29d8156c530a7b28618003d89a090c99af49751e
brianlee
  Wed Jun 1 15:58:31 2016 -0700
Adding news release announcement for density graph refs #952

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                  <font size="4"><a name="TOC"></a><b>&nbsp; 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 &#64;GenomeBrowser on Twitter" alt="Follow &#64;GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a>
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                  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>
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           <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>1 June 2016 - New Density Graph Feature!</b></font>
+  <p>
+  The Genome Browser is proud to announce a new &quot;density graph&quot; 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 &quot;Display data as a
+  density graph&quot; to see graph configurations and then click &quot;Submit&quot;.
+  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>.
+  <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
   &quot;tree&quot; 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
+        <font color="#006666" size="4"><b>1 June 2016 - New Density Graph Feature!</b></font>   
+        The Genome Browser is proud to announce a new &quot;density graph&quot; feature for
+        a variety of tracks, including BAM custom tracks, that converts data into a summary display.</p>
+        <a href="goldenPath/newsarch.html#060116">Read more</a>. 
         <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>
        <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>
-        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#042016">Read more</a>.
-
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