3e4a96791a63e5521f10311789a1a5b9bf53bad9 mspeir Fri May 30 12:07:59 2014 -0700 Adding announcement for EVS Variants track. Removed UCSC Gene and 3 assembly announcements. refs #9329 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8260ca4..9d0bc54 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -13,30 +13,51 @@ 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 --> + <hr> + <p> + <font face="courier" size="3"><b> 30 May 2014 - + New Human Variation Track Now Available</b> + </font> + </p> + + <p> + We are pleased to announce the release of the new Exome Variant Server (EVS) Variants track. The + <a href="http://evs.gs.washington.edu/EVS/" target="_blank">EVS</a>, maintained by the + <a href="http://chum.gs.washington.edu/" target="_blank">Nickerson lab</a> at the University of + Washington, contains variant annotations for over 6,500 exomes that were sequenced as part of the + <a href="https://esp.gs.washington.edu/drupal/" target="_blank">NHLBI GO Exome Sequencing Project</a> + (ESP). This annotation includes information such as function, clinical association, dbSNP rsID, + average sample read depth, and much more. You can find more information on how the data for this + track was generated on the <a href="../cgi-bin/hgTrackUi?db=hg19&g=evsEsp6500" + >track description page</a>. + + <p> + We would like to acknowledge Tim Dreszer and Matthew Speir for their hard work in creating this track. + </p> <hr> <p> <font face="courier" size="3"><b> 27 May 2014 - New Roadmap Epigenomics Integrative Analysis Hub now available</b> </font> </p> <p> We are pleased to announce the addition of the <a href="../cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt" >Roadmap Epigenomics Integrative Analysis Hub</a> to our list of publicly available track hubs. This new hub, produced by <a href="http://vizhub.wustl.edu/" target="blank">VizHub</a> at Washington University in St. Louis (WUSTL), contains hundreds of tracks that cover the wide range of epigenomic data available from the <a href="http://www.roadmapepigenomics.org/" target='blank'>Roadmap Epigenomics @@ -53,164 +74,56 @@ to access all the available Roadmap Epigenomics Project data using the UCSC Genome Browser. To access and view these hubs, navigate to the <a href="../cgi-bin/hgHubConnect">Track Hub gateway page</a> and select both the Roadmap Epigenomics Integrative Analysis Hub and Roadmap Epigenomics Data Complete Collection Hub from the Public Hubs list. </p> <p> Any queries about the data should be directed to <A HREF="mailto:twang@genetics. wustl. edu">Ting Wang</A> from VizHub. <!-- above address is twang at genetics.wustl.edu --> </p> <hr> - <p> - <font face="courier" size="3"><b> 15 May 2014 - - New UCSC Gene Track Released for GRCh38/hg38</b> - </font> - <p> - We're happy to announce the release of a new UCSC Genes track for the - GRCh38/hg38 human Genome Browser. - The new release has 104,178 transcripts, compared with 82,960 in the previous - version on hg19. The total number of canonical genes has increased from - 31,848 to 48,424. Comparing the new gene set with the previous version: - </p> - - <ul> - <li>69,691 transcripts did not change between versions.</li> - <li>619 transcripts were not carried forward to the new version.</li> - <li>8,879 transcripts are "compatible" with those in the previous set, - meaning that the two transcripts show consistent splicing.</li> - <li>3,393 transcripts overlap with those in the previous set.</li> - </ul> - <p> - More details about the new UCSC Genes track can be found on the - <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&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> + <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>:</font> - <hr> - <p> - <font face="courier" size="3"><b> 09 May 2014 - - Three New Assemblies Now Available in the Genome Browser</b> - </font> <p> - A Genome Browser is now available for the Chinese hamster (<em>Cricetulus griseus</em>) - assembly released July 2013 by the <a href="http://www.genomics.cn/en/index" - target="_blank">Beijing Genomics Institution-Shenzhen</a> - (BGI version C_griseus_v1.0, UCSC version criGri1). For more - information and statistics about this assembly, see the NCBI assembly record - for <a href="http://www.ncbi.nlm.nih.gov/assembly/40911" target="_blank"> - C_griseus_v1.0</a>. There are 52,711 scaffolds with a total size of 2,360,146,428 - bases. + <font face="courier" size="3"><b> 30 May 2014 - + New Human Variation Track Now Available</b>:</font> + We are pleased to announce the release of the new Exome Variant Server (EVS) Variants track. + <a href="goldenPath/newsarch.html#053014">Read more</a> </p> <p> - Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/criGri1/">FTP server</a> or