Date: Fri, 20 Feb 2004 12:37:23 -0700
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CBHD Newsletter Issue 8 - February 19, 2004 |
CONTENTS:
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| Welcome to the eighth issue of the Canadian Bioinformatics Help Desk (CBHD) Newsletter. Back issues of our newsletter can be viewed at our newsletter archive site (http://www.gchelpdesk.ualberta.ca/news/news.php). Our circulation base has reached 1050 subscribers. In this issue's Bioinformatics Profile, we feature an article on the Genome Canada Bioinformatics Workshop. In this issue's Software Spotlight, we highlight Programming in Perl, a collection of scripts for learning Perl. In our Commercial Software Spotlight we feature OptGene™, a novel Gene Optimizing 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 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 |
Genome Canada Bioinformatics Workshop
Feature article contributed by Brian Fristensky and Sophie Chung
Bioinformatics in the post-genomic era requires the analysis of large and diverse datasets using automated tools. While many Web-based tools are available to the wet-lab researcher, the Web is not well suited for tasks beyond single-sequence annotation. Researchers need to become productive in a server-based Unix environment with its wealth of scripting and automation tools. Even at an entry-level, this can be an intimidating task if proper guidance is not available.
The Genome Canada Bioinformatics Platform is working to empower researchers by teaching a hands-on course, outlining tried-and-proven approaches as well as new developments, with lectures by a panel of experts and integrated assignments to develop practical skills. The course is taught using tools and services which are available through the Genome Canada Bioinformatics Platform. This workshop takes place twice a year, once in Western Canada and once in Eastern Canada.
Two Genome Canada Bioinformatics workshops, entitled 'The Applied Computational Genomics Course', successfully took place in 2003. The first in the series of workshops was held last Summer in Calgary (see class photo in Figure 1), while the second workshop was held in the Fall in Toronto. Below are just a few comments received by various participants at the end of each workshop:
"Overall, a really good course. If I retain 10% it will still have been useful. A real eye opener as to what will be coming down the pipe in future years!" June 2003 workshop, Calgary, AB
"The contents of the workshop fitted my needs almost perfectly as I was looking for those bioinformatics tools myself. The workshop also upgraded and updated my knowledge and practical skills. I am sure my work will be much more efficient and could be on another higher level." June 2003 workshop, Calgary, AB
"The focus on new technologies was great. My knowledge of bioinformatics was limited to first user applications (i.e. NCBI website applications) and this 'next-phase' focus was really good for me personally!" November 2003 workshop, Toronto, ON
"Good intro to the basics. The prepared assignment handouts were indispensable for learning, and really helped my understanding." November 2003 workshop, Toronto, ON
The next workshop is scheduled to take place June 12-20, 2004, in Winnipeg, Manitoba. Topics covered will include:
- Canadian Bioinformatics Resource (CBR)
- Canadian Bioinformatics Help Desk (CBHD)
- Basic Unix skills
- Working on a network-centric Unix desktop
- BIRCH: Working with large numbers of sequences on a comprehensive bioinformatics system
- Perl scripting, BioPerl and SeqHound: Quick automation of data analysis tasks and utilization of web services
- BioMOBY: a transparent software layer that automatically finds and uses web services.
- How biological concepts are phrased in computational models and how such models can be made operational in a database
- BIND: Analyzing a gene in its biological context and retrieving lists of functionally related genes, i.e. interactors or co-regulated genes
- Retrieving datasets from public databases based on lists of functionally related genes
- Strategies to discover correlations in biological data
- High-throughput genome annotation with TimeLogic and GeneMatcher hardware
- MAGPIE: Automated genome analysis and annotation
- BLUEJAY: Genome data visualization
Figure 1. Participants from the Calgary Applied Computational Genomics Course, held in June 2003.
