c56502087bdb7d59041fe08c8ac09585ed274b92 brianlee Mon May 9 16:15:30 2016 -0700 Staging news release about new Gateway refs #15277 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 025a009..b78e373 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,176 +1,113 @@ <!-- 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> - <!-- start news --> <hr> - <a name="newGateway"</a> - <font color="#006666" size="4"><b>6 May 2016 - - New Gateway Coming 5/10/16!</b></font> - <p> - The UCSC Genome Browser team is proud to announce that we will soon release - a newly designed Gateway, which will be live on the public site Tuesday afternoon - (PDT), May 10th, 2016. Another announcement will be shared Tuesday with further - details and a demonstration video.</p> - <p> - While the main functionality remains unchanged as a gateway to all available genome - browsers, several helpful new features have been added:</p> - <li>Autocomplete search for any genome browser, genome version, or public assembly hub - <li>Browse available genome browser species by scrolling through a menu based on phylogenetic order - <li>Quick access shortcuts to popular browsers - <li>A new style and color scheme - <p> - Here is <a href="images/sneakPeekGateway.png" - target="_blank">sneak picture of the new Gateway web page</a>.</p> - <p> - We hope that you will enjoy the new Gateway page next week! As always, we invite your - questions, comments, and suggestions as directed through the details on our Contact Us web page. - <p> - - <hr> - <font color="#006666" size="4"><b>22 Apr 2016 - - Data from the Lens PatSeq Database Now Available</b></font> - <p> - We are pleased to announce the release of a set of tracks showing the genomic mapping of - biomedical sequences submitted as part of patent application documents worldwide. The sequence - data, mappings and associated patent information were obtained from the - <a href="https://www.lens.org/lens/bio" target="_blank">PatSeq</a> database provided by - <a href="https://www.lens.org/" target="_blank">The Lens</a>. The PatSeq data are - mapped to the genome, and the individual sequence features within the tracks are then - color-coded to indicate their status within the associated patent documents. - Track details pages show information about the patent documents in which the sequences - are referenced, and provide a link to The Lens PatSeq Analyzer tool for the given chromosome - range. The PatSeq data are divided into two tracks: a bulk patent track for sequences affiliated - with patents in which more than 100 sequences were submitted, and a non-bulk patent track - for all other sequences. These tracks are currently present on the human (hg19), mouse (mm10), - and Ebola virus (eboVir3) genomes. - </p> - <p> - Thanks to our collaborators at The Lens, Osmat Jefferson and Deniz Koellhofer, for providing the - data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of - the UCSC Genome Browser team, for their efforts in creating these tracks. - </p> - - <hr> - <font color="#006666" size="4"><b>20 April 2016 - - New GTEx Gene Expression Track for hg19 and hg38</b></font> - <p> - We are excited to announce the release of a new gene expression track based on data from the NIH - <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK> Genotype-Tissue Expression</a> - (GTEx) project. - This track displays tissue-specific gene expression based on RNA-seq in 53 tissues from 570 - donors obtained from the GTEx 'midpoint' data release (V6, October 2015). - The original data for this - track can be found at the <a href="http://www.gtexportal.org/home" target = _blank>GTEX Portal</a> - hosted by the Broad Institute. - <p> - This track also features a new gene expression display method that extends the traditional Genome - Browser display — a horizontal bar graph. Every gene is annotated by a graph with colored - bars, each of which corresponds to a specific tissue assayed by the GTEx project. Within - a graph, the bar color indicates the tissue type, using GTEx conventions, and the bar height - depicts the median expression level (in RPKM). - To quickly view the tissue and expression level represented by a bar in the tracks display, - mouse over the bar in the graph. - The complete tissue color legend is shown on the - <a href="../../cgi-bin/hgTrackUi?db=hg19&g=gtexGene" target=_blank>track configuration page</a>, - and can also be popped up for viewing alongside the track using the right-click menu. - Below the bar graph, a line is shown indicating the gene extent