a0cbdee739083061b0f3b65a8375443c73514c30 pauline Tue Jul 2 15:31:23 2013 -0700 Adding assembly hubs and gene alleles announcements to news page. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index df8ef8b..c78b9a0 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,168 +1,174 @@ <!--News Section-----------------------------------------------> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="#fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0> <TR><TD> <!--cheap trick to get background on row to be continuous--> <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <TR><TD ALIGN="left"> <font size="4"><a name="TOC"></a><b> News</b></font><a href="http://www.twitter.com/GenomeBrowser" target="_blank"><img src="http://twitter-badges.s3.amazonaws.com/t_small-a.png" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></TD> <TD ALIGN="right"><A HREF="goldenPath/newsarch.html"><IMG 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>2 July 2013 + - Assembly Data Hubs</b></font> + </p> + <p> + We are pleased to announce a new feature in the UCSC Genome Browser: + Assembly Data Hubs. + </p> + <p> + Assembly Data Hubs extend the functionality of Track Data Hubs to + assemblies that are not hosted natively on the Browser. Assembly Data + Hubs were developed to address the increasing need for researchers to + annotate sequence for which UCSC does not provide an annotation + database. They allow researchers to include the underlying reference + sequence, as well as data tracks that annotate that sequence. Sequence + is stored in the UCSC twoBit format, and the annotation tracks are + stored in the same manner as Track Data Hubs. + </p> + <p> + To read more about using Assembly Data Hubs, or about creating your + own, please see these guides: + </p> + <p> + <a href="http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html"> + http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html</a> + </p> + <p> + <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs"> + http://genomewiki.ucsc.edu/index.php/Assembly_Hubs</a> + </p> + <p> + Many thanks to Hiram Clawson, Brian Raney, and Pauline Fujita for their work on this feature. + </p> + + <p> + <font face="courier" size="3"><b>2 July 2013 + - New Gene Alleles feature on the details pages of UCSC genes</b></font> + </p> + <p> + We are excited to announce the release the new Gene Alleles feature on + the details pages of UCSC genes. 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." Each haplotype allele is a + distinct set of variants found on at least one of the 1000 Genomes + subject chromosomes. For each haplotype, we display its frequency in + the 1000 Genomes populations and indicate the frequency with which it + occurs homozygously in each population. Unexpected frequencies of + occurrence may thus be used to identify alleles that merit further + study. Predicted protein sequence for common haplotypes can also be + displayed, allowing differences among alleles to be used to identify + differences at the amino acid level. + </p> + <p> + To see the Gene Alleles feature, go to the details page for any + protein-coding gene in the UCSC Genes track and click the "Gene + Alleles" link in the top right cell of the "Page Index" matrix. This + will take you to the "Common Gene Haplotype Alleles" section. For + more information on this feature please see this help doc: + </p> + <p> + <a href="http://genome.ucsc.edu/goldenPath/help/haplotypes.html"> + http://genome.ucsc.edu/goldenPath/help/haplotypes.html</a> + </p> + <p> + Many thanks to Tim Dreszer, Brooke Rhead and Pauline Fujita for their work on this feature. + </p> + + <p> <font face="courier" size="3"><b>28 June 2013 - New UCSC Genes Track Released for GRCh37/hg19</b></font> </p> <p> We're happy to announce the release of an updated UCSC Genes track for the GRCh37/hg19 human Genome Browser. The new release has 82,960 total transcripts, compared with 80,922 in the previous version. The total number of canonical genes has increased from 31,227 to 31,848. Comparing the new gene set with the previous version: <ul> <li>74,657 transcripts did not change between versions. <li>88 transcripts were not carried forward to the new version. <li>5,556 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs. <li>621 transcripts overlap with those in the previous set but do not show consistent splicing, i.e., they contain overlapping introns with differing splice sites. </ul> </p> <p> More details about the new UCSC Genes