f877f97befd2b2b0ffbcc69ae83fa77689e3fb9f mspeir Wed Sep 4 10:10:59 2013 -0700 Adding announcement about oviAri3 release, refs #9409 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index f45fa18..356148c 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -13,147 +13,73 @@ SRC="images/news.jpg" ALT="" ALIGN="right" BORDER=0></A> </TD></TR></TABLE> </TD></TR></TABLE> <TABLE BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <TR><TH HEIGHT=3></TH></TR> <TR><TD WIDTH=10></TD> <TD> <P> To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the <A HREF="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> - <p> - <font face="courier" size="3"><b>22 August 2013 - - Three New Human Variation Tracks Released</b></font> - </p> - <p> - We are pleased to announce the release of three tracks that describe - human genetic variation. They are based on the - <a href="http://lovd.nl/2.0/index_list.php" target="_blank">Leiden Open - Variation Database (LOVD)</a>, the - <a href="http://www.hgmd.cf.ac.uk/ac/index.php" target="_blank">Human Gene - Mutation Database Public (HGMD)</a>, and amino acid mutations in the - <a href="http://www.uniprot.org/" target="_blank">UniProt database</a>. The - majority of the data were collected from publications by curators in the three - databases. - </p> - <p> - The three databases have varying license restrictions. UniProt provides complete - information about the mutation amino acid change, the disease and a link to the - publications that mention it. LOVD provides the mutation and a link to a website - with disease and publication details. HGMD provides some coordinates and a link to - its own website which requires registration. - </p> - <p> - These tracks are intended for use primarily by physicians and other professionals - concerned with genetic disorders, by genetics researchers, and by advanced students - in science and medicine. While the Genome Browser database is open to the public, users - seeking information about a personal medical or genetic condition are urged to consult - with a qualified physician for diagnosis and for answers to personal questions. - </p> - <p> - We'd like to thank all three databases for their help in putting the data together. The - tracks were produced at UCSC by Maximilian Haeussler and Steve Heitner. - </p> - <p> - <font face="courier" size="3"><b>22 July 2013 - - Variant Annotation Integrator</b></font> - </p> - <p> - In order to assist researchers in annotating and prioritizing thousands - of variant calls from sequencing projects, we have developed the Variant - Annotation Integrator (VAI). Given a set of variants uploaded as a - custom track (in either <a href="FAQ/FAQformat.html#format10">pgSnp</a> - or <a href="goldenPath/help/vcf.html">VCF</a> format), the VAI will - return the predicted functional effect (e.g., synonymous, missense, - frameshift, intronic) for each variant. The VAI can optionally add - several other types of relevant information, including: the - <a href="https://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a> - identifier if the variant is found in dbSNP, protein damage scores for - missense variants from the <a href="https://sites.google.com/site/jpopgen/dbNSFP" - target="_blank">Database of Non-synonymous Functional Predictions (dbNSFP)</a>, - and conservation scores computed from multi-species alignments. The VAI - also offers filters to help narrow down results to the most interesting - variants. - </p> - <p> - Future releases of the VAI will include more input/upload options, - output formats, and annotation options, and a way to add information - from any track in the Genome Browser, including custom tracks. - </p> - <p> - There are two ways to navigate to the VAI: (1) From the "Tools" - menu, follow the "Variant Annotation Integrator" link. (2) - After uploading a custom track, hit the "go to variant annotation - integrator" button. The user's guide is at the bottom of the page, - under "Using the Variant Annotation Integrator." - </p> - <p> - Thank you to Angie Hinrichs, Bob Kuhn, Brian Raney, Brooke Rhead, and - Jonathan Casper for their input and work on this feature. + <font face="courier" size="3"><b>05 September 2013 - + New Sheep (oviAri3) Assembly Now Available in the Genome Browser</b></font> + <p> + We are pleased to announce the release of a Genome Browser for the August 2012 + assembly of sheep, <em>Ovis aries</em> (ISGC Oar_v3.1, UCSC version + oviAri3). The whole genome shotgun assembly was provided by the + <a href="http://www.sheephapmap.org" + target="_blank">International Sheep Genomics Consortium</a>. + There are 5,698 scaffolds with a total size of 2,619,054,388 bases. + </p> + <p> + Bulk downloads of the sequence and annotation data are available via the Genome + Browser + <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#sheep">Downloads</a> + page. These data have + <a href="/goldenPath/credits.html#sheep_credits">specific conditions for use</a>. + The sheep (oviAri3) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + <a href="/goldenPath/credits.html#sheep_credits">Credits</a> page for a detailed + list of the organizations and individuals who contributed to this release. </p> <!-- start archives --> <hr> <p> - <!-- staged for archive use <p> <font face="courier" size="3"><b>22 August 2013 - Three New Human Variation Tracks Released:</b></font> We are pleased to announce the release of three tracks that describe human genetic variation. <a href="goldenPath/newsarch.html#082213">Read more</a>. </p> <p> <font face="courier" size="3"><b>22 July 2013 - Variant Annotation Integrator:</b></font> In order to assist researchers in annotating and prioritizing thousands of variant calls from sequencing projects, we have developed the Variant Annotation Integrator (VAI). <a href="goldenPath/newsarch.html#072213">Read more</a>. </p> - --> - - <p> - <font face="courier" size="3"><b>2 July 2013 - - Assembly Data Hubs:</b></font> Assembly Data Hubs extend the - functionality of Track Data Hubs to assemblies that are not hosted - natively on the Browser. - <a href="goldenPath/newsarch.html#070213">Read more</a>. - </p> - - <p> - <font face="courier" size="3"><b>2 July 2013 - - New Gene Alleles feature on the details pages of UCSC genes:</b></font> - For each protein-coding gene in the UCSC Genes track, variant data from - the 2,184 (per autosome) phased chromosomes from Phase 1 of the 1000 - Genomes Project have been distilled into "gene haplotype - alleles." - <a href="goldenPath/newsarch.html#070213b">Read more</a>. - </p> + <!-- staged for archive use <p> - <font face="courier" size="3"><b>28 June 2013 - - New UCSC Genes Track Released for GRCh37/hg19:</b></font> We're happy - to announce the release of an updated UCSC Genes track for the - GRCh37/hg19 human Genome Browser. - <a href="goldenPath/newsarch.html#062813">Read more</a>. + <font face="courier" size="3"><b>05 September 2013 - + New Sheep (oviAri3) Assembly Now Available in the Genome Browser</b></font> + <a href="goldenPath/newsarch.html#090513">Read more</a>. </p> - <p> - <font face="courier" size="3"><b>27 June 2013 - - New Official European Mirror Released: </b></font> Announcing - an official mirror for European users, with automatic - redirection. - <a href="goldenPath/newsarch.html#062713">Read more</a>. - </p> + --> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>