From jreecy@iastate.edu Wed Mar 1 10:44:31 2006
Date: Wed, 01 Mar 2006 10:17:29 -0600
From: James M Reecy <jreecy@iastate.edu>
Subject: NRSP-8 Bioinformatics update
Postmaster: Processed by the Listmaster
To: Multiple Recipients of <angenmap@animalgenome.org>
NRSP-8 Bioinformatics / Database Update
---=== No. 3 ===---
March 1, 2006
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1. Query the Bovine SNP Database
2. Bioinformatics utility tool box
3. Animal Genomics Software Archive
4. What is new with USDA grants in Washington, DC
5. New projects
6. Upcoming meetings
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Query the Bovine SNP Database. A database is set up using most recent bovine
SNP released by Baylor. This database contains 114,958 bovine SNPs derived
from multi-breed genome sequence information comparisons. A web interface is
set up for public users to blast against the SNP flanking sequences and
query the database for SNP details if good hits are found. URL:
http://www.animalgenome.org/bioinfo/resources/util/q_bovsnp.html
Bioinformatics utility tool box. A bioinformatics utility tool box is set up
at the NAGRP Bioinformatics site. Currently there are 6 utility tools in the
"box": 1. Expeditor: Design primers gene structure and EST information from
different species. 2. Prim2: Design primers on the consensus of 2 similar
sequences. 3. A sequence alignment diagram drawing tool. 4. Gene ontology
(GO) terms classifications counter. 5. DNA Sequence Reverse Complement
Converter 6. Query the Bovine SNP Database by blast. URL:
http://www.animalgenome.org/bioinfo/resources/util/
Animal Genomics Software Archive. We have set up an animal genomics software
archive site for publicly shared software
(http://db.genome.iastate.edu/ftp/share/). Those who wish to share their
software with the community, please feel free to contact bioinfo-
team@animalgenome.org for information on how to deposit your software to
this archive.
What is new with USDA grants in Washington, DC. The new USDA-NRI request for
applications is available. You can access it at
http://www.csrees.usda.gov/funding/rfas/nri_rfa.html. We want to remind
everyone that this year there is a specific call for bioinformatics
proposals.
The Bioinformatics program requests applications for the
development of bioinformatic tools that will assist in functional
genomics, annotation and comparative genomics of agriculturally
important animals. These tools need to be designed to integrate with
existing data/databases (not create new ones), serve as tools for
genome analysis, provide for practical applications of genomic data
and have a biological framework.
FY 2006 Priorities for Research
1) Tools that integrate genome sequence, genome annotations and
pedigree information with biological function and phenotypic
information for a single species or across multiple species; and
2) Animal bioinformatics tools to efficiently and effectively handle
and interpret the genomic/ genetic data being generated to accelerate
the knowledge discovery process. (Examples include technology
platforms, computational resources and analytical tools for
integrative and comparative research.)
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.
<mailto:Jreecy@iastate.edu>Jreecy@iastate.edu
UPCOMING BIOINFORMATICS MEETINGS
March 05 - March 10, 2006
Event: Biology: Integrating Biology, Technology, and Computation
Location: Taos, NM, USA
Web: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingIDx9
April 02 - April 05, 2006
Event: 10th Annual International Conference on Research in
Computational Molecular Biology (RECOM)
Location: Venice, Italy
Web: http://recomb06.dei.unipd.it/
May 16 - May 19, 2006
Event: 2nd International Symposium on Animal Functional Genomics
Location: Henry Center, Michigan State University, East Lansing, MI
Web: http://www.isafg.msu.edu/
May 24 - May 28, 2006
Event: Genomes, Evolution, & Bioinformatics (GEB2006)
Location: Arizona State University, Tempe, Arizona
Web: http://www.smbe.org/geb/
June 15 - June 18, 2006
Event: 7th International Conference on Bioinformatics 2006
Location: hus, Denmark
Web: http://www.birc.au.dk/bioinformatics2006/
August 04 - August 05, 2006
Event: The 6th annual Bioinformatics Open Source Conference (BOSC 2005)
Location: Fortaleza, Brasil
Web: http://www.open-bio.org/bosc2005/
August 06 - August 10, 2006
Event: Intelligent Systems for Molecular Biology (ISMB)
Location: Fortaleza, Brazil
Web: http://ismb2006.cbi.cnptia.embrapa.br/
August 13 - August 18, 2006
Event: 8th World Congress on Genetics Applied to Livestock Production
Location: Belo Horizonte, MG, Brazil
Web: http://www.wcgalp8.org.br/paginaInicial.do
August 20 - August 25, 2006
Event: 30th International Conference on Animal Genetics (ISAG 2006)
Location: Porto Seguro, Bahia State, Brazil
Web: http://www.cbra.org.br/eventos/XXXisag.do
August 30 - September 03, 2006
Event: 28th Annual International Conference of the IEEE Engineering
in Medicine and Biology Society
Location: Marriott Hotel at Times Square, New York, NY
Web: http://embc2006.njit.edu/
September 04 - September 08, 2006
Event: 4th International Workshop on Biological Data Management - BIDM 06
Location: Krakow, Poland
Web: <http://embc2006.njit.edu/>http://embc2006.njit.edu/
September 10 - October 13, 2006
Event: 4th European Conference on Computational Biology (ECCB/05)
Location: Eilat, Isreal
Web: http://www.eccb06.org/
September 13 - September 17, 2006
Event: Genome Informatics
Location: Hinxton, UK
Web: http://meetings.cshl.edu/meetings/infouk06.shtml
September 28 - September 29, 2006
Event: Computational Intelligence in Bioinformatics and Computational Biology
Location: San Diego, California
Web: http://eldar.mathstat.uoguelph.ca/dashlock/CIBCB2006/
October 16 - October 18, 2006
Event: IEEE Symposium on Bioinformatics and Bioengineering (BIBE)
Location: Washington D.C
Web: http://birg.cs.wright.edu/bibe06/
November 08 - November 14, 2006
Event: COMPUTATIONAL & COMPARATIVE GENOMICS
Location: Cold Spring Harbor Laboratory, NY
Web: http://meetings.cshl.edu/courses/c-ecg06.shtml
November 11 - November 15, 2006
Event: Biomedical and Health Informatics
Location: Hilton Wahington & Towers, Wahington, DC
Web: http://embc2006.njit.edu/
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