track can be found on the <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene" >UCSC Genes track description page</a>. </p> <p> Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo for their work on this track! </p> <p> - <font face="courier" size="3"><b>27 June 2013 - - New Official European Mirror Released</b></font> - </p> - - <p> - The UCSC Genome Browser is pleased to announce the - introduction of a new mirror site to serve our users - in Europe. Genome-euro is an official European mirror - site of the UCSC Genome Browser, at - <A HREF = "http://genome-euro.ucsc.edu" TARGET = _BLANK> - http://genome-euro.ucsc.edu</A>. The server is physically - located at the Universität Bielefeld Center for - Biotechnology in Bielefeld, Germany, and is administered - by UCSC. Genome-euro is meant to be an alternate, faster - access point for those Browser users who are geographically - closer to central Europe than to the western United States. - </p> - <p> - All functionality will be the same as on the US server, - although Custom Tracks will not be transfered. Saved Sessions - containing Custom Tracks will require some manual <A HREF = - "http://genome.ucsc.edu/goldenPath/help/genomeEuro.html#sessions" - TARGET = _BLANK>intervention</A>. - </p> - <p> - When European users navigate to the US server home page - and click the "Genomes" menu item, they will receive a - notification that they have been - redirected to the more geographically-appropriate server. - They will have the option to remain on the US server, as - described in our - <A HREF = "http://genome.ucsc.edu/goldenPath/help/genomeEuro.html" - TARGET = _BLANK>documentation</A>. - </p> - <p> - The backup mirror in <A HREF = "http://genome-mirror.moma.ki.au.dk/" - TARGET = _BLANK>Aarhus, Denmark</A> will continue to serve as an - emergency site in the event of the official sites in California - and Germany malfunctioning. - </p> - <p> - We wish to express our special thanks to our colleagues at the - Universität Bielefeld Bioinformatics, especially Jens Stoye, - for making this possible. - </p> - - <p> - <font face="courier" size="3"><b>26 June 2013 - - Suggestion Box Released</b></font> - </p> - <p> - Due to popular demand, we have created a suggestion box for track, assembly, - tool, and other requests. All suggestions will be assigned a reference - number so that you may follow up on their progress with our staff. Please - limit the use of this form to requests for new features; questions and reports - of problems about existing features and data should continue to be directed to - our mailing lists. You may reach the suggestion box from the - <a href="contacts.html">Contact Us</a> page or by - <a href="cgi-bin/hgUserSuggestion">clicking here</a>. - </p> - <p> - - <!-- start archives --> <hr> - <!-- staged for archive use - <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> + <a href="goldenPath/newsarch.html#062713">Read more</a>. </p> <p> <font face="courier" size="3"><b>26 June 2013 - Suggestion Box Released:</b></font> Due to popular demand, we have created a suggestion box for track, assembly, tool, and other feature requests. <a href="goldenPath/newsarch.html#062613">Read more</a>.</p> - --> - <p> - <font face="courier" size="3"><b>12 June 2013 - - Ferret Genome Browser Released:</b></font> - A Genome Browser is now available for the Ferret - (<em>Mustela putorius furo</em>) assembly released by the Ferret Genome Sequencing Consortium - April 2011 (version MusPutFur1.0, UCSC version musFur1). - <a href="goldenPath/newsarch.html#061213">Read more</a>.</p> + <!-- start archives --> + <hr> + <!-- staged for archive use + <p> + <font face="courier" size="3"><b>2 July 2013 + - Assembly Data Hubs</b></font> + </p> + <p> + <a href="goldenPath/newsarch.html#070213">Read more</a>. + </p> + <p> - <font face="courier" size="3"><b>22 May 2013 - - Gibbon Genome Browser Released:</b></font> - A Genome Browser is now available for the Gibbon - (<em>Nomascus leucogenys</em>) assembly released by the Gibbon Genome Sequencing Consortium - October 2012 (version Nleu_3.0, UCSC version nomLeu3). - <a href="goldenPath/newsarch.html#052213">Read more</a>.</p> + <font face="courier" size="3"><b>2 July 2013 + - New Gene Alleles feature on the details pages of UCSC genes</b></font> + </p> + <a href="goldenPath/newsarch.html#070213b">Read more</a>. + </p> -==> <a href="goldenPath/newsarch.html">News Archives</a> + + --> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>