From listmaster animalgenome.org Wed Aug 31 09:03:22 2016
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#3,
2016)
Date: Wed, 31 Aug 2016 09:03:22 -0500
What's new on the NAGRP animal genome web site (#3, 2016)
o Animal QTLdb updates:
Announcing Release 30 of the Animal QTLdb. A sum of 11,571 new
QTL/associations have been added to the database. The current total number
of QTL/association data in the database: 106,028 [Breakdown: Cattle: 81,652;
Chicken: 5,683; Horse: 1,197; Pig: 16,033; Sheep: 1,336; Rainbow trout: 127]
(New additions: Cattle: 10,205; Chicken: 221; Horse: 58; Pig: 924; Sheep:
163).
We thank Giuseppina Schiavo from University of Bologna, Italy, and Paulina
Eusebi from Universitat Autònoma de Barcelona of Spain for their efforts
entering data into the QTLdb.
URL: http://www.animalgenome.org/QTLdb/
Developmental updates:
(1) Introducing the new chicken genome build (GG_5.0) to the QTLdb. We have
completed the first trial of lifting the QTL/association coordinates to the
new build. Continued efforts will be made to verify the transferred data in
the upcoming weeks. Please note the availability of chicken QTL/association
data for download and for graphic visualization online may be affected.
URL: http://www.animalgenome.org/QTLdb/chicken
(2) New file format examples are being added to the "Minimum information
required for Animal QTLdb data entry" page in the form of Excel worksheets.
Click the icon on the right hand side to see an example, and scroll to the
bottom of the page to download all Excel templates. More such templates are
still being added to provide a convenient way for users to prepare their
data for upload into the QTLdb.
URL: http://www.animalgenome.org/QTLdb/doc/minfo/
o New server:
The AnimalGenome.ORG site is being moved to a new server with more computing
power, which will help us to meet new challenges. The move affects multiple
services (more than two dozen hosted web sites, databases, virtual domains,
etc). The complete migration of the services and development platform has
been going relatively smoothly and is expected to be complete in the next
couple months.
With multiple computer servers, we can now offer more services to the
community, such as virtual machines (i.e., a computer space where you have
complete control over what you would like to develop, your own domain name,
etc.).
URL: http://www.animalgenome.org/...rs/service
o VCF data repository development:
We are engaged with EBI (EMBL European Bioinformatics Institute) for
collaborative VCF (variant call format) file archives. At EBI/EVA (European
Variation Archive), all VCF data will be validated prior to entry in their
repository, then further streamed to NCBI/dbSNP. See the NAGRP VCF Data
Repository for updates in the coming months.
URL: http://www.animalgenome.org/...i-bin/util/vcf/index
o CorrDB development:
New curation tools are under active development and expected to be released
soon. This development is intended to couple with the QTLdb in terms of
sharing developed resources and tools, and providing a central resource for
livestock genotype-phenotype information.
URL: http://www.animalgenome.org/CorrDB
Check out the daily "what's new" (http://www.animalgenome.org/news/) items
for up-to-date information on this site. We appreciate user reports on broken
links or web errors to help us ensure a smooth transition of services to the
new server.
Your input is always important to us. Feel free to contact us any time with
your needs, requests, and/or suggestions. You can reach us in multiple ways:
contact Jim Reecy (+1-515-294-9269) for new projects/priorities, send us
email at bioinfo-teamanimalgenome.org, or go to the online Helpdesk
(http://www.animalgenome.org/...fo/services/helpdesk) to get timely
assistance.
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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