What's New on the NAGRP Animal Genome Web Site


 

New, modified, or content updated pages in the last 30 days

  1. Dec 12, 2017 (10:56): http://www.animalgenome.org/blast
  2. Dec 12, 2017 (07:58): http://www.animalgenome.org/community/angenmap (7)
  3. Dec 08, 2017 (10:00): http://www.animalgenome.org/repository/pub (11)
  4. Dec 07, 2017 (10:51): http://www.animalgenome.org/community/angenmap/stata (9)
  5. Dec 07, 2017 (08:22): http://www.animalgenome.org/../meetings/LivestockHTP.video (2)
  6. Dec 06, 2017 (11:06): http://www.animalgenome.org/QTLdb/release/index (9)
  7. Dec 06, 2017 (04:05): http://www.animalgenome.org/../angenmap/hmail/thread (2)
  8. Dec 06, 2017 (04:05): http://www.animalgenome.org/../angenmap/hmail/subject
  9. Dec 06, 2017 (04:05): http://www.animalgenome.org/community/angenmap/hmail/date
  10. Dec 06, 2017 (04:05): http://www.animalgenome.org/../angenmap/hmail/author
  11. Dec 04, 2017 (13:56): http://www.animalgenome.org/community/FAANG/video (3)
  12. Nov 30, 2017 (08:39): http://www.animalgenome.org/community/FAANG/index (10)
  13. Nov 30, 2017 (04:03): http://www.animalgenome.org/share/meetings
  14. Nov 28, 2017 (11:38): http://www.animalgenome.org/QTLdb/doc (7)
  15. Nov 28, 2017 (09:40): http://www.animalgenome.org/community/projects/eQTL/index
  16. Nov 27, 2017 (19:48): http://www.animalgenome.org/bioinfo/index (8)
  17. Nov 27, 2017 (19:40): http://www.animalgenome.org/bioinfo/resources/ncbitut
  18. Nov 27, 2017 (14:33): http://www.animalgenome.org/repository (2)
  19. Nov 27, 2017 (14:27): http://www.animalgenome.org/share/meetings/LivestockHTP (2)
  20. Nov 27, 2017 (07:52): http://www.animalgenome.org/community/omia-support/info
  21. Nov 24, 2017 (09:42): http://www.animalgenome.org/../meetings/LivestockHTP.reg (4)
  22. Nov 24, 2017 (09:42): http://www.animalgenome.org/../meetings/LivestockHTP.abs
  23. Nov 15, 2017 (07:59): http://www.animalgenome.org/bioinfo/services/index (13)
* Red number in parenthesis indicates multiple updates in the area represented by that URL [Dec 12, 2017 (21:01PM CST)]
 
Major updates / permanent additions:
  • "AnGenMap Frequenly Asked Questions" is updated with new entries to address problems seen for new users, relationships between the Directory and the listserv.
  • Updated, Oct 6, 2017
  • A "Frequently Asked Questions" page is being developed for the NAGRP Community Data Repository platform.
  • New, Oct 2, 2017
  • The Animal QTLdb has a new feature: a "gene centric view" and a "trait centric view" of QTL/association data where underlining gene information is available. This helps users to relatively quickly to interrogate and understand genotype-to-phenotype information in a synopsis. A quick way to use the tool to view information is to try a search by genes or by traits (e.g. try "grand search", then go to "genes" or "traits"), or go from a "Trait Details" view to following links on "List all QTL/association data where a gene may exist". The returned query results are displayed in one of the two ways - "gene centric" or "trait centric" view - at user's choice.
  • New, Sep 17, 2017
  • The NAGRP Data Repository is undergoing another round of restructuring by setting up new data areas for each aquaculture species. The current data area "aquaculture" is planned to deprecate, while existing data in this area are being moved to their respective species areas. The data moved will be also kept available in their current "aquaculture" area until March 1, 2018. As part of the move, data areas for "catfish" and "rainbow trout" have been set up with data inherited from "aquaculture" area.
