52b721ced395f7bcefb6e9ce4c1b8ac803f3c7a8 steve Tue Jul 15 08:58:05 2014 -0700 Modified static docs for ochPri3 and sorAra2 release (redmine #9347,9348) diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 9a972c2..42a15a6 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,129 +1,126 @@ <!-- 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>. + <font face="courier" size="3"><b> 15 July 2014 - + New Shrew (sorAra2) Assembly Now Available in the Genome Browser</b> + </font> </p> - <p> - With the release of this new conservation track, we have changed the default rat browser on - our website from rn4 to rn5. In general, the Genome Browser will continue to display - whichever rat assembly you have already been viewing, and will default to the rn5 assembly - only for those users who haven't recently viewed a rat assembly. However, there are - circumstances in which the browser may update the view to the newer version, for instance - if you reset your browser settings to the default values. 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 expected assembly. + We are pleased to announce the release of a Genome Browser for the August 2008 + assembly of shrew, <em>Sorex araneus</em> (Broad SorAra2.0, UCSC version + sorAra2). The whole genome shotgun assembly was provided by + <a href="http://www.broadinstitute.org/" + target="_blank">The Broad Institute</a>. + There are 12,845 scaffolds with a total size of 2,423,158,183 bases. </p> - <p> - We would like to thank Pauline Fujita, Matthew Speir, and Hiram Clawson for their efforts in - creating this track. + Bulk downloads of the sequence and annotation data are available via the Genome + Browser + <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/sorAra2/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#shrew">Downloads</a> + page. These data have + <a href="/goldenPath/credits.html#shrew_credits">specific conditions for use</a>. + The shrew (sorAra2) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + <a href="/goldenPath/credits.html#shrew_credits">Credits</a> page for a detailed + list of the organizations and individuals who contributed to this release. </p> <hr> + <p> - <font face="courier" size="3"><b> 30 May 2014 - - New Human Variation Track Now Available</b> + <font face="courier" size="3"><b> 15 July 2014 - + New Pika (ochPri3) Assembly Now Available in the Genome Browser</b> </font> </p> - <p> - We would like 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>. - + We are pleased to announce the release of a Genome Browser for the May 2012 + assembly of pika, <em>Ochotona princeps</em> (Broad OchPri3.0, UCSC version + ochPri3). The whole genome shotgun assembly was provided by + <a href="http://www.broadinstitute.org/" + target="_blank">The Broad Institute</a>. + There are 10,420 scaffolds with a total size of 2,229,835,716 bases. + </p> <p> - We would like to acknowledge Tim Dreszer and Matthew Speir for their hard work in creating - this track. + Bulk downloads of the sequence and annotation data are available via the Genome + Browser + <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#pika">Downloads</a> + page. These data have + <a href="/goldenPath/credits.html#pika_credits">specific conditions for use</a>. + The pika (ochPri3) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + <a href="/goldenPath/credits.html#pika_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> <p> - <font face="courier" size="3"><b> 19 June 2014 - - Conservation Track Released for Rat (rn5)</b>: </font> - We have released a new Conservation track based on the rat (rn5) assembly. - <a href="goldenPath/newsarch.html#061914">Read more</a>. + <font face="courier" size="3"><b> 15 July 2014 - + New Shrew (sorAra2) Assembly Now Available in the Genome Browser</b>: </font> + We are pleased to announce the release of a Genome Browser for the August 2008 + assembly of shrew, <em>Sorex araneus</em> (Broad SorAra2.0, UCSC version + sorAra2). <a href="goldenPath/newsarch.html#071514">Read more</a>. </p> <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>. + <font face="courier" size="3"><b> 15 July 2014 - + New Pika (ochPri3) Assembly Now Available in the Genome Browser</b>: </font> + We are pleased to announce the release of a Genome Browser for the May 2012 + assembly of pika, <em>Ochotona princeps</em> (Broad OchPri3.0, UCSC version + ochPri3). <a href="goldenPath/newsarch.html#071514">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>. + <font face="courier" size="3"><b> 19 June 2014 - + Conservation Track Released for Rat (rn5)</b>: </font> + We have released a new Conservation track based on the rat (rn5) assembly. + <a href="goldenPath/newsarch.html#061914">Read more</a>. </p> <p> - <font face="courier" size="3"><b> 15 May 2014 - - New UCSC Gene Track Released for GRCh38/hg38</b>: </font> - We're happy to announce the release of a new UCSC Genes track for the - GRCh38/hg38 human Genome Browser. - <a href="goldenPath/newsarch.html#051514">Read more</a>. + <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> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>