 2) Software Spotlight |
Programming in Perl: A Perl tutorial for new programmers
Feature article contributed by Ian J. Forsythe and Paul Stothard
In your day-to-day lab activities, have you ever found yourself carrying out the same set of calculations over and over? Imagine having to perform the same operation a thousand times. Data analysis can be an important part of a biologist's job, especially once all the data has been gathered and it is time to make sense of it and write a paper or submit a report. Have you ever wondered if there is a better way to get the job done? A set of calculations that is performed over and over can easily be automated using a scripting language such as Perl. Perl has been very popular with bioinformaticians because of its flexibility, its ease of use, and its powerful pattern matching features—perfect for finding a specific DNA or protein sequence motif. Perl enables users to write "quick and dirty" programs that get the job done. At the Help Desk, we have developed a set of sample scripts that demonstrate some simple applications of Perl in biological data analysis and also teach the biologist how to get started in writing their own Perl scripts.
This collection of programs is intended to introduce the Perl programming language to students with little or no programming experience. Included with every script are detailed comments that describe what each line of code does when executed. Students are encouraged to type (minus the comments), edit, and run these programs. By doing so they will become familiar with the notations used by Perl, and the error messages that arise from common typos. These programs are not meant to illustrate the best way to complete a particular task. Several features of Perl have been omitted for the sake of simplicity. Students are encouraged to write faster or more compact versions of these programs using subroutines, objects, or more complex regular expressions. As Larry Wall, the inventor of Perl, would say, "There's more than one way to do it!"
After typing out a script, Unix users can make it executable by typing chmod +x script_filename at the command line. Windows users need to install ActivePerl from ActiveState (http://aspn.activestate.com/ASPN/Downloads/ActivePerl/Source) and enter perl script_filename at the Windows command prompt. The programs can be run using the sample input data provided or the user's own data. Figure 2 shows a simple script, called 1_typeseq.pl, which prompts the user for the name of a DNA sequence and the corresponding raw DNA sequence. The comments included with each script provide a high level description about what the individual statements do when they are executed by the Perl interpreter. The scripts in the Programming in Perl tutorial become progressively more complex. By script four of part II, students will be using Perl to communicate with NCBI's BLAST servers. For information about the other scripts that make up this tutorial, please refer to Table 1 below.
Figure 2. An example of an extensively commented Perl script from the Programming in Perl tutorial. The commented lines start with a '#' sign while the interpreted lines of Perl code do not. The comments help the new programmer learn about the structure of a typical Perl script and provide an explanation of how different Perl statements are used.
| Name of Script | Function |
| Part I Scripts | |
| 1_typeseq.pl | -This script prompts the user for a name and a DNA sequence
and then prints the information to the screen. -Demonstrates the use strict and use warnings pragmas (these are compiler options), declaring variables, basic syntax, print statement, standard input and output, and the chomp statement. |
| 2_seqfromfile.pl | -This script reads a DNA sequence (in FASTA format) from a
file, parses its individual components, and prints them to the screen. -Demonstrates opening and reading of files, opening and closing file handles, and the die statement. |
| 3_readmany.pl | -This script reads multiple DNA sequences (in FASTA format)
from a file and prints the name, length, and %GC content of each
sequence. -Demonstrates arrays, the special variables $/ and $1, the while loop, the if statement, the else statement, the next statement, the matching operator, the substitution operator, the length function for strings, the string equality operator eq, the push statement for adding elements to an array, the sort function for sorting the elements of an array, the reverse function for reversing the elements of an array, the sprintf function for formatting strings, and the scalar function for determining the number of elements in an array. |
| 4_translate.pl | -This script reads multiple DNA sequences (in FASTA format)
from a file and translates the DNA into protein in reading frame 1. -Demonstrates hash tables (associative arrays), the lowercase function lc, the for loop, the substring function substr, the exists function for hash tables, and the join function for combining the elements of an array into a string. |
| 5_revcomp.pl | -This script reads a single DNA sequence (in FASTA format)
from a file and converts the DNA sequence into its
reverse-complement form. Sequence composition statistics are printed
for the original and reverse-complement sequence. -Demonstrates various regular expressions for use with the matching and substitution operators, the translation operator (tr), and the split function for converting a string into an array. |
| 6_orfs_a.pl |
-This script reads a single DNA sequence (in FASTA format)
from a file and finds the open reading frames (ORFs) on the direct
strand using pattern matching (regular expressions). The ORF ranges are
then printed. -Demonstrates the pos function for monitoring the regular expression search, the elsif statement, the modulus operator, the pop function for removing and returning the last element in an array, the last statement for exiting a loop, the foreach loop, and the special variable $_. |
| 6_orfs_b.pl | -This script is
similar to 6_orfs_a.pl, except that it uses for loops
to scan the DNA
sequence in each of the three reading frames on the direct strand for
start and stop codons.
