22f9f870631d27d22d4bc5a51dd6b30b026103eb kuhn Fri Jul 6 10:29:27 2012 -0700 added link to original hgTables release announcement in archives diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index bc419c3..fda0d88 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,164 +1,165 @@
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06 July 2012 - hgText CGI To Be Retired

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 + 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.

19 June 2012 - Many New Assemblies Available in the Browser!

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.

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).

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 contact us for more information.

Newly released assemblies:

  • Cow (Bos taurus) bosTau7 – Btau_4.6.1 (Oct. 2011) from the Bovine Genome Sequencing Consortium and Baylor College of Medicine
  • Rat (Rattus norvegicus) rn5 – RGSC Rnor_5.0 (Oct. 2011) from the Rat Genome Sequencing Consortium
  • Chicken (Gallus gallus) galGal4 – Gallus_gallus-4.0 (Nov. 2011) from the International Chicken Genome Consortium
  • Western painted turtle (Chrysemys picta bellii) chrPic1 – Chrysemys_picta_bellii-3.0.1 (Dec. 2011) from the International Painted Turtle Genome Sequencing Consortium
  • Lesser hedgehog tenrec (Echinops telfairi) echTel1 – echTel1 (Jul. 2005) from the Broad Institute (pending)
  • Dog (Canis familiaris) canFam3 – v3.1 (Sep. 2011) from the Broad Institute (pending)
Released in the past half year:
  • Mouse (Mus musculus) mm10 – GRCm38 (Dec. 2011) from the Mouse Genome Reference Consortium
  • Cow (Bos taurus) bosTau6 – Bos_taurus_UMD_3.1 (Nov. 2009) from the University of Maryland
  • Fugu (Takifugu rubripes) fr3 – FUGU5 (Oct. 2011) from the International Fugu Genome Sequencing Consortium
  • Gibbon (Nomascus leucogenys) nomLeu1 – Nleu1.0 (Jan. 2010) from the Gibbon Genome Sequencing Consortium
  • Gorilla (Gorilla gorilla gorilla) gorGor3 – gorGor3.1 (May 2011) from the Wellcome Trust Sanger Institute
  • Microbat (Myotis lucifugus) myoLuc2 – Myoluc2.0 (Jul. 2010) from the Broad Institute
  • Naked mole-rat (Heterocephalus glaber) hetGla1 – HetGla_1.0 (Jul. 2011) from the Beijing Genomics Institute
  • Tammar wallaby (Macropus eugenii) macEug2 – Meug_1.1 (Sep. 2009) from the Tammar Wallaby Genome Sequencing Consortium
  • Turkey (Meleagris gallopavo) melGal1 – Turkey_2.01 (Dec. 2009) from the Turkey Genome Consortium
  • Western clawed frog (X. tropicalis) xenTro3 – v4.2 (Nov. 2009) from the DOE Joint Genome Institute
  • C. elegans ce10 – WS220 (Oct. 2010) from WormBase
  • S. cerevisiae sacCer3 – SacCer_Apr2011 (Apr. 2011) from the Saccharomyces Genome Database

Bulk downloads of the sequence and annotation data for these assemblies are available via the Genome Browser FTP server or the Downloads page. Be sure to check the credits page for data use restrictions and acknowledgments.

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.

15 May 2012 - New Fugu (fr3) Assembly Now Available in the Genome Browser: We are pleased to announce the release of a Genome Browser for the October 2011 assembly of the Fugu, Takifugu rubripes (JGI v5.0, UCSC version fr3). Read more.

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