun's solution partners provide a range of software options.

For more information, listen to a NetTalk webinar on the Sun Discovery Cluster for Life Sciences, featuring the designer of the Sun Fire "Galaxy" series servers, Andy Bechtolsheim, Sun Chief Architect and Senior Vice President, Network Systems. For more information visit www.sun.com/nettalk, www.sun.com/discoverycluster, or email discoverycluster@sun.com.

Sun, Sun Microsystems, the Sun logo, Sun Fire, Solaris are trademarks or registered trademarks of Sun Microsystems, Inc. in the United States and other countries. AMD and Opteron are trademarks or registered trademarks of Advanced Micro Devices.

Please note: If you are part of a bioinformatics research group, know of any bioinformatics software, hardware, meetings, workshops, training sessions, degree programs or web servers that we should feature in future issues of this newsletter, please email Ian Forsythe (ianf@cs.ualberta.ca).

The Canadian Bioinformatics Workshops Series is offering its second workshop of the 2006 season: Genomics. Until March 7th, you can apply on-line at: http://www.bioinformatics.ca/apply.php.

Genomics Workshop

Date: May 1 - 6, 2006
Location: SFU Harbour Centre, Vancouver
Course Fee: $1,700.00 CAD
Prerequisite: Bioinformatics Workshop or equivalent experience

Participants will gain practical skills and understanding to:

Microarray Data Analysis (Expression and chIP- chip)
EnsEMBL and the Perl API
Gene Network Analysis
Regulatory Sequence Analysis

A comprehensive lecture and lab manual will be provided to all participants. This workshop will also be counted toward your eligibility in receiving the Certificate in Bioinformatics, which is accredited by the University of British Columbia, the University of Toronto, and the University of New Brunswick.

For more information please visit our website at: http://bioinformatics.ca/course_work/workshops/ or e-mail course_info@bioinformatics.ca, CBW Manager, Shum Sidhu (ssidhu@cgdn.ca).

Sponsored by:		Presented by:

Accredited by:

Unleashed Informatics' Free DogBox Online - Unleashed Informatics Limited announced the release of DogBox Online, a free and open access version of DogBox^TM. According to the company's press release, "DogBox Online offers researchers a free, integrated data service with a re-designed interface allowing for complex text query execution, on-the-fly data exports in various formats, and an integrated view of sequence records including pre-calculated BLAST results." In addition to DogBox^TM Online, Unleashed Informatics is also offering two other open access products and services, namely BIND^TM and SMIDSuite^TM Lite. As of March 2, 2006, Unleashed Informatics has implemented a simple, one-time registration process for users of it open access products and services. Source: Unleashed Informatics Limited News Release

Review on Federated Databases in Bioinformatics and Translational Medical Research - Dr. Richard M. Casey, Founder and Chief Scientific Officer of RMC Biosciences Inc., has written a very informative review article entitled "Federated Databases in Bioinformatics and Translational Medical Research". In this article, Dr. Casey provides some real examples of how federated databases are being used in the fields of bioinformatics and translational medical research, which seeks to bridge the gap between basic medical research and clinical trials research. Dr. Casey describes three examples: The Structural Proteomics in the Northeast (SPINE2), the Cancer Biomedical Informatics Grid (caBIG), and Rodeo. To read this review article, visit http://www.b-eye-network.com/view/2366. For other recent review articles by Dr. Casey, visit http://www.b-eye-network.com/authors/index.php?a=52. Source: Business Intelligence Network

Winner of the 2006 Benjamin Franklin Award - Bioinformatics.Org announced Michael Ashburner of Cambridge University as the winner of the 2006 Benjamin Franklin Award for his work on the following open access bioinformatics projects: FlyBase, the GASP project, the Gene Ontology project, and the Open Biomedical Ontologies project. He also played a key role in the establishment of the European Bioinformatics Institute. Source: Bioinformatics.Org Press Release