It is approximately 30 times slower than 6_orfs_a.pl. The speed
difference is probably due to the optimization of the built in pattern
matching functions, which are used in 6_orfs_a.pl. -Demonstrates the foreach loop and the special variable $_. |
| 7_transorfs.pl | -This script reads a single DNA sequence (in FASTA format)
from a file and then generates the protein translations of ORFs found
in any of the six reading frames. The protein ORFs are displayed in
FASTA format with an informative title. A minimum ORF length prevents
short ORFs from being displayed. -Uses portions of the early programs, with slight modifications. |
| Part II Scripts | |
| 1_orf_finder_sequence.pl | -This script submits a sequence to NCBI's ORF finder and
writes the unparsed results to a file. -Demonstrates Library for the WWW in Perl, the unless statement, and writing to a .html file. |
| 2_orf_finder_parser.pl | -This script parses the output produced by 1_orf_finder_sequence.pl, extracts the ORF information, and writes it to a text file. |
| 3_genscan.pl | -This script reads a single DNA sequence (in FASTA format)
from a file and sends the sequence to MIT's Genscan web server; the
predicted gene translations returned by Genscan are written to a file. -Further demonstrates and discusses the Library for the WWW in Perl. |
| 4_blast.pl | -This script reads multiple protein sequences (in FASTA
format) from a file and submits them to NCBI's BLAST server; the
results for each sequence are written to a file. -Demonstrates the application program interface (API) for accessing the NCBI BLAST server, how to use Perl to submit BLAST queries, and how to retrieve the results using the assigned request ID. |
| 5_MW.pl | -This script reads multiple protein sequences (in FASTA
format) from a file, determines the amino acid usage and molecular
weight of each sequence, and determines the combined amino acid usage
for all the
sequences. The results are written to a file. -Further demonstrates hash tables and writing to a file. |
Table 1. This table provides a brief description of the scripts that make up Parts I and II of Programming in Perl.
To download your free copies of Programming in Perl, Parts I and II, please visit our Software Repository:
Part I http://www.gchelpdesk.ualberta.ca/repository/VersionDetails.php?fileId=38&submissionId=29
Part II http://www.gchelpdesk.ualberta.ca/repository/VersionDetails.php?fileId=39&submissionId=30
Recommended references:
- Beginning Perl for
Bioinformatics
- Learning Perl, 3rd Edition—Making Easy Things Easy and Hard Things Possible
- Teach Yourself Perl in 21 Days
- Mastering Perl for Bioinformatics
Featured Commercial Software: OptGene™
Feature
article contributed
by Lindsay Moir
Production
of genetically modified organisms to achieve higher productivity,
disease resistance and other desirable properties is still based on
naturally occurring gene sequences. Naturally occurring sequences prove
futile in modern biotechnology with increased focus on safety
requirement for recombinant products and at the same time higher
flexibility in protein design. These gene sequences seldom meet the
ever growing demand for optimized yields in heterogeneous systems.
OptGene™ is a
novel Gene Optimizing tool that optimizes naturally occurring genes to
achieve higher productivity, at the same time giving higher flexibility
for protein design. The tool optimizes the genes using only the
sequence information and the choice of expression system. OptGene™
allows the researcher to adapt genes and their products precisely to
their specific requirements.