  • New, Sep 07, 2017
  • What's new on the NAGRP animal genome web site (#3, 2017)
  • New, Aug 29, 2017
  • The NAGRP Data Repository for publication supplementary data files has been restructured with: (1) addition of customized file description area to allow authors to better reflect what are hosted (optional; in addition to what they can put in their publications); This was made retrospectively compatible for 10+ publications having custom file descriptions. (2) modification of the web interface for supplementary data uploads for better collection of meta-data when initiating the data host process; (3) addition of a new machanism to allow only reviewers to access a set of deposited data while the data is considered confidential prior to publication (i.e. public access to the data is not possible during the review period, or until authors give a green light to lift the restriction).
  • New, Aug 10, 2017
  • The web services on https://www.AnimalGenome.ORG is now completely served by a SSL implemented web server, after 5 months test run period during which both HTTP and HTTPS visits were served. Now all traffic to the HTTP protocol (http://www.AnimalGenome.ORG) is now automatically forwarded to HTTPS server.
  • New, Aug 3, 2017
  • The web site for the Functional Annotation of ANimal Genomes (FAANG) consortium, https://www.faang.org, is now operated on a Secure Sockets Layer (SSL) implemented web server.
  • New, Aug 1, 2017
  • A "permanent record locator" is implemented on the AnimalQTLdb to provide unique and stable links to all curated QTL/association data on a publication. The new "permanent record locator" is a replacement of an "URL Link" function introduced two years ago to overcome some of its shortcomings. It can be used by the authors to refer to their published data, to provide proof of evidence of data entry at the Animal QTLdb to journal editors/manuscript reviewers, and to serve other purposes. All QTLdb curators/editors have access to this tool for their curated data.
  • New, Jun 14, 2017
  • The new NCBI pig genome annotation data for the assembly build version 11.1 is made available at the NAGRP shared data repository.
  • New, Jun 1, 2017
  • What's new on the NAGRP animal genome web site (#2, 2017)
  • New, Apr 28, 2017
  • The Secure Sockets Layer (SSL) is implemented on https://www.AnimalGenome.ORG web server for encrypted data transfer from/to the server.
  • New, Mar 27, 2017
  • The new pig genome assembly build version 11.1 is installed on the NAGRP Blast server, for blast searches, available on both blastn and megablast engines. The genome sequence is also available for download from the NAGRP/Pig data repository. Annotations to this build is not yet available.
  • New, Mar 10, 2017
  • Selected NCBI and Ensembl video tutorials on how to use their sites/tools are summarized for user's covenience.
  • New, Feb 19, 2017
  • An online tool is made to batch match Illuminar SNP names to rs numbers.
  • New, Feb 14, 2017
  • A Wordle representation of QTL/association-mapped traits by years can be found in the data summary area of each species on the Animal QTLdb.
  • New, Jan 10, 2017
  • What's new on the NAGRP animal genome web site (#1, 2017)
  • New, Jan 11, 2017
  • The Animal QTLdb curation tools are improved to allow automatic verification and streamlined curation of SNP information as part of the QTL/association annotations. The improvements involved data quality control processes in which multiple genome builds are maintained for cattle, chicken, and sheep.
  • New, Dec 21, 2016
  • The hosted publication supplementary data is now merged with NAGRP Shared Data Repository. Its contents can be found by searching the data repository.
  • Update, Dec 14, 2016
  • The Animal QTLdb curation protocols are modified that preliminary SNPs (with 'ss' numbers only) are allowed to be entered to anchor QTL/association mapping locations. The QTL/association mapping data represented by the 'ss' SNPs are subject to normal data release procedure while the 'ss' SNP information will eventually be replaced with their 'rs' SNP information once the 'rs' numbers are assigned by dbSNP.
  • New, Nov 08, 2016
  • The AnGenMap listserv moderator's switchbox was improved to include functions to aid list moderator's reviewing and posting jobs. These included functions/tools to clean mail text mixed with quoted-printables, and to decode MIME coded text.
  • New, Oct 25, 2016
  • Thanks to Ben Rosen from the USDA/ARS and his colleagues for their efforts putting together a new goat genome assembly. The new goat assembly is now loaded to JBrowse for map alignment views. Currently added tracks include NCBI gene model annotations and NCBI gene structure Gnomon.