that was used to generate the - annotation, colored by gene class using GENCODE conventions - (e.g. <span style='color: #0c0c78'>blue</span> for protein-coding, - <span style='color: #006400'>green</span> for non-coding). - <p> - <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/gtexAnnouncementSession.txt" - target=_blank> - <center><img src="images/gtexAnnounceExample.png" width=75%></center></a> - <p> - User alert: In the figure above, do you notice how the bar graph sometimes extends past the - righthand end of the associated gene annotation? This is because all bar graphs in the - display are the same width (and have the same tissue ordering) to facilitate comparison. - For example, in this figure (which may also be viewed - <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/gtexAnnouncementSession.txt" - target=_blank>here</a>), - the three tall bars in the annotation of the TCAP gene indicate that this <em>entire</em> gene is - highly expressed in cardiac and skeletal muscle. It does <em>not</em> indicate that there are - expression peaks in the intergenic region beyond the gene! - <p> - Similar to other Genome Browser track displays, clicking on the graph will bring up a description - page that shows a detailed box-and-whiskers plot of - the RPKM data, as well as a description of the methods used to generate the data. - <p> - Credit goes to Kate Rosenbloom and Christopher Lee for the implementation and testing of this - feature. - </p> + <!-- start news --> + <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 designed + <a href="../cgi-bin/hgGateway" target="_blank">Gateway web page</a>. + While the main functionality remains unchanged as a gateway to all available + genome browsers on all available genome assemblies, several helpful new + features have been added:</p> + <ul> + <li>Autocomplete search for any genome browser, genome version, or public hub</li> + <li>Browse available genome browser species by scrolling through a 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 new <a href="https://youtu.be/5zc9sqd4SD4" + target="_blank">UCSC Genome Browser Gateway video</a> + for an introduction to these new features. As we continue to expand our + collection of high-quality, reviewed data by adding more genome assemblies + to our public site, the new autocomplete search functionality provides an + improved method for navigating to genome assemblies. As an alternative to + scrolling through long drop-down menus of genome assembly options, you can + now simply enter assembly search terms for autocomplete recognition, + providing quick access to your genome assembly of interest.</p> + <p> + Please note the following differences in navigation, which used to appear + as links directly from the previous version of the Gateway web page. New + navigation for the following tools can all be found in the top horizontal + blue 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>10 May 2016 - New Gateway Page!</b>: </font> + The UCSC Genome Browser team is proud to announce a newly designed + <a href="../../cgi-bin/hgGateway" target="_blank">Gateway web page</a>. + Please see our <a href="https://youtu.be/5zc9sqd4SD4" + target="_blank">UCSC Genome Browser Gateway video</a> + for an introduction to these new features. + <a href="goldenPath/newsarch.html#051016">Read more</a>. +--> + <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> <font color="#006666" size="4"><b>19 April 2016 - - New Genotyping Tissue Expression Track for hg19 and hg38!</b></font> - <p> + - New Genotyping Tissue Expression Track for hg19 and hg38!</b>: </font> We are excited to announce the release of a new track based on data from the <a href="http://commonfund.nih.gov/GTEx/index" TARGET = _BLANK>Genotyping Tissue Expression Consortium</a> V6 data freeze. - <a href="goldenPath/newsarch.html#04202016">Read more</a>. ---> - - <p> - <font color="#006666" size="4"><b> 15 April 2016 - - dbSNP 146 Available for hg19 and hg38</b>: </font> - We are pleased to announce the release of four tracks derived - from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/">dbSNP</a> Build 146 data. - <a href="goldenPath/newsarch.html#041516_2">Read more</a>. - </p> - - <p> - <font color="#006666" size="4"><b>15 April 2016 - - Genome Browsers for Gorilla, Rhesus, and Crab-Eating Macacque Now Available.</b></font> - <a href="goldenPath/newsarch.html#041516_1">Read more</a>. - </p> + <a href="goldenPath/newsarch.html#042016">Read more</a>. </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>