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 @@ -<!-- News Section ============================================- --> -<TABLE style="background-color:#888888; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px"> - <TR><TD> - <TABLE style="background-color:#fffee8; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px"> - <TR><TD> - <TABLE style="background-color:#D9E4F8; background-image: url('images/hr.gif'); width: 100%; border: 0px"> - <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" title="Follow @GenomeBrowser on Twitter" alt="Follow @GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a> - <a title="Genome Browser Facebook page" - href="http://www.facebook.com/ucscGenomeBrowser" - target="_blank"><img - src="/images/FB-f-Logo__blue_22.jpg" - style="vertical-align:text-bottom; margin-left: 15px;" - alt="Genome Browser Facebook page"></a> - <a href="https://plus.google.com/107643636314131661344" rel="publisher"></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 style="background-color:#fffee8; width: 100%; padding: 0px"> - <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="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" - TARGET=_blank>genome-announce</A> mailing list. Please see our - <a href="http://genome.ucsc.edu/blog" - target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more. - </p> +<!-- News item template: - <hr> - <!-- start news --> + <div class="jwNewsItem"> + __DATE__ - + <a href="goldenPath/newsarch.html#__MMDDYY__"> + __HEADLINE__ + </a></div> - <font color="#006666" size="4"><b>30 June 2016 - CRAM Files Now Supported!</b></font> - <p> - <p> - We are excited to announce the support of CRAM files on the Browser! - Read more <a href="goldenPath/newsarch.html#0630B16">here</a>.</p> - <p> - See complete details on the <a href="goldenPath/help/cram.html" target="_blank">CRAM Track Format</a> - 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, - <a href="/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&hgct_customText=track%20type=bam%20name=%22CRAM%20Example%22%20description=%22A%201000%20Genomes%20CRAM%20file%22%20visibility=full%20bigDataUrl=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00139/exome_alignment/HG00139.mapped.ILLUMINA.bwa.GBR.exome.20121211.bam.cram%20doWiggle=1" - target="_blank">click here</a>. - <p> - Thanks to Jonathan Casper and Brian Raney for the implementation of this feature.</p> - <hr> - - <font color="#006666" size="4"><b>30 June 2016 - Updated Gene Tracks Available for - the Human (hg38) and Mouse (mm10) Assemblies</b></font> - <p> - 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: - </p> - <p> - <ul> - <li>193,647 transcripts did not change.</li> - <li>128 transcripts were not carried forward to the new version.</li> - <li>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.</li> - <li>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).</li> - </ul> - <p> - More details about the GENCODE Genes track can be found on the - <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene"> - GENCODE v24 track description page</a>. - </p> - <p> - Many thanks to Brian Raney and Luvina Guruvadoo for their work on this track! - </p> - --- - <p> - 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: - <ul> - <li>60,827 transcripts did not change between versions.</li> - <li>148 transcripts were not carried forward to the new version.</li> - <li>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.</li> - <li>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).</li> - </ul> - </p> - <p> - More details about the new UCSC Genes track can be found on the - <a href="../cgi-bin/hgTrackUi?db=mm10&g=knownGene">UCSC Genes track - description page</a>. - </p> - - <p> - Many thanks to Jonathan Casper and Christopher Lee for their work on this track! - </p> - <hr> - - - <font color="#006666" size="4"><b>27 June 2016 - New Way to Share Sessions - Public Sessions!</b></font> - <p> - We are excited to announce the release of the - <a href="cgi-bin/hgPublicSessions">Public Sessions</a> - 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. - </p> - - <p> - The Genome Browser <a href="cgi-bin/hgSession">session management</a> 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. - </p> - - <p> - 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. - </p> - - <p> - For more information about using sessions to share snapshots of the UCSC Genome Browser, - please see the <a href="goldenPath/help/hgSessionHelp.html">User Guide</a> or our blog post, - "<a href="http://genome.