  • New, Oct 5, 2016
  • Room share bulletin board for PAG, PAG-Asia and other meetings are improved by adding several administrator tools and a security layer to prevent robot-like hackers.
  • Update, Sep 15, 2016
  • What's new on the NAGRP animal genome web site (#3, 2016)
  • New, Aug 31, 2016
  • 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.
  • Update, Aug 28, 2016
  • The AnimalGenome.ORG site is being moved to a new server with more computing powers which will help us to meet new challenges. The move of multiple services (more than a couple dozen hosted web sites, databases, virtual domains, etc). The complete migration of the services and development platform has been going with relatively smoothly and expected to complete in the next couple months.
  • Update, Aug 2, 2016
  • We have engaged with EBI (EMBL European Bioinformatics Institute) for collaborative VCF file archives. At EBI/EVA (European Variation Archive) all VCF data will be validated to to enter their archive repository, and further streamed to NCBI/dbSNP. See NAGRP VCF Data Repository for updates in the coming months.
  • New, Jul 30, 2016
  • File formate examples are being added to the "Minimum information required for Animal QTLdb data entry" page in the form of Excel work sheets. 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 entering into the QTLdb.
  • Update, May 26, 2016
  • What's new on the NAGRP animal genome web site (#2, 2016)
  • New, Apr 30, 2016
  • The WebApollo were revived on a dedicated NAGRP virtual machine platform as part of the efforts to develop cyber resources for the Striped Bass Genome project led by Benjamin Reading and Charles Opperman at the North Carolina State University.
  • Update, Mar 6, 2016
  • TOM-connectivity related cattle genes: 137,887,921 connectivities among 16,608 probe sets representing 11,125 genes. TOM-connectivity is measured by weighted correlation network analysis on the GEO archive data using "Topological Overlap Measure (TOM)" ( Langfelder P, Horvath S: WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 2008, 9:559) to find "related" genes.
  • New, Feb 24, 2016
  • EpiDB goes online. The development of EpiDB is a collaboration with James Koltes of University of Arkansas to provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock.
  • New, Feb 04, 2016
  • We have set up a private data share area for Dr. Zhou's group at University of California-Davis on the NAGRP Data Repository. This provides a model for individual NRSP-8 labs to have their data share utilizaing the NAGRP bioinformatics platform.
  • New, Jan 21, 2016
  • The Animal QTLdb was present at PAG 2016 Booth on the Plant and Animal Genome XXIV in San Diego, Jan 9-10, 2016.
  • New, Jan 9, 2016
  • What's new on the NAGRP animal genome web site (#1, 2016)
  • New, Jan 04, 2016
  • A new plot tool for whole-genome view of QTL/association data was created. This is to overcome the space limitations of the current plot tool. To use it, start from browing by traits, click on a "link out" icon by a trait name to go to "Find all QTL for this trait type" will do.
  • New, Dec 22, 2015
  • Working with Dr. Frank Nicholas and Matthew Hobbs of Sydney University, we are in a process to migrate the Online Mendelian Inheritance in Animals from it original Sydney University site to Iowa State University (http://OMIA.AnimalGenome.ORG). We expect the full migration will be completed in the coming months.
  • New, Dec 3, 2015
  • We have been developing a livestock breed ontology (LBO) which was started with its utilities in Animal QTLdb. A most recent copy of the LBO is deposited in Bioportal.ORG, and also made available through AmiGO hosted on AnimalGenome.ORG.
  • New, Dec 1, 2015
  • We have recently developed a number of web modules to support the research activities of the FAANG community in terms of structured working groups, grant application oriented collaborations and communications. The same functions/tools can be applied to other groups if such interests exist.
  • New, Nov 16, 2015
  • The Animal QTLdb now can accept user inputs to improve the quality, and add values to the QTLdb data content. The types of user inputs may include additional annotations, comments, or report problems.
  • New, Oct 29, 2015
  • The Animal QTLdb has rolled out new information pages on minimum information required and steps needed to upload large quantity of new QTL/association data.
