8549c7efab6dec1e1dcbde6546a5c145f3a4c3d4
mspeir
  Tue May 6 14:32:17 2014 -0700
adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
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 <!-- News Section ============================================- -->  
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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" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></a></TD>
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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.</P>
 
     <!-- start news -->
 
         <hr>
         <p>
+        <font face="courier" size="3"><b> 5 May 2014 -
+        Introducing the new stacked overlay for multi-wiggle tracks</b></font>
+        <p>
+        We are excited to announce the release of the new stacked
+	overlay method for multi-wiggle tracks. This new stacked overlay
+	method displays each graph stacked on top of each other.
+	</p>
+	<img style="border: 2px solid black; margin-left:auto;
+                    margin-right:auto; display: block;"
+	     src="images/stackedMultiWig_screenshot.png"
+	     alt="Stacked screenshot">
+        <p>
+	Navigate to the track settings for <A HREF="cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegMarkH3k27ac"
+	>H3K27Ac Mark</A> on the human hg19 assembly to view this new stacked
+	overlay method on a multi-wiggle track. On the track settings page,
+	from the "Overlay method" drop-down menu select "stacked". Make sure
+	that the display mode is not set to hide, and click submit.
+        </p>
+	<p>
+	Credit for the implementation and testing of this new feature goes to
+	Brian Raney and Matthew Speir.
+	</p>
+
+        <hr>
+        <p>
         <font face="courier" size="3"><b> 29 Apr 2014 - 
         100-species Conservation track re-release</b></font>
         <p>
         We released the initial version of the 100-species Conservation track
         for the hg19 human assembly in November 2013. Over the past few months,
         we found a couple of inconsistencies and decided, for the integrity of
         the data, that we should rerun the computation pipeline and re-release
         the data. The fixes required minimal changes, and resulted in a more
         precise data set. We published the new version of the hg19 100-species
         Conservation track on 15 April 2014.
         </p>
         <p>
         Here are more details about the two fixes that we made:
         </p>
         <p>
         1. We tracked down the cause of some unusual gaps in the alignments to a 
         bug in the multiz program used in our alignment pipeline. The Penn State 
         Bioinformatics Group provided us with a fixed version of multiz that we 
         used to rerun the pipeline.
         </p>
         <p>
         2. We inadvertently used the pre-release assembly for one of the species 
         in the 100-way alignment: the panda. We replaced this assembly with the 
         correct version and verified that the data sets for all other species 
         were correct before rerunning the pipeline.
         </p>
         <hr>
 
-        <p>
-        <font face="courier" size="3"><b> 18 April 2014 - 
-        New Motif Displays for Transcription Factor ChIP-seq Track and New Genome Segmentations from ENCODE</b></font>
-        <p>
-        The Browser's default displayed Transcription Factor ChIP-seq track is updating to the
-        <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">latest data release</a>,
-        which has been enhanced with the display of Factorbook motifs.  Within a cluster, a green
-        highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the
-        corresponding factor. Upon clicking a transcription factor's cluster with a motif, the details page
-        now displays the motif's sequence logo, alignment and underlying Positional Weight Matrix. Also,
-        the track configuration page now enables the filtering of factors.
-        </p>
-        <p>
-        The newly added <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation">
-        Genome Segmentations from ENCODE</a> tracks display multivariate genome-segmentation performed on
-        <a target=ucscVocab href="http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?term=GM12878,H1-hESC,K562,HeLa-S3,HepG2,HUVEC">six human cell types</a>
-        (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for
-        <a target=ucscVocab href="http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?term=CTCF,H3K4me1,H3K4me2,H3K4me3,H3K27ac,H3K9ac,H3K36me3,H4K20me1,H3K27me3,Pol2,Input">
-        eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data</a>. In total,
-        twenty-five states were used to segment the genome, and these states were then grouped and colored to
-        highlight predicted functional elements. These Genome Segmentations are the same data as
-        found in the Analysis Working Group Hub, but are now hosted natively in the Browser with enhanced
-        filtering capability where desired segmented states can be selected using the
-        'Filter by Segment Type' control on the track configuration page.
-        </p>
-
-        <hr>
-
         <!-- staged for archive use.  NOTE: condense header line from .... </b></font><p> to </b></font>: 
 
+        <font face="courier" size="3"><b> 29 Apr 2014 -
+        100-species Conservation track re-release</b>:</font>
+        We released the initial version of the 100-species Conservation track
+        for the hg19 human assembly in November 2013. Over the past few months,
+        we found a couple of inconsistencies and decided, for the integrity of
+        the data, that we should rerun the computation pipeline and re-release
+        the data. <a href="goldenPath/newsarch.html#042914">Read more</a>
+
+	<font face="courier" size="3"><b> 5 May 2014 -
+        Introducing the new stacked overlay for multi-wiggle tracks</b>:</font>
+        We are excited to announce the release of the new &quot;stacked&quot;
+        overlay method for multi-wiggle tracks.
+	<a href="goldenPath/newsarch.html#050614">Read more</a>
+                -->
+        <!-- start archives -->
 	<p>
         <font face="courier" size="3"><b>18 April 2014 - 
         New Motif Displays and New Genome Segmentations from ENCODE</b></font>:
         The Browser's default displayed 
         <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">Transcription Factor ChIP-seq track</a>
         updated to the latest release, enhanced with the display of Factorbook motifs. And the Browser added
         <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation">Genome
         Segmentations from ENCODE</a> tracks, which segment the genome into twenty-five states that were then grouped
         and colored to highlight predicted functional elements.
         <a href="goldenPath/newsarch.html#041814">Read more</a>.
         </p>
 	
-        <font face="courier" size="3"><b> 29 Apr 2014 - 
-        100-species Conservation track re-release</b></font>
-        <p>
-        We released the initial version of the 100-species Conservation track
-        for the hg19 human assembly in November 2013. Over the past few months,
-        we found a couple of inconsistencies and decided, for the integrity of
-        the data, that we should rerun the computation pipeline and re-release
-        the data. <a href="goldenPath/newsarch.html#042914">Read more</a> 
-
-                -->
-        <!-- start archives -->
-
 	<p>
         <font face="courier" size="3"><b>15 April 2014 -
         New Minke Whale (balAcu1) Assembly Now Available in the
         Genome Browser</b></font>:
         A Genome Browser is now available for the minke whale
         (Balaenoptera acutorostrata scammoni) assembly released 
         October 2013 by the Korea Ocean Research &amp; Development Institute.
         <a href="goldenPath/newsarch.html#041514">Read more</a>.
         </p>
 
-
-        <p>
-        <font face="courier" size="3"><b>11 April 2014 -
-        New UCSC Genes Track Released for GRCm38/mm10</b></font>:
-         We're happy to announce the release of an updated UCSC Genes
-        track for the GRCm38/mm10 mouse Genome Browser.
-        <a href="goldenPath/newsarch.html#041114">Read more</a>.
-        </p>
-
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