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" - target="_blank">How to share your UCSC screenthoughts</a>." - </p> - - <p> - Thanks to Jonathan Casper and Matthew Speir for their work on this new tool. - </p> - - <hr> - - <font color="#006666" size="4"><b>15 June 2016 - New Official Asian Mirror Released</b></font> - <p> - We are pleased to announce the introduction of a new supported Genome Browser mirror - to serve our users in Asia. The genome-asia server - <a href="http://genome-asia.ucsc.edu" target="_blank">(http://genome-asia.ucsc.edu)</a>, - which is administered by UCSC, is physically located at the - <a href="http://www.yokohama.riken.jp/english/" target="_blank">RIKEN Yokohama Campus</a> - in Japan. - </p> - <p> - 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. - </p> - <p> - 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 - <a href="http://genome-euro.ucsc.edu" target="_blank">(http://genome-euro.ucsc.edu)</a> - in Bielefeld, Germany. A third-party mirror in - <a href="http://genome-mirror.moma.ki.au.dk/" target="_blank">Aarhus, Denmark</a>, - is available as an emergency backup in the rare event - that our three supported sites are offline. - </p> - <p> - We wish to express our special thanks to Dr. Hideya Kawaji at the - <a href="http://www.riken.jp/en/research/labs/accc/" target="_blank">RIKEN Advanced - Center for Computing and Communication</a> 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. - </p> - <hr> - -<!-- start archives --> -<!--staged for future release - - <p> - <font color="#006666" size="4"><b>30 June 2016 - Updated Gene Tracks Available for - the Human (hg38) and Mouse (mm10) Assemblies </b> </font> - We are pleased to announce the release of updated GENCODE Genes and UCSC Genes tracks - for the Human (GRCh38/hg38) and Mouse (GRCm38/mm10) assemblies. - <a href="goldenPath/newsarch.html#063016">Read more</a>. - </p> + 1. replace __DATE__ with something like 'Apr. 29, 2016' + 2. replace __MMDDYY__ with something like '042916' + 3. replace __HEADLINE__ with the news item's headline like 'Awesome New Feature' +--> - <p> - <font color="#006666" size="4"><b>27 June 2016 - New Way to Share Sessions - Public Sessions!</b> </font> - We are excited to announce the release of the - <a href="cgi-bin/hgPublicSessions">Public Sessions</a> - page, the newest way to share your UCSC Genome Browser snapshots with your colleagues - and the world. - <a href="goldenPath/newsarch.html#062816">Read more</a>. - </p> + <div class="jwNewsItem"> + Jun. 30, 2016 - + <a href="goldenPath/newsarch.html#063016"> + CRAM Files Now Supported! + </a></div> - <p> - <font color="#006666" size="4"><b>15 June 2016 - New Official Asian Mirror Released</b>: </font> - We are pleased to announce the introduction of a new supported Genome Browser mirror - to serve our users in Asia. - <a href="goldenPath/newsarch.html#061516">Read more</a>. - </p> ---> + <div class="jwNewsItem"> + Jun. 30, 2016 - + <a href="goldenPath/newsarch.html#063016"> + Updated Gene Tracks Available for the Human (hg38) and Mouse (mm10) Assemblies + </a></div> - <p> - <font color="#006666" size="4"><b>6 June 2016 - New video: Exon-only mode</b></font> - We are proud to announce a new <a href="https://www.youtube.com/watch?v=mNEJBOkf_Gk" target="_blank">video</a> demonstrating the - exon-only feature. This feature is useful in gene-expresson studies and - for those doing whole-exome sequencing. - <a href="goldenPath/newsarch.html#060616">Read more</a>. - </p> + <div class="jwNewsItem"> + Jun. 28, 2016 - + <a href="goldenPath/newsarch.html#062816"> + New Way to Share Sessions - Public Sessions! + </a></div> - <p> - <font color="#006666" size="4"><b>1 June 2016 - New Density Graph Feature!</b></font> - 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. - <a href="goldenPath/newsarch.html#060116">Read more</a>. - </p> - </TD><TD WIDTH=15> - </TD></TR></TABLE> - <BR></TD></TR></TABLE> -</TD></TR></TABLE>