  • New, Oct 20, 2015
  • Video recorded sessions of GO-FAANG are put onine. The GO-FAANG was held October 7-8, 2015 at the US National Academy of Sciences Building in Washington, DC
  • New, Oct 14, 2015
  • A Jbrowse and a WebApollo were up running on a dedicated NAGRP virtual machine platform as part of the efforts to develop cyber resources for the Striped Bass Genome project led by Benjamin Reading and Charles Opperman at the North Carolina State University.
  • New, Sep 15, 2015
  • What's new on the NAGRP animal genome web site (#3, 2015)
  • New, Aug 31, 2015
  • User interface for NAGRP File Sharing Platform is improved for easy use.
  • Update, Aug 17, 2015
  • New items are added to the AnGenMap FAQ: who can post recruitment advertisements and why? Now the FAQ has 32 items.
  • New, Jul 24, 2015
  • A new pre-compiled CRI-MAP (version 2.5.07) for MacOSX-10.10.4 is made available by Jill Maddox from Australia.
  • New, Jul 22, 2015
  • A horse genotype VCF file is shared by Mohammed Al Abri (Cornell University) and Samantha Brooks (University of Florida). See the NAGRP VCF File Repository for details
  • New, Jul 06, 2015
  • New horse genotype data are shared by Jessica Petersen from the University of Nebraska-Lincoln and Mohammed Al Abri from Cornell University. Jessica's data is part of their recent publication "The American Quarter Horse: Population structure and relationship to the Thoroughbred" on Journal of Heredity. (2014) 105:148-162.
  • New, Jun 26, 2015
  • What's new on the NAGRP animal genome web site (#2, 2015)
  • New, Apr 28, 2015
  • A new version of CRI-MAP is made available by Jill Madox on the CRI-MAP Improvement web site. The main change in this version pertains to the implementation of a version of parallelisation using forks and pipes for the get_likelihoods function. This means that flips, all and build will use multiple cpus when more than one order is being tested.
  • New, Apr 16, 2015
  • Support for OMIA continues -- A virtual machine site is set up for hosting OMIA. The site has a new URL: http://omia.animalgenome.org
  • New, Mar 12, 2015
  • The NAGRP Data Share Repository now has over 1000 files for sharing. A new search function is implemented in the data repository site to help users quickly narrow down the area for targeted files s/he is looking for.
  • New, Feb 7, 2015
  • GenomeWeb interviewed with Jim Reecy: NAGRP Bioinformatics Arm Seeks Input from Livestock Genomics Community to Set Future Priorities.
  • New, Feb 5, 2015
  • A new web site is set up for the international consortium on Functional Annotation of Animal Genomes (FAANG), a.k.a. http://www.faang.org, which supports the collaborative efforts with wiki sites, member forums, communications for working committees. All project related information can also be found on the site.
  • New, Jan 8, 2015
  • What's new on the NAGRP animal genome web site (#1, 2015)
  • New, Jan 6, 2015
  • A preliminary application programming interface (API) platform (developing) has been added to the Animal QTLdb
  • New, Dec 30, 2014
  • A dedicated virtual machine platform is setup to develop cyber resources for the Striped Bass Genome Database (http://stripedbass.animalgenome.org/), a project led by Benjamin Reading and Charles Opperman at the North Carolina State University.
  • New, Dec 15, 2014
  • Horse QTL data is now streamed to UCSC Genome Browser for alignment display and data mining using the tools available at UCSC.
  • New, Nov 05, 2014
  • The NAGRP VCF Data Repository is actively used. The most recent additions are eight (8) VCF files from Drs. Ottmar Distl, Joern Wrede (Institute of Animal Breeding and Genetics, Hannover), Dr. Ludovic Orlando (University of Copenhagen, Centre for GeoGenetics), and Dr. Danika Bannasch (University of California Davis).. Thanks to Dr. Carrie Finno from University of California-Davis to help facilitating with this.
  • New, Oct 25, 2014
  • The state of art online alignment tool - Jbrowse - has been setup for QTL/association data alignment with annotated genes among other genome features. The advantage of Jbrowse is that it allows easy user quantitative data - XYPlot, Density, in BAM or VCF format - to be loaded for comparisons directly to users browser in users local environment.
