44b656609fe0b77c1162f052d94217bc04ccb916 luvina Wed Jun 15 14:26:32 2016 -0700 added news announcement for genome-mirror diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index a0201d9..1aed149 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,168 +1,155 @@ <!-- 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> <hr> <!-- start news --> + <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 (see documentation). 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> + <font color="#006666" size="4"><b>6 June 2016 - New video: Exon-only mode</b></font> </P> We are pleased to announce the release to our YouTube channel of a new training <A HREF = "https://www.youtube.com/watch?v=mNEJBOkf_Gk" TARGET = _BLANK>video</A>, in which we demonstrate the recently released Multi-Region feature in exon-only mode. This feature is useful for those studying gene expression or undertaking whole-exome sequencing. By removing intronic and intergenic regions, exon-only mode shows the portion (sometimes as little as a few percent) of the genome most useful for these analyses. </P> <P> This video is <A HREF ="training/vids/#vid09" TARGET = _BLANK>indexed</A> to allow easy access to relevant sections and comes with a transcript for the hard-of-hearing. </P> <P> Thanks to Robert Kuhn and David Gibson for production. </P> <hr> <font color="#006666" size="4"><b>1 June 2016 - New Density Graph Feature!</b></font> <p> 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.</p> <p> The density graph feature enables certain track types to be displayed as a bar graph where the height is proportional to the number of reads mapped to each genomic position. Through dynamic calculation of items in the current window, this feature plots a line similar to a wiggle graph that can be customized with a number of <a href="goldenPath/help/hgWiggleTrackHelp.html" target="_blank">graph-based configuration options</a> such as drawing indicator lines, smoothing plots, adjusting graph height and vertical range, and switching from bars to points. Please note that the feature is best displayed with Display mode set to full and that the default is auto-scale data to view. Please note that using this feature on a <a href="goldenPath/help/gbib.html#GbibMirroring" target="_blank">virtual machine Genome Browser in a Box (GBiB)</a> may benefit from increasing memory.</p> <p> To turn on the feature click into the track controls for certain track types, such as a BAM custom track, and check the box next to "Display data as a density graph" to see graph configurations and then click "Submit". To see the new density graph feature in use, please see this example <a href="cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.densityGraph&hgct_customText=track%20type=bam%20name=bamExample%20visibility=full%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam%20doWiggle=1" target="_blank">session</a>. <p> Thanks to Brian Raney for the implementation of this feature.</p> <hr> - <font color="#006666" size="4"><b>10 May 2016 - New Gateway Page!</b></font> - <p> - The UCSC Genome Browser team is proud to announce a newly redesigned - <a href="../cgi-bin/hgGateway" target="_blank">Genome Browser Gateway</a> page. - The Gateway retains its original functionality as a central access point for all genome assemblies - available on our site, while sporting several helpful new features and updates:</p> - <ul> - <li>Autocomplete searching for any genome browser, genome version, or public hub</li> - <li>Species browsing through a scrollable visual - "tree" menu based on phylogenetic order</li> - <li>Quick access shortcuts to popular browsers</li> - <li>New style and color scheme</li> - </ul> - <p> - Please see our <a href="https://youtu.be/5zc9sqd4SD4" - target="_blank">Gateway video</a> for an introduction to these new features. - </p> - <p> - The new Gateway addresses the need for streamlined access to the rapidly - growing number of genome assemblies available on our public site. - As an alternative to scrolling through long drop-down menus of genome assemblies, you can - now simply type in assembly search terms for autocomplete recognition, visually scroll - through our collection, or click a button to access our most popular species. - </p> - <p> - Note that a few browser utilities that were previously accessed through links and buttons on the - Gateway page have been moved to the top menu bar: - </p> - <ul> - <li>Browser reset: Genome Browser > Reset All User Settings</li> - <li>Track search: Genome Browser > Track Search</li> - <li>Add custom tracks: My Data > Custom Tracks</li> - <li>Track hubs: My Data > Track Hubs</li> - <li>Configure tracks and display: Genome Browser > Configure</li> - </ul> - <p> - We would like to acknowledge the following people for their contributions - to the new Gateway: original art by Jeff West Design, concept by Robert Kuhn, - software design by Angie Hinrichs, and quality assurance by Cath Tyner.</p> - <hr> - <!-- start archives --> <!--staged for future release <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 = "">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> <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> - +--> <p> <font color="#006666" size="4"><b>10 May 2016 - New Gateway Page!</b>: </font> The UCSC Genome Browser team is proud to announce a newly redesigned <a href="../../cgi-bin/hgGateway" target="_blank">Genome Browser Gateway page</a>. Please see our <a href="https://youtu.be/5zc9sqd4SD4" target="_blank">Gateway video</a> for an introduction to these new features. <a href="goldenPath/newsarch.html#051016">Read more</a>. </p> ---> - <p> - <font color="#006666" size="4"><b>22 Apr 2016 - - Data from the Lens PatSeq Database Now Available</b>: </font> - We are pleased to announce the release of a set of tracks containing data from the - <a href="https://www.lens.org/" target="_blank">Lens</a> - PatSeq database in the UCSC Genome Browser. - <a href="goldenPath/newsarch.html#042216">Read more</a>. - </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>