From jreecy@iastate.edu Thu Nov 3 16:10:50 2005
From: James M Reecy <jreecy@iastate.edu>
Date: Thu, 03 Nov 2005 16:01:39 -0600
Subject: NRSP-8 Bioinformatics Update #2
Postmaster: Processed by the Listmaster
To: Multiple Recipients of <angenmap@animalgenome.org>
NRSP-8 Bioinformatics / Database Update
---=== No. 2 ===---
November 1, 2005
----------------------------------------------------------------------
1. Development of Genetic/Genomics Software Database
2. What is new with USDA grants in Washington, DC
3. The Online Mendelian Inheritance in Animals (OMIA) is revamped
4. Generation of Comparative Maps
5. Mouse Genome Informatics announced a new release of MGI
6. Update on the Pig QTL database
7. The livestock sequence Blast server
8. New projects
9. Upcoming bioinformatics meetings (13 items)
----------------------------------------------------------------------
Development of Genetic/Genomics Software Database. In collaboration with Dr.
Wentian Li, North Shore LIJ Research Institute, we have developed a database
of more that 330 programs designed to analyze genetic/genomic data
(http://www.animalgenome.org/soft). To improve the ease of finding available
software, the database was designed so that it can be queried by keywords or
browsed alphabetically. Please contact Zhiliang Hu (zhu@iastate.edu) with
any suggested improvements or additional data to add to the database.
-*- -*- -*- -*-
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. 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.)
The total amount of support available for the Bioinformatics program element
will be approximately $1.5 million. The program element plans to make 1 or 2
awards of up to $1 million each (including indirect costs) for up to 4 years
in duration.
-*- -*- -*- -*-
The Online Mendelian Inheritance in Animals (OMIA) has been revamped and
upgraded. The main change has been to move the master database to a MySQL
platform at the Australian National Genomic Information Service (ANGIS). The
results are: 1) a new web page (http://omia.angis.org.au) that dynamically
queries the master database; 2) access to abstracts (and sometimes full
papers) for papers with a pubmed ID; 3) far greater possibilities for
reciprocal linking with other web sites and 4) on-line curation, which will
enable input from colleagues with specialist knowledge; and which, in time,
will give OMIA a life beyond that of its creator, Frank Nicholas. Another
important development is that at the request of NCBI, OMIA has been
integrated into NCBI?s Entrez search interface at
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIA. This has given
several new dimensions to OMIA, providing enhancements that are not
available from the ANGIS site. The content of the NCBI version will be
updated with regular dumps from the master database. These developments have
been achieved through the sterling efforts of many people (see
http://omia.angis.org.au/acknowledgements.html). The new master database is
still in its infancy. Input from interested colleagues to make OMIA
continually better is encouraged. The efforts
of Frank Nicholas are greatly appreciated (Kindly provided by Dr.
Rothschild).
-*- -*- -*- -*-
Generation of Comparative Maps. A graphic mapping presentation tool has been
developed to generate comparative RH-linkage maps on the fly
(http://www.animalgenome.org/cattle/maps/ RHMap3/). The tool has been used
for the online presentation of the data set from the recently published
cattle RH maps (SIAG-SUNbRH maps, Itoh et al., Genomics, 85(4):413-24). We
plan to develop the tool further to facilitate comparative mapping efforts.
-*- -*- -*- -*-
Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) is pleased
to announce the release of Version 3.3 of the database. Version 3.3
integrates the data on mouse models of human disease and human disease
etiology from OMIM with existing data for mouse genes and strains in MGI.
This enhances the exploration of phenotypes, sequence, expression,
orthology, and other related data. You can now use three of the MGI query
forms (Phenotypes and Alleles, Genes and Markers, Mouse Sequence) to search
for existing or potential mouse models of a particular human disease and all
human diseases that a particular mouse (genotype plus strain background) can
be used to model. Version 3.3 also incorporates data on mouse models sought
without success, such as models free from particular confounding diseases or
phenotypic traits. The database now links to Online Mendelian Inheritance in
Man (OMIM) descriptions of human diseases, syndromes, and conditions. The
updated query forms are for Phenotypes and Alleles is:
http://www.informatics.jax.org/searches/allele_form.shtml, for Genes and
Markers: http://www.informatics.jax.org/searches/marker_form.shtml; for
Mouse Sequence: http://www.informatics.jax.org/searches/sequence_form.shtml
and Human Disease Vocabulary Browser:
http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=omimVocab&subset
=A (kindly provided by David Shaw)
-*- -*- -*- -*-
Update on the Pig QTL database. The pig quantitative trait loci (QTL)
database (PigQTLdb) (http://www.animalgenome.org/QTLdb/) has been recently
published http://dx.doi.org/10.1007/s00335-005-0060-9. On average about
11,000 web hits per month have been made to PigQTLdb in the last few months.
Several hundreds of new QTL data have been added to the database. Stay tuned
for next release soon. Please contact Zhiliang Hu (zhu@iastate.edu) with any
suggested improvements or additional data to add to the database. We are
currently also working with the Aquaculture community to expand the utility
of this resource. In addition, we are working to incorporate the RH map and
BAC end sequence information as well.
-*- -*- -*- -*-
The 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.
-*- -*- -*- -*-
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
November 9-12, 2005. 8th Annual Conference on Computational Genomics
Location: Cambridge, Massachusetts, USA Web:
http://www.jax.org/courses/events/coursedetails.do?id=137
November 14-15, 2005. Computational Intelligence in Bioinformatics and
Computational Biology Location: San Diego, CA, USA Web: http://ieee-
cis.org/cibcb2005/
December 8-11, 2005. 1st International Biocurator Meeting Location: Pacific
Grove, CA, USA Web:
http://tesuque.stanford.edu/biocurator.org//intnlbiocurator.html
January 3-7, 2006. PSB 2006 - Pacific Symposium on Biocomputing Location:
Hawaii, USA Web: http://psb.stanford.edu/
January 21-25 2006. Lan Automation 2006 Location: Palm Springs, CA, USA Web:
http://labautomation.org/LA/LA06/
March 5-10, 2006. Systems Biology: Integrating Biology, Technology, and
Computation Location: Taos, NM, USA Web:
http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=789
April 2-5, 2006. 10th Annual International Conference on Research in
Computational Molecular Biology Location: Venice, Italy Web:
http://recomb06.dei.unipd.it/
April 3-7, 2006. ICDE 2006 - International Conference on Data Engineering
Location: Atlanta, GA,USA Web: http://icde06.cc.gatech.edu/index.html
June 6-8, 2006. International Conference On Computing & Informatics
Location: Kuala Lumpur, Malaysia Web:
http://www.conferencealerts.com/seeconf.mv?q=ca1a03h3
April 12-15, 2006. International Conference on Database Systems for Advanced
Applications Location: Hilton Hotel, Singapore Web:
http://www.comp.nus.edu.sg/~dasfaa06/
June 15-18, 2006. The 8th international bioinformatics meeting Location:
Aarhus, Denmark Web: http://www.birc.au.dk/bioinformatics2006/
July 2-7, 2006. Information Processing and Management of Uncertainty in
Knowledge-Based Systems Location: Paris, France Web:
http://ipmu2006.lip6.fr/
August 6-10, 2006. The 14th Annual International conference on Intelligent
Systems for Molecular Biology. Location: Fortaleza, Brazil Web:
http://ismb_2006.cbi.cnptia.embrapa.br/
-*- -*- -*- -*-
Items for the next update can be sent to me by no later than January 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