OptGene™
achieves optimization through
- Adaptation of codon usage to that of host
- Directed Mutagenesis
- Introduction of restriction sites
- Knockout of cryptic splice sites, RNA destabilizing sequences and other undesirable sequence signals
- Removal of secondary structures in RNA
- Reduction of transcription regions in unused frames
If you need a) to
optimize expression from a transgenic organism (e.g. alfalfa, canola,
mouse, goat, etc.), b) a management tool that can take you through the
process, c) to manage all of the information, d) to explore a large
number of possible alternatives, then OptGene™ is likely in your
future. For further information on OptGene™, please visit www.ubi.ca/optgene.htm.
Information on other bioinformatic products that UBI offers can be
found at www.ubi.ca/products.htm.
 3)
What's New? |
| 19 Feb 2004 | CBHD Bioinformatics
Needs Survey Report - We
recently conducted a Canada-wide bioinformatics needs survey. We asked
Genome Canada researchers what their bioinformatics and computational
biology needs were. I wish to thank all who participated in this
survey. Click here to view our report [PDF]
[DOC]. |
| 16 Feb 2004 | S2K Chooses
GeneLinker Products for Advanced Data Analysis - "S2K
is a consortium of highly recognized researchers from across Canada
funded by a $15 million grant from Genome Canada, Genome Quebec and
Ontario Genomics Institute. The S2K program, which is hosted by the
Université de Montréal, aims to study the functional
genomics, pharmacogenomics and proteomics of the immune response
regarding HIV and HCV infections, SARS, transplant rejection and
rheumatoid arthritis diseases. The ultimate goal of this program is to
develop a bioinformatic model to predict susceptibility and progression
of the targeted diseases as well as the response to a given therapy." Source: http://www.prweb.com/releases/2004/2/prweb104338.htm |
| 16 Feb 2004 | Bioinformatics
Network Cheered -
"European Virtual Institute for Genome Annotation will have a global
impact. An initiative
to tackle the current fragmentation of bioinformatics research across
Europe has been welcomed by scientists in both Europe and the United
States." Source: http://www.biomedcentral.com/news/20040216/03/ |
| 14 Feb 2004 | BIOKNOPPIX
Distribution
- The
High Performance Computing Facility at the University of Puerto Rico
has released a Knoppix Linux Live CD distribution customized for the
molecular biologist. Here is some of the software included with BIOKNOPPIX: EMBOSS 2.8.0,
jemboss, artemis, clustal, Cn3D, ImageJ, BioPython, Rasmol, Bioperl,
Bioconductor. Source: http://bioinformatics.org/forums/forum.php?forum_id=2500 |
| 12 Feb 2004 | RNAsoft
Release - Researchers in the
Department of Computer Science at the University of British Columbia
recently released online versions of RNAsoft,
"software
for RNA/DNA secondary structure prediction and design." RNAsoft
consists of three main programs: PairFold, CombFold, and RNA Designer.
For further details, see their recent publication in Nucleic Acids
Research (http://nar.oupjournals.org/cgi/content/full/31/13/3416). Source: http://bioinformatics.ca/weblogs/ |
| 10 Feb 2004 | Venter submits
whole genome shotgun assemblies to GenBank - "The sequences of the
whole genome shotgun assemblies (WGSA) generated by Venter
et al.
at Celera Genomics and The Center for the Advancement of Genomics
(TCAG) have been deposited in the GenBank database (see accession nos.
AADD00000000, AADC00000000, and AADB00000000). This data release
accompanies a paper in
PNAS comparing the sequence from the International
Human Genome Sequencing Consortium (NCBI Build 34) with the
WGSA." Source: http://www.bioinformatics.ca/weblogs/log.php?wid=128 |
| 06 Feb 2004 | Science Issue on
Mathematics in Biology - The Feb. 6 issue of
Science is devoted to Mathematics in Biology. Several Genome
Canada researchers co-authored this issue's paper entitled "Global
Mapping of the Yeast Genetic Interaction Network". Source: http://www.bioinformatics.ca/weblogs/log.php?wid=127 |
BIOINFORMATICS TRAINING
A DNA Microarray Workshop will be held at the University of Saskatchewan on February 26-27, 2004. Due to limited space, participants should register before February 20. To register, please send your name, institution, and email address to Faouzi.Bekkaoui%x%nrc-cnrc.gc.ca. For further details, please see the workshop announcement [PDF].
