9aeac47bc63bebdada9050038b6f6ade8a9823db kuhn Fri Jul 6 10:18:08 2012 -0700 adding announcement about retiring hgText. added some end-paragraph tags diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html old mode 100644 new mode 100755 index 7187f55..bc419c3 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,155 +1,164 @@ <!--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 --> <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 2004. 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. + 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). + 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. + 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> + </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. + 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. + 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>. - <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> <P> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>