8d3723380a50dafc3d17cc29b8605c0a8e669aef luvina Mon Jul 16 11:36:23 2012 -0700 Added sarHar1 announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index fda0d88..45d28e2 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,165 +1,87 @@ <!--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="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> + + <FONT FACE="courier" SIZE="3"><B>16 July 2012 - Tasmanian Devil + Assembly Now Available in Genome Browser </B></FONT> + <P>We are pleased to announce the release of a Genome Browser + for the February 2011 Tasmanian devil assembly, <em>Sarcophilus harrisii</em> + (WTSI version Devil_refv7.0, UCSC version sarHar1). The Tasmanian devil, + which is native to the island of Tasmania, is at risk of extinction due + to a transmissable facial cancer. The devil population in Tasmania has declined by more + than 80% since the first time the disease was observed 14 years ago. + This draft assembly, created by the <a href="http://www.sanger.ac.uk/" + >Wellcome Trust Sanger Institute</a>, + was sequenced using Illumina reads. This completed genome is the first step + towards finding genetic mutations in the transmissible cancer, which will help + researchers understand the disease and its spread. + <P> + Bulk downloads of the sequence and annotation data are available + via the Genome Browser + <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/sarHar1/" TARGET=_blank + >FTP server</A> or the + <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#tasmanian_devil" TARGET=_blank + >Downloads</A> page. The Tasmanian devil browser + annotation tracks were generated by UCSC and collaborators worldwide. + See the + <A HREF="http://genome.ucsc.edu/goldenPath/credits.html#tasmanian_devil_credits" TARGET=_blank + >Credits</A> page for a detailed list of the organizations and + individuals who contributed to the success of this release. + <HR> + <P> <FONT FACE="courier" SIZE="3"><B>06 July 2012 - hgText CGI To Be Retired </B></FONT> </P> <P>We are announcing the imminent retirement of the hgText CGI. hgText was the original version of the Table Browser, and was replaced by the new CGI, hgTables, in <A HREF = "goldenPath/newsarch.html#100104">2004</A>. A very small number of our users are still accessing the database using the old hgText CGI. Beginning July 24, 2012, we will be removing the hgText CGI from our site. All users will need to use hgTables after that time. </P> - <HR> - <P> - <FONT FACE="courier" SIZE="3"><B>19 June 2012 - Many New - Assemblies Available in the Browser! </B></FONT> - </P> - <P> - With the abundance of new vertebrate assemblies available in - GenBank, the UCSC Genome Browser team has streamlined its - browser release pipeline in the effort to keep pace. In the past - week we have released a new browser on the Western painted - turtle and updated assemblies for the cow, rat, and chicken. - Browsers for the lesser hedgehog tenrec and the latest dog - assembly should be available later this week, for a total of 18 - assemblies released in the past half year. You can - expect many new assemblies to show up on our website in upcoming - months, along with broader multiple alignment annotations on - selected organisms that include many of the new assemblies.</P> - <P> - Keep in mind that some of these new assemblies may not yet be - fully populated with annotation tracks. Some data, such as the - data underlying genes and SNPs tracks, may not be immediately - available, and other annotations (e.g., comparative genomics - tracks) may take a while to generate. As always, our mandated - focus is on vertebrates, with a particular emphasis on richly - annotating the human genome, although we do provide occasional - updated assemblies for other selected model organisms (fly, - worm, yeast).</P> - <P> - We regret that we don't have the resources to support the many - other genomics research communities who would like us to - visualize their data in our browser, but we can provide you - with information for setting up your own browser or track hub - to display your data, as well as links to other visualization - resources on the web that are specific to your genome of - interest. Feel free to <A HREF="contacts.html">contact us</A> - for more information.