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 @@ -14,126 +14,142 @@

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- - - 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 fugu, Takifugu rubripes - (JGI v5.0, UCSC version fr3). Whole genome shotgun assembly was provided by the - International Fugu Genome Sequencing - Consortium, led by JGI and the - Singapore Institute of Molecular and Cell Biology (IMCB).

- -

Bulk downloads of the sequence and annotation data are available via the Genome Browser - FTP server or the - Downloads page. - These data have specific conditions - for use. The fugu (fr3) browser annotation tracks were generated by UCSC and - collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed - to the success of this release.

- -
- - 15 May 2012 - Naked Mole-Rat - Assembly Now Available in the Genome Browser -

We are pleased to announce the release of a Genome Browser - for the July 2011 naked mole-rat, Heterocephalus glaber - (BGI version HetGla1.0, UCSC version hetGla1). This draft assembly, - produced by the - Beijing Genomics Institute, 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".

- Bulk downloads of the sequence and annotation data are available - via the Genome Browser - FTP server or the - Downloads page. These data have - specific conditions for use. The naked mole-rat browser - annotation tracks were generated by UCSC and collaborators worldwide. - See the - Credits page for a detailed list of the organizations and - individuals who contributed to the success of this release. -

- - 8 May 2012 - OpenHelix - to Conduct Free Genome Browser Webinars in May + 19 June 2012 - Many New + Assemblies Available in the Browser!

- OpenHelix - is conducting two free webinars on the UCSC Genome Browser: -

    -
  • UCSC Genome Browser: An Introduction - (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. -
  • UCSC Table Browser and Custom Tracks - (Thursday, May 24, at 1pm EDT) -- advanced Genome Browser - topics, including creating Custom Tracks and using the Table - 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.

- 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).

- Seating is limited and - registration is required. Slides may be - downloaded from the OpenHelix website 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 contact us + for more information.

- 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 - UCSC - training page. + 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.

- - - - 2 May 2012 - OpenHelix - Releases Updated Genome Browser Tutorials: - OpenHelix - has released updated versions of two Genome Browser tutorial - suites. - Read more.

- 18 April 2012 - GRC Planning Phase - for GRCh38 Human Reference Assembly: - The Genome Reference Consortium (GRC) plans to - update the human reference assembly to GRCh38 in the summer of - 2013. - Read more. + 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. +

+ 15 May 2012 - Naked Mole-Rat + Assembly Now Available in the Genome Browser: + We are pleased to announce the release of a Genome Browser + for the July 2011 naked mole-rat, Heterocephalus glaber + (BGI version HetGla1.0, UCSC version hetGla1). + Read more.

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