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 @@ -1,216 +1,129 @@ <!-- 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 --> + <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 Project</a>. This hub contains data from over 40 different assays carried out on over 250 different cell and sample types. These assays include RNA-seq, MeDIP-seq, MRE-seq, methylC-seq, DNase hypersensitivity, chromHMM segmentation, ChIP-seq, and more than 30 histone modifications. The data contained in this hub is complementary to the ENCODE data available at UCSC and in the ENCODE Integrative Analysis public hub. </p> <p> You can view more data produced by the Roadmap Epigenomics Project in their other publicly available track hub, the Roadmap Epigenomics Data Complete Collection. You can use these two hubs together 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>