From angenmap-request@db.genome.iastate.eduWed Mar 2 13:38:46 2005
Message-ID: <20050302193844.351.qmail@db.genome.iastate.edu>
From: James M Reecy <jreecy@iastate.edu>
Date: Wed, 02 Mar 2005 13:06:17 -0600
Postmaster: processed by hu@db.genome.iastate.edu
Subject: NRSP-8 Bioinformatics Update #1
To: Multiple Recipients of <angenmap@db.genome.iastate.edu>
NRSP-8 Bioinformatics / Database Update
---=== No. 1 ===---
March 1, 2005
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1. Development of Pig QTL database
2. Development of a PCR primer development tool
3. Development of a livestock sequence Blast server
4. Upcoming bioinformatics meetings (16 items)
5. Upcoming short courses (5 items)
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Development of Pig QTL database. The pig quantitative trait loci (QTL)
database (PigQTLdb) has been well used since its release last December
(http://www.animalgenome.org/QTLdb/). On average about 6,000 web hits
per month were made to PigQTLdb. The database contains all pig QTL
data published during the past 10+ years. The database and its
peripheral tools were made to compare, confirm, and locate on pig
chromosomes the most feasible location for a candidate gene responsible
for quantitative trait(s) important to pig production. To date, 791 QTL
from 73 publications have been curated into the database. Please
contact Zhiliang Hu (zhu@iastate.edu) with any suggested improvements
or additional data to add to the database.
-*- -*- -*- -*-
Development of a PCR primer development tool. The Expeditor tool has
received some good comments and been used by some 200+ users since its
release last October (http://www.genome.iastate.edu/~hu/expeditor).
Expeditor is a web-based tool which combines human intron/exon
structural information and EST sequence information of the target
species to design primers for amplification of genomic segments of a
given gene.
-*- -*- -*- -*-
Development of a livestock sequence Blast server. A NAGRP Blast Server
is now in service (http://www.animalgenome.org/blast/). This blast
server uses a local copy of NCBI blast suite, which includes bl2seq,
blastall, megablast, blastpgp, blastclust, netblast, etc. The local
sequence data sets include all non-human, non-mouse EST sequences from
the Genbank, Whole Genome Shotgun (WGS) sequence assemblies for
different organisms from Genbank. These data sets are updated from
Genbank every night. The local sequence data sets also include TIGR
Gene Indices for Cattle, Chicken, Pig, Salmon, Catfish, and Rainbow
Trout. The TIGR Indices are updated weekly (done every Saturday
night). Currently users can use the web server for their blast. Links
to the blast server are included on each of the species pages under
resources. We can develop a service portal for batch blast if there
are such needs in the community. Please email Jreecy@iastate.edu to
discuss.
-*- -*- -*- -*-
The Aquaculture genomics web site has a new home and look. The URL to
the current web site is http://www.genome.iastate.edu/aquaculture/ .
Please send information that you would like added to Rexroad, Caird
(crexroad@ncccwa.ars.usda.gov) or Zhiliang Hu (zhu@iastate.edu).