the - <a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_hamster">Downloads</a> page. - Please observe the <a href="goldenPath/credits.html#chinese_hamster_use">conditions for use</a> when - accessing and using these data sets. The annotation tracks for this browser were - generated by UCSC and collaborators woldwide. See the <a - href="goldenPath/credits.html#chinese_hamster_credits">Credits</a> page for a detailed list of the - organizations and individuals who contributed to this release. - </p> - --- - <p> - A Genome Browser is now available for the hedgehog (<em>Erinaceus europaeus</em>) - assembly released May 2012 by the <a href="http://www.broadinstitute.org/" - target="_blank">Broad Institute</a> - (Broad version EriEur2.0, UCSC version eriEur2). For more - information and statistics about this assembly, see the NCBI assembly record - for <a href="http://www.ncbi.nlm.nih.gov/assembly/426148" target="_blank"> - EriEur2.0</a>. There are 5,802 scaffolds with a total size of 2,715,720,925 - bases. - </p> - - <p> - Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/eriEur2/">FTP server</a> or the - <a href="http://hgdownload.soe.ucsc.edu/downloads.html#hedgehog">Downloads</a> page. - Please observe the <a href="goldenPath/credits.html#hedgehog_use">conditions for use</a> when - accessing and using these data sets. The annotation tracks for this browser were - generated by UCSC and collaborators woldwide. See the <a - href="goldenPath/credits.html#hedgehog_credits">Credits</a> page for a detailed list of the - organizations and individuals who contributed to this release. - </p> - --- - <p> - A Genome Browser is now available for the zebra finch (<em>Taeniopygia guttata</em>) - assembly released February 2013 by <a href="http://genome.wustl.edu/genomes/detail/taeniopygia-guttata/" - target="_blank">The Genome Institute at Washington University</a> - (WUSTL version Taeniopygia_guttata-3.2.4, UCSC version taeGut2). For more - information and statistics about this assembly, see the NCBI assembly record - for <a href="http://www.ncbi.nlm.nih.gov/assembly/524908" target="_blank"> - Taeniopygia_guttata-3.2.4</a>. There are 37,096 scaffolds with a total size of 1,232,135,591 - bases. - </p> - - <p> - Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/taeGut2/">FTP server</a> or the - <a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebra_finch">Downloads</a> page. - Please observe the <a href="goldenPath/credits.html#zebra_finch_use">conditions for use</a> when - accessing and using these data sets. The annotation tracks for this browser were - generated by UCSC and collaborators woldwide. See the <a - href="goldenPath/credits.html#zebra_finch_credits">Credits</a> page for a detailed list of the - organizations and individuals who contributed to this release. - </p> - - <hr> - - <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b></font>: - <font face="courier" size="3"><b> 22 May 2014 - New Roadmap Epigenomics Integrative Analysis Hub now available</b>:</font> We are pleased to announce the addition of the <a href="../cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt" >Roadmap Epigenomics Integrative Analysis Hub</a> to our list of publicly available track hubs. <a href="goldenPath/newsarch.html#052714">Read more</a> + </p> + --> + <!-- start archives --> + + <p> <font face="courier" size="3"><b> 15 May 2014 - We're happy to announce the release of a new UCSC Genes track for the - GRCh38/hg38 human Genome Browser. + GRCh38/hg38 human Genome Browser.</b></font> <a href="goldenPath/newsarch.html#051514">Read more</a> + </p> + <p> <font face="courier" size="3"><b> 09 May 2014 - Three New Assemblies Now Available in the Genome Browser</b>:</font> A Genome Browser is now available for the Chinese hamster (<em>Cricetulus griseus</em>), hedgehog (<em>Erinaceus europaeus</em>), and zebra finch (<em>Taeniopygia guttata</em>). <a href="goldenPath/newsarch.html#050914">Read more</a> - --> - - <!-- start archives --> - - <p> - <font face="courier" size="3"><b> 08 May 2014 - - New Elephant Shark (calMil1) Assembly Now Available in the Genome - Browser</b>:</font> - A Genome Browser is now available for the elephant shark (<em>Callorhinchus milii</em>) - assembly released December 2013 by the Singapore Institute of Molecular - and Cell Biology. - <a href="goldenPath/newsarch.html#050814">Read more</a> - </p> - - <p> - <font face="courier" size="3"><b> 06 May 2014 - - Introducing the new stacked overlay for multi-wiggle tracks</b>:</font> - We are excited to announce the release of the new "stacked" - overlay method for multi-wiggle tracks. - <a href="goldenPath/newsarch.html#050614">Read more</a> </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>