  • New, Oct 3, 2014
  • QTL/Association discovery trends - a Wordle representation (experimenting...)
  • New, Sep 19, 2014
  • What's new on the NAGRP animal genome web site (#3, 2014)
  • New, Sep 2, 2014
  • The complete implementation of livestock animal QTL tracks at the UCSC site took extended time and they are finally made available in the recent new release of UCSC Genome browser.
  • New, Aug 3, 2014
  • A horse genotype VCF file is shared from Claire Wade (University of Sydney) and Jessica Petersen (University of Nebraska-Lincoln). See the NAGRP VCF Data Repository for details
  • New, Jul 12, 2014
  • A video tutorial is made available on workarounds to a VCmap menu dysfunction on MacOS platform
  • New, Jul 10, 2014
  • We have begun to create video tutorials to introduce new tools developed for Animal QTLdb users to easily access and analyse the QTL data curated into the database. More tutorials are to be added in the coming weeks.
  • New, Jun 30, 2014
  • Thanks to Jeremy Walker [JWalker@neogen.com] the pig 70K SNP chip annotations are now available from the NAGRP data repository
  • New, Jun 10, 2014
  • A new search tool is added to the Animal QTLdb to allow query of neighboring QTL/associations by a user-defined view window. Its utility comes with a sliding window, also defined by user on viewing size and slide distance. The tool also included a graphical representation of the two window positions relative to their chromosome locations. Hyper links enable users to bring the QTL/associations to visualize for their alignments in GBrowse.
  • New, May 27, 2014
  • A new QTLdb curator tool is added to help users batch deposit their QTL/association data.
  • New, May 22, 2014
  • The latest releases of NCBI genome annotations within the last 12 months for several livestock species (cattle: 2013-08-06; chicken: 2013-06-19; pig: 2013-09-29; horse: 2013-09-23) have been made available through the NAGRP shared data repository (look for "Genome_annotations" sub-folder in respective species folders). Information are also linked from each NAGRP species home pages.
  • Update, May 16, 2014
  • The CateGOrizer is now bundled with a new external tool, Revigo, for the convenience of users to take CateGOrizer outputs directly to Revigo for a semantic representative subset analysis.
  • Update, May 16, 2014
  • What's new on the NAGRP animal genome web site (#2, 2014)
  • New, Apr 21, 2014
  • Two annotation data sets in '.bed' format are made available by Heather Holl and Samantha Brooks from Cornell University to share with the horse genomics community. The data sets are on a de novo assembly of three lamellar transcriptomes. Alignment was performed to EquCab2 using BLAT and has been repeats filtered.
  • New, Apr 11, 2014
  • An user contributed FAQ item is added to the Animal QTLdb FAQ list thanks to Shangang Jia. This user kindly shared his experience how to transfer QTL location coordinatyes from the current genome build to an older version using LiftOver. This FAQ also listed a few other similar tools for the same task.
  • New, Apr 5, 2014
  • The Animal QTLdb is improved to include pleiotropic QTL/association data. The pleiotropy data can be accessed through data summaries of a publication. i.e. go to details of a publication (abstract), then click on "List QTL" links, as shown in this example.
  • New, Mar 31, 2014
  • The Animal QTLdb is improved to allow users analyze the QTL by their trait types (i.e. "feed intake" has included "average daily feed intake", "days on feed", "dry matter intake", and "residual feed intake"). To use it, browse the trait hierarchy to find trait of your interests, click on its linkout icon () to "find all QTL on this trait type". This brings up a genome view of all chromosomes showing all mapped QTL in the genome. When there are more QTL on a chromosome than the available space could hold, a "more" link will show to bring you to that particular chromosome in order to display all QTL of the trait type on that chromosome. Currently this function is implemented only in Cattle QTLdb. Stay tuned...
  • New, Mar 22, 2014
  • The Animal QTLdb map view is improved to allow users to view QTL of user's choice on a chromosome for alignment display. To do so, first come up with a list of QTL IDs from your data mining process, then copy all QTL IDs into the "Search" box on a QTLdb chromosome view page, then click "go".
