7fd3e07e801c35b7345e1219b70280f0c860310d donnak Wed Jun 27 13:21:57 2012 -0700 Added news announcement about several new assemblies, and archived some items. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index cd27a97..7187f55 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,139 +1,155 @@ <!--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> - 15 May 2012 - New Fugu (fr3) Assembly Now Available in the Genome Browser - </b></font> - - <p>We are pleased to announce the release of a Genome Browser - for the October 2011 fugu, <i>Takifugu rubripes</i> - (JGI v5.0, UCSC version fr3). Whole genome shotgun assembly was provided by the - <a target="_blank" href="http://www.fugu-sg.org/">International Fugu Genome Sequencing - Consortium,</a> led by JGI and the <a target="_blank" href="http://www.imcb.a-star.edu.sg/"> - Singapore Institute of Molecular and Cell Biology</a> (IMCB).</p> - - <p>Bulk downloads of the sequence and annotation data are available via the Genome Browser - <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/">FTP server</a> or the - <a href="http://hgdownload.cse.ucsc.edu/downloads.html#fugu">Downloads</a> page. - These data have <a href="../goldenPath/credits.html#fugu_credits">specific conditions - for use</a>. The fugu (fr3) browser annotation tracks were generated by UCSC and - collaborators worldwide. See the <a href="../goldenPath/credits.html#fugu_credits" - >Credits</a> page for a detailed list of the organizations and individuals who contributed - to the success of this release.</p> - - <hr> - - <FONT FACE="courier" SIZE="3"><B>15 May 2012 - Naked Mole-Rat - Assembly Now Available in the Genome Browser </B></FONT> - <P>We are pleased to announce the release of a Genome Browser - for the July 2011 naked mole-rat, <i>Heterocephalus glaber</i> - (BGI version HetGla1.0, UCSC version hetGla1). This draft assembly, - produced by the - <A HREF="http://en.genomics.cn/" - TARGET=_blank>Beijing Genomics Institute</A>, has been sequenced using - Illumina reads with a sequencing depth of >20x. There are - 39,266 scaffolds with a total size of 2,643,961,837 bases. - The N50 size of the scaffolds is 1,603,177 bases with 502 - scaffolds larger, and 38,764 scaffolds smaller. The mitochondrial - sequence is also available as the virtual chromosome "chrM". <P> - Bulk downloads of the sequence and annotation data are available - via the Genome Browser - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/hetGla1/">FTP server</A> or the - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#naked_mole-rat" - TARGET=_blank>Downloads</A> page. These data have - <A HREF="../goldenPath/credits.html#naked_mole-rat_use" - >specific conditions for use</A>. The naked mole-rat browser - annotation tracks were generated by UCSC and collaborators worldwide. - See the - <A HREF="../goldenPath/credits.html#naked_mole-rat_credits" - >Credits</A> page for a detailed list of the organizations and - individuals who contributed to the success of this release. - <HR> - - <FONT FACE="courier" SIZE="3"><B>8 May 2012 - OpenHelix - to Conduct Free Genome Browser Webinars in May</B></FONT> + <FONT FACE="courier" SIZE="3"><B>19 June 2012 - Many New + Assemblies Available in the Browser! </B></FONT> <P> - <A HREF="http://www.openhelix.com" TARGET=_blank>OpenHelix</A> - is conducting two free webinars on the UCSC Genome Browser: - <UL> - <LI><A HREF="http://www.openhelix.com/cgi/webinarInfo.cgi?id=43" - TARGET=_blank>UCSC Genome Browser: An Introduction</A> - (Thursday, May 17, 1pm EDT) -- designed for new users - of the UCSC Genome Browser and those who want to improve their - skills at basic navigation and display. - <LI><A HREF="http://www.openhelix.com/cgi/webinarInfo.cgi?id=44" - TARGET=_blank>UCSC Table Browser and Custom Tracks</A> - (Thursday, May 24, at 1pm EDT) -- advanced Genome Browser - topics, including creating Custom Tracks and using the Table - Browser. - </UL> + 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> - The webinars will last approximately 1hr 15min. + 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> - Seating is limited and - <A HREF="http://www.openhelix.com/cgi/webinar.cgi" - TARGET=_blank>registration is required</A>. Slides may be - downloaded from the <A HREF="http://www.openhelix.com/ucsc" - TARGET=_blank>OpenHelix website</A> prior to the webinar. + 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> - OpenHelix provides training materials and programs on hundreds - of free, publicly accessible bioinformatics and genomics - resources. To browse their entire collection of UCSC genomics - tutorials, go to the OpenHelix - <A HREF="http://www.openhelix.com/ucsc" TARGET=_blank>UCSC - training page</A>. + 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> + 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> + 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. <HR> - - <!-- start archives --> - - <FONT FACE="courier" SIZE="3"><B>2 May 2012 - OpenHelix - Releases Updated Genome Browser Tutorials: </B></FONT> - <A HREF="http://www.openhelix.com" TARGET=_blank>OpenHelix</A> - has released updated versions of two Genome Browser tutorial - suites. - <A HREF="goldenPath/newsarch.html#050212">Read more</A>. <P> - <FONT FACE="courier" SIZE="3"><B>18 April 2012 - GRC Planning Phase - for GRCh38 Human Reference Assembly: </B></FONT> - The <A HREF="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/" - TARGET=_blank>Genome Reference Consortium</A> (GRC) plans to - update the human reference assembly to GRCh38 in the summer of - 2013. - <A HREF="goldenPath/newsarch.html#041812">Read more</A>. + <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>. + <P> + <FONT FACE="courier" SIZE="3"><B>15 May 2012 - Naked Mole-Rat + Assembly Now Available in the Genome Browser: </B></FONT> + We are pleased to announce the release of a Genome Browser + for the July 2011 naked mole-rat, <i>Heterocephalus glaber</i> + (BGI version HetGla1.0, UCSC version hetGla1). + <A HREF="goldenPath/newsarch.html#051512a">Read more</A>. <P> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>