BioneQ's "A Biologist's Introduction to UNIX" workshop is now full. However, additional registrations will be added to a waiting list for future offerings of this workshop. For further information, please visit BioneQ's training web pages ("A Biologist's Introduction to UNIX") (other BioneQ workshops).
The next Applied Computational Genomics Course will be held in Winnipeg, Manitoba, on June 12-20, 2004. Early bird registrations must be received before May 1, 2004. For more information, see this issue's Bioinformatics Profile article or visit the course web page.
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
Canadian Bioinformatics Workshops (CBW): In 2004, CBW will be offering three remaining bioinformatics workshops on: 1. Developing the Tools (Deadline: March 6, 2004), 2. Proteomics (Deadline: May 22, 2004), and 3. Genomics (Deadline: June 19, 2004). These courses may count toward a Certificate in Bioinformatics. For further details, please visit http://www.bioinformatics.ca/workshops.php
Cold Spring Harbor Laboratory (CSHL) is offering a special 2 day course, spring, summer, and fall courses. The deadlines for summer and fall courses are March 15, 2004 and July 15, 2004, respectively. For more information, please visit http://meetings.cshl.org/2004/2004courses.htm
BIOINFORMATICS MEETINGS
| 12-16 May 2004 | 2004 CSH 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 '04, MONTREAL,
CANADA: The
Fourth International Conference of the Canadian Proteomics Initiative
(CPI)
will be held in Montreal, Canada, on May 14-16, 2004. The deadline for
abstracts is March 15, 2004. For other key deadlines, please visit http://www.pence.ualberta.ca/CPI/index.php?keydates.
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. For further details, please visit http://www.iscb.org/ismbeccb2004/ |
| 16-20 Aug 2004 | CSB 2004: "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. For more details, 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". The deadline
for the submission of papers is March 31, 2004. For further
details, please visit http://www.softwareresearch.ca/ecai-bio/index.html
and http://www.dsic.upv.es/ecai2004/ |
 5)
Help Desk Software Repository |
The
Help Desk
software repository is where researchers may upload or download
bioinformatics programs of interest. Currently the repository has 50
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
resource. Downloads are encouraged and submissions are always welcome.
The repository can be found at: http://gchelpdesk.ualberta.ca/repository/.
Attention all
programmers—we encourage you to submit your favourite bioinformatics
software to the Help Desk Software Repository
Please email Ian Forsythe
(ian^gchelpdesk.ualberta.ca)
if you would
like to deposit software into the software repository. To deposit
software now, please visit http://www.gchelpdesk.ualberta.ca/repository/SubmitRealSoftware.php
In case you missed it, this issue's Software Spotlight article highlights parts one and two of the Programming in Perl tutorial from our Software Repository.
 6)
Bioinformatics Jobs |
This is a resource for advertising positions in bioinformatics and computational biology. If you have a job you would like posted in this newsletter please email curators a bioinformatics.ca directly. 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/media/CareerOpportunities.pdf) and their latest job postings (http://genomecanada.ca/careers/index.asp?l=e).
| Job Title | Location | Date Posted |
| BIOINFORMATICS
SOFTWARE SPECIALIST |
Montreal
(Saint-Laurent), PQ |
February 19, 2004 |
| DNA
Sequence Finisher, RAII |
Vancouver, BC |
February 16,
2004 |
| Bioinformatics
position (Assistant Professor tenure track) |
Toronto, ON | February 9, 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 twelve additional positions
at Genome Sciences Centre) |
Vancouver, BC | January
26, 2004 |
| Computational
Biology position (Assistant/Associate
Professor tenure track) |
Hamilton, ON | January 24, 2004 |
| SHARCNet
Chair in Bioinformatics |
London, ON | January
7, 2004 |
| Future
positions: Bioinformatics, molecular microbiology, and genomics |
Burnaby,
BC |
Starting
in 2004-2005 |
Source: http://www.bioinformatics.ca/jobs
except for the Bioinformatics tenure track, 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:
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Ian J.
Forsythe, MSc
Phone: (780)
492-5969
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:
