314824361dc21136bc421b310438a481e8b74883 mspeir Thu Jun 19 16:09:24 2014 -0700 adding announcement for rn5 conservation track, refs #8212 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 9d0bc54..0d69181 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,129 +1,119 @@ <!-- 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> 19 June 2014 - + Conservation Track Released for Rat</b> + </font> + </p> + + <p> + We are pleased to announce the release of a new Conservation track based on the rat (RGSC 5.0/rn5) assembly. + This track shows multiple alignments of 13 vertebrate species and measurements of evolutionary + conservation using two methods (phastCons and phyloP) from the PHAST package for all species. The + multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics + comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed + in this track. For more details, visit the <a href="../cgi-bin/hgTrackUi?db=rn5&g=cons13way"> + track description page</a>. + </p> + + <p> + With the release of this new conservation track for the rat (RGSC 5.0/rn5) assembly, we have changed the + default rat browser on our website from rn4 to rn5. In general, if you are currently using the rn5 (or + older) browser, the Genome Browser will continue to display that assembly for you when you start it up. + However, there are circumstances in which the assembly may switch to the newer version (for instance, if + you reset your browser to the defaults). If you find yourself in a situation where some of your favorite + browser tracks have "disappeared", you may want to check that you're viewing the right assembly. + </p> + + <p> + We would like to thank Pauline Fujita, Matthew Speir, and Hiram Clawson for their efforts in creating this track. + </p> + + <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> + <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>:</font> <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 --> + <font face="courier" size="3"><b> 19 June 2014 - + Conservation Track Released for Rat (rn5)</b>:</font> + We are pleased to announce the release of a new Conservation track based on the rat (rn5) assembly. </p> - <hr> - - <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>:</font> - <p> <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> + --> + + <!-- start archives --> <p> <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.</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> - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>