-*- -*- -*- -*-
New projects: As always if you have suggestions about what needs to be
developed/improved or how we can help please do not hesitate to contact
us. Jreecy@iastate.edu
-*- -*- -*- -*-
UPCOMING BIOINFORMATICS MEETINGS
March 19-23, 2005 - 3rd Symposium on Computational Cell Biology
Web: http://www.ccbsymposium.org/index.html
Place: Cranwell Resort & Golf Club, Lenox, MA
April 8-13, 2005 - Keystone Symposia: Proteomics and Bioinformatics
Web: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingIDs4
Place: Keystone, Colorado, USA
April 24-25, 2005 - Computational Challenges in Systems Biology
Web: http://www.systemsbiology.org/symposium2005/
Organized by Institute for Systems Biology
Place: Seattle
May 17-19, 2005 - Bio-IT World Conference & Expo
Web: http://www.bioitworldexpo.com/
Organized by IDG World Expo
Place: Hynes Convention Center, Boston
June 9-12, 2005 - 7th International Conference on Bioinformatics 2005
Web: http://bioinfo.ebc.ee/bio2005/indexen.php
Place: Tartu, Estonia
June 17, 2005 - Bioinformatics: Knowledge Discovery in Biology 2005
Web: http://xldb.fc.ul.pt/bkdb2005/
Place: Lisboa, Portugal
June 25- 29, 2005 - Intelligent Systems for Molecular Biology (ISMB 2005)
Web: http://www.iscb.org/ismb2005/
Location: Detroit, Michigan
Satellite event (June 24, 2005):
Eighth Annual Bio-Ontologies Meeting
Web: http://bio-ontologies.man.ac.uk/
Submission Deadline: 29th April 2005
June 31-5, 2005 - 14th International Conference on Cytochromes P450:
Biochemistry, Biophysics, and Bioinformatics
Web: http://www.p450dallas2005.us/
Place: UT Southwestern Medical Center, Dallas
July 10-13, 2005 - 9th World Multi-Conference on Systemics, Cybernetics
and Informatics
Web: (http://www.iiisci.org/sci2005), which will
Place: Orlando, Florida
July 21-26, 2005 - 6th International Symposium on Computational Biology
and Genome Informatics
Web: http://www.jcis.org/pages/subconference/cbgi/cbgi.aspx
Place: Marriott City Center, Salt Lake City, CO
August 8-11, 2005 - IEEE Computational Systems Bioinformatics
Conference (CSB 2005)
Web: http://conferences.computer.org/bioinformatics/
Place: Stanford, CA
August 22-25, 2005 - 5th International Workshop on Bioinformatics and
Systems Biology (IBSS 2005)
Web: http://www.biologie.hu-berlin.de/~gk/events/ibsb2005/index.htm
Place: Berlin, Germany
September 22-25, 2005 - Integration of Structural and Functional Genomics
Web: http://www.bb.iastate.edu/%7Egfst/homepg.html
Place: Ames, Iowa
September 28 - October 1, 2005 - 4th European Conference on Computational
Biology (ECCB/05)
Web: http://www.eccb05.org/
Place: Madrid
October 26-30, 2005 - Genome Informatics
Web: http://meetings.cshl.edu/meetings/info05.shtml
Organized by CSHL
Place: Cold Spring Harbor
November 14-15, 2005 - Computational Intelligence in Bioinformatics and
Computational Biology
Web: http://www.cibcb.org/
Organized by IEEE Computational Intelligence Society
San Diego, California
-*- -*- -*- -*-
UPCOMING SHORT COURSES
Fortran programming and Bayesian implementation via Markov Chain Monte
Carlo (MCMC) techniques
Time: May 16-27, 2005
Location: Department of Animal and Dairy Science, University of Georgia
Lecturer: Romdhane Rekaya and Ignacy Misztal
ASREML Workshop
Time: June 13-14, 2005
Location: Iowa State University, Ames, IA
Lecturer: Steve Kachman, University of Nebraska
C++ Programming for Animal Breeding
Time: June 15-24
Location: Iowa State University, Ames, IA
Lecturer: Steve Kachman (Nebraska) and Rohan Fernando (Iowa State)
Design and Analysis of Microarray Experiments
Time: July 11-12
Location: Iowa State University, Ames, IA
Lecturer: Dan Nettleton (Dept. Statistics, Iowa State)
NCBI PowerScripting
Time: April 20-22, 2005
Location: Lister Hill Center (Bldg 38A), NLM, NIH, Bethesda, MD
Lecturer: Andrei Gabrielian, Eric Sayers, and David Wheeler
Scopes: A 3-day course including both lectures and computer workshops
on effectively using the NCBI E-utilities within scripts to automate
search and retrieval operations across the entire suite of Entrez
databases.
-*- -*- -*- -*-
Items for the next update can be sent to me by no later than May 15
please.
James Reecy
U.S. Database/Bioinformatics Coordinator
2255 Kildee Hall
Department of Animal Science
Iowa State University
Ames, Iowa 50011-3150
Phone: 515-294-9269
Fax: 515-294-2401
Jreecy@iastate.edu
http://www.genome.iastate.edu