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, visit http://www.iscb.org/events/event_board.php
15-19 Mar 2006	Phylogenomics Conference - This conference will be held in Sainte-Adele, Quebec on March 15-19, 2006. This conference aims to bring together experts focusing on two distinct aspects of phylogenomics: the use of genome data to infer species phylogeny and the use of phylogenetics approaches to gain insights into gene functions. For more information, visit the conference website: http://www.bioinfo.umontreal.ca/evenements/phylogenomics.html.
2-5 Apr 2006	RECOMB 2006 - The Tenth Annual International Conference on Research in Computational Molecular Biology will be held in Venice, Italy on April 2-5, 2006. For more details, visit http://recomb06.dei.unipd.it/.
10-12 May 2006	CPI 2006 - The Sixth International Conference of the Canadian Proteomics Initiative (CPI) will take place at the University of Alberta in Edmonton, Canada, on May 10-12, 2006. The Canadian Proteomics Initiative is part of a cross-Canada effort to build on Canada's growing strengths in the field of proteomics and protein chemistry. The CPI Conference provides a general forum for disseminating the latest developments in proteomics and protein chemistry to Canadian scientists. It is a multidisciplinary conference that brings together ~350 researchers with expertise in all areas of proteomics including functional proteomics, structural proteomics, protein display, protein expression, protein chemistry and protein interactions. Its scope includes the development and application of novel experimental or computational methods for studying the proteome of cells, tissues or organisms. Register by March 15, 2006 to save $75. For more information, visit the conference website at http://cpicanada.org.
28 May-1 June 2006	ICRM 2006 - The Fourth International Chemometrics Research Meeting will be on May 28 to June 1, 2006, in Veldhoven, Netherlands. For more details, visit http://www.icrm.info/.
6-10 Aug 2006	ISMB 2006 - The Fourteenth Annual International Conference on Intelligent Systems for Molecular Biology will take place on August 6-10, 2006, in Fortaleza, Brazil. For more details, visit http://ismb2006.cbi.cnptia.embrapa.br/.
14-18 Aug 2006	CSB2006 - The 2006 Life Sciences Society Computational Systems Bioinformatics Conference will be held on August 14-18, 2006, at Stanford University, California. For more information, visit http://www.lifesciencessociety.org/CSB2006/.
10-13 Sep 2006	ECCB 2006 - The Fifth European Conference on Computational Biology will be held in Eilat, Israel on September 10-13, 2006. For more details, visit http://www.eccb06.org/.
28-29 Sep 2006	2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - This symposium will be held at the Renaissance Hotel Downtown, Toronto, Ontario, Canada on September 28-29, 2006. This symposium will bring together top researchers, practitioners, and students from around the world to discuss the latest advances in the field of computational intelligence and their application to real-world problems in biology. For more information, visit http://www.cibcb.org or download the symposium flyer.

Bioinformatics Training

Canadian Bioinformatics Workshops (Bioinformatics Workshop) - The Canadian Bioinformatics Workshops Series is offering its second workshop of the 2006 season: Genomics. This workshop will be held in Vancouver on May 1-6, 2006. Until March 7th, you can apply on-line at: http://www.bioinformatics.ca/apply.php. For more information see the above Workshop Spotlight article.

Computational and Statistical Aspects of Microarray Analysis (CSAMA) - The fourth edition of this course will be held in Bressanone-Brixen, Italy, on June 18-23, 2006, and is being organized jointly by the Universities of Milan and Padua, Italy, in collaboration with the Bioconductor project and the R Foundation for Statistical Computing. This five-day course will include: an introduction to genomic data, microarray experiments, statistical methods applied to microarray data, proteomics, and other high throughput methods. For more information, visit http://www.economia.unimi.it/marray/2006/ or email stefano.iacus@unimi.it.

Bioinformatics Degree Programs

University of Alberta's Undergraduate Programs in Bioinformatics - Degree programs in Bioinformatics are offered at the University of Alberta through the Department of Biological Sciences and through the Department of Computing Science.

University of British Columbia's Bachelor of Computer Science (Integrated Computer Science) Program - This new, full-time, 20-month, second degree program provides the opportunity to integrate computer science with one's existing expertise. This program is attracting many considering a career in bioinformatics. For more information, see the Degree Spotlight article from the May 5 issue.

British Columbia's 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.

Simon Fraser University's B.A.Sc. Joint Major Program in Computing Science and Molecular Biology and Biochemistry (CS-MBB) - This program provides excellent training for a bioinformatics career (it was the basis for a White Paper on Bioinformatics training for Canada), but allows you to keep your options open to many other career options in the computational and life sciences. The CS-MBB program is geared for exceptional students who want a high-caliber, intensive, broad-based education that forms a solid platform for further advanced training and/or a cutting-edge, flexible career. See http://www.bioinformatics.sfu.ca/undergrad.html for more information.

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/.

Queen's University Biomedical Computing Degree - "The future of medicine is here, in Canada's first and only specialized program in computational and medical informatics." For more information, visit http://www.cs.queensu.ca/biomed/.

Carleton University's Undergraduate Program in Bioinformatics - Carleton University offers Bachelor of Science (Honours) programs in Computational Biology, Computational Biochemistry and Computational Chemistry with research and Co-op options. These programs deliver a solid theoretical and practical background in bioinformatics, biology, chemistry, biochemistry, computer science, mathematics and statistics that provides graduates with exceptional opportunities in biotechnology and drug discovery. See http://www.carleton.ca/biochem/bioinformatics.html for more information.