  • New, Mar 18, 2014
  • The NAGRP VCF File Repository (beta version) is open to public to accept file deposits. This platform is designed for collaborative VCF file storage, handling, information abstraction, querying, and data re-use. See our poster at the 2014 PAG for details: VCF Miner: A Platform and Tools for Collaborative Information Mining from Next-Generation Sequence Variant Data.
  • New, Mar 10, 2014
  • Search for Vertebrate Trait (VT) Ontology, Product Trait (PT) Ontology, and Clinical Measurement Ontology (CMO) within the Animal QTLdb is made possible. Use the current search tool "Find if your trait has a QTL" or "Grand search" to start. On the results page, VT/PT/CMO are now shown where mapped. Note on this page there are new choices on the top search box to limit the search "In VT/PT/CMO traits" or "all". e.g. when "In VT/PT/CMO traits" is checked, the results will be limited to, AND grouped by, VT/PT/CMO traits only. - In addition, if any QTL for the trait exists in "other" species, it is also listed, for exploration of the same trait into a different species. Another way to start the search is from respective VT/PT/CMO project home pages, by the heading "Utility: Animal QTLdb", click expansion arrow to open a search box.
  • New, Feb 21, 2014
  • Thanks to Brian Dalrymple, Sean McWilliam, and James Kijas of CSIRO for providing sheep STS marker mapping information, now we have made available the genome coordinate estimates of sheep QTL/association data. Check the sheep QTLdb to find more.
  • New, Feb 07, 2014
  • Vertibrate Trait (VT), Production Trait (PT), and Clinical Measurement Trait (CMO) terms are included on QTLdb searches. See QTLdb trait search to try it out.
  • New, Feb 06, 2014
  • Several Ensembl functional annotated SNP chip data sets are made available via NAGRP Data Repository. These include Ensembl VEP annotated bovine high density (770K) SNP data, bovine low density (6K) SNP data, 50K SNP chip data, chicken 600K SNP chip data, horse 50K SNP chip data, and pig 60K SNP chip data (Thanks to James Koltes for forwarding the information)
  • New, Jan 18, 2014
  • Frustrated by too many Animal QTLdb search options/tools to choose from? Now there is a "grand search" tool available to simplify the database-wide search for you. The searched results are linked to each specialized search tools for you to explore further. Find it on the top of each species page, as well as the "Search Tools" pages.
  • New, Jan 08, 2014
  • What's new on the NAGRP animal genome web site (#1, 2014)
  • New, Jan 06, 2014
  • Animal QTLdb is expanded to include horse for QTL/association data collections.
  • New, Dec 15, 2013
  • Animal QTLdb Search Tools page is reformated for users to easily locate a data search tool for information, for exploration, or for data analysis.
  • Update, Nov 18, 2013
  • A new tool is added to the Animal QTLdb -- which allows users to search for traits of interests for their location distributions throughout the genome. Go to "Search", under "Data Analysis Tools", look for item "Find QTL genome distributions on a particular trait".
  • New, Nov 15, 2013
  • New SNP genotype analysis/process scripts from Guangtu Gao, et al. are added to the NAGRP Tools repository
  • New, Nov 12, 2013
  • New rainbow trout SNP data from publication by Yniv Palti, Guangtu Gao, et al. is added to aquaculture genomics data repository
  • New, Nov 12, 2013
  • A new tool is added to the Animal QTLdb -- for species that has a genome build (currently cattle, chicken, and pig), users now can search and download QTL data by their genome locations (in terms of "bp"). Go to "Search", under "Data Analysis Tools", look for item "Find QTL by their genome locations" to try it out.
  • Update, Oct 22, 2013
  • Animal QTLdb data is synchronized to Ensembl. Users can now utilize Ensembl genome viewer for gene feature/phenotype variation aliagnments. Choose a species where its genome is available (e.g. cattle, chicken, sheep, or pig) and search for traits of your interests to find more.
  • New, Oct 10, 2013
  • NAGRP-8 species/bioinformatics coordinators information updated to reflect the renewed NAGRP coordination structure for the next 5 years.
  • Update, Sep 25, 2013
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