c43bcc0e7251182c280ed8c1a1fdf592ccf827c4 angie Tue Apr 12 13:56:18 2016 -0700 New home page designed by Jim & others, using styles from the new gateway page design. refs #17470, #15277 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 21cc401..e5c455e 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,237 +1,31 @@ - - -

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- To receive announcements of new genome - assembly releases, new software features, updates and - training seminars by email, subscribe to the - genome-announce mailing list. Please see our - blog for posts about Genome Browser tools, features, projects and more. -

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- 30 June 2016 - CRAM Files Now Supported! -

- We are excited to announce the support of CRAM files on the Browser! - Read more here.

- See complete details on the CRAM Track Format - page. To load an example CRAM file from the 1000 Genomes Project where reads are displayed as - a bar graph using the "Display data as a density graph" option, - click here. -

- Thanks to Jonathan Casper and Brian Raney for the implementation of this feature.

- - 30 June 2016 - Updated Gene Tracks Available for - the Human (hg38) and Mouse (mm10) Assemblies -

- We are pleased to announce the release of an updated GENCODE Genes - track for the Human (GRCh38/hg38) assembly. - The GENCODE v24 gene set has 197,782 total transcripts, compared with - 195,178 in the previous version. - The total number of canonical genes has increased from 49,534 to 49,948. - Comparing the new gene set with the previous version: -

193,647 transcripts did not change.
128 transcripts were not carried forward to the new version.
997 transcripts are "compatible" with those in the previous set, - meaning that the two transcripts show consistent splicing. In most cases, - the old and new transcripts differ in the lengths of their UTRs.
406 transcripts overlap with those in the previous set, but do not - show consistent splicing (i.e., they contain overlapping introns with - differing splice sites).

- More details about the GENCODE Genes track can be found on the - - GENCODE v24 track description page. -

- Many thanks to Brian Raney and Luvina Guruvadoo for their work on this track! -

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- We are pleased to announce the release of an updated UCSC Genes track for the - Mouse (GRCm38/mm10) assembly. - The new release has 63,759 total transcripts, compared with 63,244 - in the previous version. The total number of canonical genes has increased from 32,958 - to 33,079. Comparing the new gene set with the previous version: -

60,827 transcripts did not change between versions.
148 transcripts were not carried forward to the new version.
1,929 transcripts are "compatible" with those in the previous set, meaning - that the two transcripts show consistent splicing. In most cases, the old and new - transcripts differ in the lengths of their UTRs.
340 transcripts overlap with those in the previous set, but do not show consistent - splicing (i.e., they contain overlapping introns with differing splice sites).

- More details about the new UCSC Genes track can be found on the - UCSC Genes track - description page. -

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- Many thanks to Jonathan Casper and Christopher Lee for their work on this track! -

- - - 27 June 2016 - New Way to Share Sessions - Public Sessions! -

- We are excited to announce the release of the - Public Sessions - page, the newest way to share your UCSC Genome Browser snapshots with your colleagues - and the world. The Public Sessions page collects sessions that users have elected to share - publicly. Sessions on this page can be filtered based on assembly, name, or a phrase from - the description. Sessions can also be sorted based on their popularity or creation date. - To add your own sessions to this Public Sessions page, just check the box under "post in - public listing" on the session management page. -

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- The Genome Browser session management page has also received an - update with the release of the new Public Sessions page. Sessions are now arranged in a table, - where varying numbers of sessions can be displayed on a page of this table. Sessions can now be - filtered and ordered based on session name, primary assembly, and creation date. Clicking on the - session name now displays that session in the Genome Browser. Session details, such as the name - or the description, can be changed using the "details" button in the new table layout. -

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- The release of the new Public Sessions page also marks a change in our session expiration policy. - We no longer expire sessions and associated custom tracks four months after their last use. - Please note, however, that the UCSC Genome Browser is not a data storage service and that we - encourage you to keep local copies of your session contents and custom track data. -

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- For more information about using sessions to share snapshots of the UCSC Genome Browser, - please see the User Guide or our blog post, - "How to share your UCSC screenthoughts." -

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- Thanks to Jonathan Casper and Matthew Speir for their work on this new tool. -

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- - 15 June 2016 - New Official Asian Mirror Released -

- We are pleased to announce the introduction of a new supported Genome Browser mirror - to serve our users in Asia. The genome-asia server - (http://genome-asia.ucsc.edu), - which is administered by UCSC, is physically located at the - RIKEN Yokohama Campus - in Japan. -

- Genome-asia is intended as an alternate, faster access point for those Browser users - who are geographically closer to Asia than to the western United States. The mirror - is functionally identical to the U.S.-based server, with one exception. Custom tracks - residing on the U.S. server are not automatically accessible from the genome-asia mirror; - therefore, the use of these custom tracks and saved sessions containing them will require - some manual intervention. -

- Genome Browser users located in Asia will be automatically redirected to genome-asia - when they click the "Genomes" menu item on the Genome Browser home page, but will have - the option to remain on the U.S.-based server. In addition to the - genome-asia mirror, we continue to support a Europe-based Genome Browser mirror - (http://genome-euro.ucsc.edu) - in Bielefeld, Germany. A third-party mirror in - Aarhus, Denmark, - is available as an emergency backup in the rare event - that our three supported sites are offline. -

- We wish to express our special thanks to Dr. Hideya Kawaji at the - RIKEN Advanced - Center for Computing and Communication for making this possible. We would also - like to acknowledge the following members of the UCSC Genome Browser team for their efforts: - Galt Barber, Robert Kuhn, Jorge Garcia, and Luvina Guruvadoo. -

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- 27 June 2016 - New Way to Share Sessions - Public Sessions! - We are excited to announce the release of the - Public Sessions - page, the newest way to share your UCSC Genome Browser snapshots with your colleagues - and the world. - Read more. -

+ Jun. 30, 2016 - + + CRAM Files Now Supported! +

- 15 June 2016 - New Official Asian Mirror Released: - We are pleased to announce the introduction of a new supported Genome Browser mirror - to serve our users in Asia. - Read more. -

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+ Jun. 30, 2016 - + + Updated Gene Tracks Available for the Human (hg38) and Mouse (mm10) Assemblies +

- 6 June 2016 - New video: Exon-only mode - We are proud to announce a new video demonstrating the - exon-only feature. This feature is useful in gene-expresson studies and - for those doing whole-exome sequencing. - Read more. -

+ Jun. 28, 2016 - + + New Way to Share Sessions - Public Sessions! +

- 1 June 2016 - New Density Graph Feature! - The Genome Browser is proud to announce a new "density graph" feature for - a variety of tracks, including BAM custom tracks, that converts data into a summary display. - Read more. -