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

McGill University's Undergraduate Minor in Computational Biology and Graduate Option in Bioinformatics - "Currently, at McGill there is a Minor in Computational Biology offered by the Department of Computer Science. This minor is intended for students majoring in 'biological sciences' (e.g., biology, biochemistry, immunology and microbiology) who are also serious about the computational and mathematical aspects of Bioinformatics." McGill also offers a Graduate Option in Bioinformatics at the M.Sc. and Ph.D. levels. For more information, visit http://www.mcb.mcgill.ca/academics/index.php.
Source: http://www.mcb.mcgill.ca/academics/index.php

Please note: If you know of any bioinformatics meetings, workshops, training sessions, or degree programs that we should feature in future issues of this newsletter, please email Ian Forsythe (ianf@cs.ualberta.ca).

The Help Desk software repository is where researchers may upload or download bioinformatics programs of interest. Currently the repository has 75 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 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.

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 ianf@cs.ualberta.ca. Job postings will be carried for a maximum of 4 issues (8 weeks) unless the position is filled prior to that date.

Special Announcement: Dr. Andrew Grant of the Universite de Sherbrooke would like to identify persons here in Canada who are interested in data standardisation in bioinformatics and, in particular, wish to participate in the ISO standards development work with respect to the Polymorphism Markup Language (PML) and Single Nucleotide Polymorphisms (SNPs) [details].

Source: http://bioinformatics.ca/bioinformatics_resources/jobs/ except the Software Developer position

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, 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
Dept. of Biological Sciences, CW 405
Edmonton, AB, T6G 2E9, Canada

Job Title	Location	Date Posted
TIER 1 CANADA RESEARCH CHAIR IN BIOINFORMATICS	London, ON	March 8, 2006
Postdoctoral Fellowship in Bioinformatics	Toronto, ON	March 6, 2006
Postdoctoral Positions in Bioinformatics, Genomics and Proteomics	Ottawa, ON	February 21, 2006
Informatics Scientist	Vancouver, BC	February 20, 2006
Postdoctoral Fellowships (in Pathway Modelling, Pathway Modelling Curation, Proteomics, Text Mining)	Oslo, Norway	February 17, 2006
Software Developer	Oslo, Norway	February 17, 2006
Informatician - Pleiades Project	Vancouver, BC	February 15, 2006
Job Title: Salmon gene ID, assembly, expression and arrays	Victoria, BC	February 14, 2006
Post-doc in Bioinformatics	Vancouver, BC	February 7, 2006
Database Developer	Toronto, ON	January 27, 2006
Postdoc Positions at University of Toronto	Toronto, ON	January 25, 2006
Bioinformatician	Sherbrooke, PQ	January 25, 2006
Postdoc in Bioinformatics	Greater Vancouver, BC	January 22, 2006
Canada Research Chair in Bioinformatics	Ottawa, ON	January 19, 2006

22 Feb 2006	Unleashed Informatics' Free DogBox Online - Unleashed Informatics Limited announced the release of DogBox Online, a free and open access version of DogBox^TM. According to the company's press release, "DogBox Online offers researchers a free, integrated data service with a re-designed interface allowing for complex text query execution, on-the-fly data exports in various formats, and an integrated view of sequence records including pre-calculated BLAST results." In addition to DogBox^TM Online, Unleashed Informatics is also offering two other open access products and services, namely BIND^TM and SMIDSuite^TM Lite. As of March 2, 2006, Unleashed Informatics has implemented a simple, one-time registration process for users of it open access products and services. Source: Unleashed Informatics Limited News Release
21 Feb 2006	Review on Federated Databases in Bioinformatics and Translational Medical Research - Dr. Richard M. Casey, Founder and Chief Scientific Officer of RMC Biosciences Inc., has written a very informative review article entitled "Federated Databases in Bioinformatics and Translational Medical Research". In this article, Dr. Casey provides some real examples of how federated databases are being used in the fields of bioinformatics and translational medical research, which seeks to bridge the gap between basic medical research and clinical trials research. Dr. Casey describes three examples: The Structural Proteomics in the Northeast (SPINE2), the Cancer Biomedical Informatics Grid (caBIG), and Rodeo. To read this review article, visit http://www.b-eye-network.com/view/2366. For other recent review articles by Dr. Casey, visit http://www.b-eye-network.com/authors/index.php?a=52. Source: Business Intelligence Network
15 Feb 2006	Winner of the 2006 Benjamin Franklin Award - Bioinformatics.Org announced Michael Ashburner of Cambridge University as the winner of the 2006 Benjamin Franklin Award for his work on the following open access bioinformatics projects: FlyBase, the GASP project, the Gene Ontology project, and the Open Biomedical Ontologies project. He also played a key role in the establishment of the European Bioinformatics Institute. Source: Bioinformatics.Org Press Release