48c16d5636ff8c81f5054d10aa66f76edc97dd0c
mspeir
  Tue Jan 14 10:25:23 2014 -0800
Adding E coli hub announcements, refs #11889
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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>
 
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         <p>
+        <font face="courier" size="3"><b>14 January 2014 -
+        Two E. coli comparative assembly hubs now available</b></font>
+        </p>
+        <p>
+        We're pleased to add two new assembly hubs produced by the UCSC
+        <A HREF="https://cbse.soe.ucsc.edu/hausslerlab" TARGET="_BLANK">David Haussler lab</A> 
+        to our collection of publicly available hubs. The new hubs feature over 60 bacterial assemblies, 
+        including more than 55 different E. coli strains. The assembly annotations include genes, pathogenic
+        genes, conservation, GC percent, repetitive elements and much more.
+        </p>
+        <p>
+        These hubs focus on comparative genomics and showcase the new "snake" track type. Snakes, which
+        visualize alignments from
+        <A HREF="http://genome.ucsc.edu/FAQ/FAQformat.html#format20">Hierarchical Alignment</A>
+        (HAL) files, provide a way to view sets of pairwise gapless alignments that may overlap on both
+        the chosen genome (reference) and the query genome, and show various types of genomic variations
+        such as insertions, substitutions, and duplications. More details about the new snake track display
+        and its configuration options can be found on our Genome Browser
+        <a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html" target="_blank">help</a> page.
+        </p>
+        <p>
+        To access and view these hubs, navigate to the
+        <A HREF="http://genome.ucsc.edu/cgi-bin/hgHubConnect">Track Hub gateway page</A>
+        and select one of the two E. coli comparative assembly hubs from the Public Hubs list.
+        </p>
+        <p>
+        We would like to acknowledge Ngan Nguyen, Glenn Hickey, Brian Raney, Joel Armstrong, Benedict Paten,
+        Matt Speir, and Luvina Guruvadoo for their hard work in creating these hubs. 
+        </p>
+        <hr>
+
+       <p>
         <font face="courier" size="3"><b>27 November 2013 -
         100 Species Conservation Track now available on hg19</b></font>
         </p>
         <p>
         After 15.4 years of CPU run-time in 9,905,594 individual 'jobs' and 99 cluster runs for lastz 
         pair-wise alignment...we are excited to announce the release of a 100 species alignment on the 
         hg19/GRCh37 human Genome Browser.
         </p>
         <p>
         This new Conservation track shows multiple alignments of 100 species and measurements of 
         evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. 
         This adds 40 more species to the existing 60-way on the mm10 mouse browser. For more information 
         about the 100 species Conservation track, see its 
         <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons100way" target="_blank">description page</a>.
         </p>
         <p>
         We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together 
         the information for this track: Hiram Clawson and Pauline Fujita.
         </p>
-        <hr>
 
+        <!-- staged for archive use
         <p>
-        <font face="courier" size="3"><b>24 October 2013 -
-        Job Opening: UCSC Genome Browser Trainer</b></font>
-        <p>
-	The <a href="http://cbse.ucsc.edu/" target="_blank">Center for Biomolecular Science
-	and Engineering</a> (CBSE) at University of California Santa Cruz
-	seeks an articulate, self-motivated educator for the two-year position of UCSC Genome
-	Browser trainer. The trainer develops curriculum and provides in-person training on the UCSC
-	Genome Browser at universities, hospitals, institutes, and professional
-	meetings in the United States and internationally. Typical audiences include graduate 
-	and post-graduate biologists and doctors, with Genome Browser experience ranging from novice
-	users to bioinformatics specialists. Presentations include formal talks, problem-solving 
-	sessions, and two-day workshops. </p>
- 	<p>
-	This position requires a Master's degree in a biological science, depth in molecular
-	biology, experience in a research environment, working knowledge of the UCSC Genome Browser,
-	understanding of its role in research methodology, and experience teaching or training in a
-	scientific environment. Preferred qualifications include a PhD in a relevant field,
-	experience with video production, and experience with HTML or web content management
-	systems. </p>
-	<p>
-	For more information and to apply for this position, see
-	<a href="http://bit.ly/browserJob" target="_blank">Job #1304619</a> on the UCSC Staff 
-	Employment website.  </p>
+        <font face="courier" size="3"><b>14 January 2014 -
+        Two E. coli comparative assembly hubs now available</b></font>
+        We're pleased to add two new assembly hubs produced by the UCSC
+        <A HREF="https://cbse.soe.ucsc.edu/hausslerlab" TARGET="_BLANK">David Haussler lab</A> 
+        to our collection of publicly available hubs.
+        <a href="goldenPath/newsarch.html#011414">Read more</a> 
+        </p>
 
-        <!-- staged for archive use
         <p>
         <font face="courier" size="3"><b>27 November 2013 -
         100 Species Conservation Track now available on hg19</b></font>
         </p>
        
         <p>
         We're happy to announce the release of a new track on the hg19/GRCh37 human Genome Browser. 
         The new Conservation track shows multiple alignments of 100 species and measurements of 
         evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. 
         </p> 
+        -->
 
+        <!-- start archives -->
+        <hr>
         <p>
         <font face="courier" size="3"><b>24 October 2013 -
         Job Opening: UCSC Genome Browser Trainer</b></font>
-        <p>
 	The <a href="http://cbse.ucsc.edu/" target="_blank">Center for Biomolecular Science
 	and Engineering</a> (CBSE) at University of California Santa Cruz
 	seeks an articulate, self-motivated educator for the two-year position of UCSC Genome
 	Browser trainer. 
         <a href="goldenPath/newsarch.html#102413">Read more</a>.
         </p>
-        -->
-
-        <!-- start archives -->
-        <hr>
         
         <p>
         <font face="courier" size="3"><b>23 October 2013 -
         dbSNP 138 Available for hg19: </b></font>
 	We are pleased to announce the release of four tracks derived from NCBI
  	<a href="http://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a> Build 138
  	data, available on the human assembly (GRCh37/hg19). 
         <a href="goldenPath/newsarch.html#102313">Read more</a>.
         </p>
 
-	<p>
-        <font face="courier" size="3"><b>11 October 2013 -
-        Updated DGV Structural Variation Track: </b></font>
-        The UCSC Genome Browser team is pleased to announce an updated DGV Structural Variation
-        track to reflect the official launch of the new <a href="http://dgv.tcag.ca/dgv/app/home"
-        target="_blank">Database of Genomic Variants</a>.
-        <a href="goldenPath/newsarch.html#101113">Read more</a>.
-        </p>
-        
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