</P> - <P> - Newly released assemblies: - <UL> - <LI><B>Cow</B> (<em>Bos taurus</em>) <B>bosTau7</B> – - Btau_4.6.1 (Oct. 2011) from the Bovine Genome Sequencing - Consortium and Baylor College of Medicine - <LI><B>Rat</B> (<em>Rattus norvegicus</em>) <B>rn5</B> – - RGSC Rnor_5.0 (Oct. 2011) from the Rat Genome Sequencing - Consortium - <LI><B>Chicken</B> (<em>Gallus gallus</em>) <B>galGal4</B> - – Gallus_gallus-4.0 (Nov. 2011) from the International - Chicken Genome Consortium - <LI><B>Western painted turtle</B> (<em>Chrysemys picta bellii</em>) - <B>chrPic1</B> – Chrysemys_picta_bellii-3.0.1 (Dec. 2011) - from the International Painted Turtle Genome Sequencing Consortium - <LI><B>Lesser hedgehog tenrec</B> (<em>Echinops telfairi</em>) - <B>echTel1</B> – echTel1 (Jul. 2005) from the Broad - Institute (pending) - <LI><B>Dog</B> (<em>Canis familiaris</em>) <B>canFam3</B> - – v3.1 (Sep. 2011) from the Broad Institute (pending) - </UL> - - Released in the past half year: - <UL> - <LI><B>Mouse</B> (<em>Mus musculus</em>) <B>mm10</B> – - GRCm38 (Dec. 2011) from the Mouse Genome Reference Consortium - <LI><B>Cow</B> (<em>Bos taurus</em>) <B>bosTau6</B> – - Bos_taurus_UMD_3.1 (Nov. 2009) from the University of Maryland - <LI><B>Fugu</B> (<em>Takifugu rubripes</em>) <B>fr3</B> – - FUGU5 (Oct. 2011) from the International Fugu Genome Sequencing - Consortium - <LI><B>Gibbon</B> (<em>Nomascus leucogenys</em>) <B>nomLeu1</B> - – Nleu1.0 (Jan. 2010) from the Gibbon Genome Sequencing - Consortium - <LI><B>Gorilla</B> (<em>Gorilla gorilla gorilla</em>) <B>gorGor3</B> - – gorGor3.1 (May 2011) from the Wellcome Trust Sanger - Institute - <LI><B>Microbat</B> (<em>Myotis lucifugus</em>) <B>myoLuc2</B> - – Myoluc2.0 (Jul. 2010) from the Broad Institute - <LI><B>Naked mole-rat</B> (<em>Heterocephalus glaber</em>) - <B>hetGla1</B> – HetGla_1.0 (Jul. 2011) from the Beijing - Genomics Institute - <LI><B>Tammar wallaby</B> (<em>Macropus eugenii</em>) <B>macEug2</B> - – Meug_1.1 (Sep. 2009) from the Tammar Wallaby Genome - Sequencing Consortium - <LI><B>Turkey</B> (<em>Meleagris gallopavo</em>) <B>melGal1</B> - – Turkey_2.01 (Dec. 2009) from the Turkey Genome Consortium - <LI><B>Western clawed frog</B> (<em>X. tropicalis</em>) - <B>xenTro3</B> – v4.2 (Nov. 2009) from the DOE Joint - Genome Institute - <LI><B><em>C. elegans</em></B> <B>ce10</B> – WS220 - (Oct. 2010) from WormBase - <LI><B><em>S. cerevisiae</em></B> <B>sacCer3</B> – - SacCer_Apr2011 (Apr. 2011) from the Saccharomyces Genome Database - </UL> </P> - <P> - Bulk downloads of the sequence and annotation data for these - assemblies are available via the Genome Browser - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/" - TARGET=_blank>FTP server</A> or the - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html" - TARGET=_blank>Downloads</A> page. Be sure to check the - <A HREF="goldenPath/credits.html" TARGET=_blank>credits</A> - page for data use restrictions and acknowledgments. </P> - <P> - Many thanks to the sequencing and assembly groups, as well as - NCBI's GenBank, for making these genomes available for public - use. We'd also like to acknowledge Hiram Clawson, Chin Li, and - our hard-working QA team for putting together these browsers. </P> - <HR> <!-- start archives --> <P> - <font face="courier" size="3"><b> 15 May 2012 - New Fugu (fr3) - Assembly Now Available in the Genome Browser: </b></font> - We are pleased to announce the release of a Genome Browser - for the October 2011 assembly of the Fugu, <i>Takifugu rubripes</i> - (JGI v5.0, UCSC version fr3). - <A HREF="goldenPath/newsarch.html#051512b">Read more</A>. + <font face="courier" size="3"><b>19 June 2012 - Many New + Assemblies Available in the Browser!</b></font> + With the abundance of new vertebrate assemblies available in + GenBank, the UCSC Genome Browser team has streamlined its + browser release pipeline in the effort to keep pace. + <A HREF="goldenPath/newsarch.html#061912">Read more</A>. </P> <P> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>