13a3177e706f25defbc80a58e96ca0057d58b082
mspeir
  Mon Mar 21 14:38:33 2016 -0700
Adding announcement for ce11 and aptMan1. Staging announcement for Lens Patent track. refs #15209 #16029

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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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           <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"
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           <a href="http://genome.ucsc.edu/blog"
           target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more.
           </p>
 
     <!-- start news -->
+    <!-- start news -->
+<!-- Staged for later release
+  <hr>
+  <font color="#006666" size="4"><b>16 Mar 2016
+  - Data from the Lens PatSeq Database Now Available</b></font>
+  <p>
+  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. These tracks contain data from the
+  <a href="https://www.lens.org/lens/bio" target="_blank">PatSeq</a>
+  database mapped to the genome and then colored based on where the sequence appears in
+  the patent document. Details pages contain the patent titles with links to the patents in the
+  Lens database. The data from PatSeq is divided into two tracks, one includes those sequences
+  that were submitted in bulk patents containing 100 or more sequences and the other containing
+  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>21 Mar 2016
+  - Genome Browsers for <i>C. elegans</i> and Brown Kiwi Now Available</b></font>
+  <p>
+  A Genome Browser is now available for the <em>Caenorhabditis elegans</em>
+  assembly released August 2014 by the C. elegans Sequencing Consortium, which is led by the
+  <a href="http://genome.wustl.edu/"
+  target="_blank">Genome Sequencing Center at Washington University, St. Louis</a>
+  and the <a href="http://www.sanger.ac.uk/" target="_blank">Wellcome Trust Sanger Institute</a>.
+  You can read more about their sequencing efforts
+  <a href=http://genome.wustl.edu/genomes/detail/caenorhabditis-elegans/
+  target="_blank">here</a>.
+  For more information and statistics about this assembly, see the NCBI assembly record
+  for <a href="http://www.ncbi.nlm.nih.gov/assembly/554278" target="_blank">WBcel235</a>. Note
+  that the sequences in WBcel235 are identical to the sequence in WBcel245/ce11. This means
+  that WBcel245 only has different annotations, but is the exact same sequence as WBcel235.
+  There are 7 complete chromsomes with a total size of 100,286,401 bases.
+  </p>
+
+  <p>
+  Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
+  <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ce11/">FTP server</a> or the
+  <a href="http://hgdownload.soe.ucsc.edu/downloads.html#c_elegans">Downloads</a> page.
+  Please observe the <a href="credits.html#ce_credits">conditions for use</a> when
+  accessing and using these data sets. The annotation tracks for this browser were
+  generated by UCSC and collaborators worldwide. See the <a
+  href="credits.html#ce_credits">Credits</a> page for a detailed list of the
+  organizations and individuals who contributed to this release.
+  </p>
+  ---
+  <p>
+  A Genome Browser is now available for the brown kiwi (<em>Apteryx australis</em>)
+  assembly released June 2015 by the
+  <a href="http://www.eva.mpg.de/index.html"
+  target=_blank>Max-Plank Institute for Evolutionary Anthropology</a>.
+  For more information and statistics about this assembly, see
+  <a href="http://www.ncbi.nlm.nih.gov/assembly/GCF_001039765.1"
+  target="_blank">AptMant0</a> in the NCBI Assembly database. There are
+  24,719 scaffolds with a total size of 1,523,986,457 bases.
+  </p>
+
+  <p>
+  Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
+  <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/aptMan1/">FTP server</a> or the
+  <a href="http://hgdownload.soe.ucsc.edu/downloads.html#brown_kiwi">Downloads</a> page.
+  Please observe the <a href="credits.html#brown_kiwi_use">conditions for use</a> when
+  accessing and using these data sets. The annotation tracks for this browser were
+  generated by UCSC and collaborators worldwide. See the <a
+  href="credits.html#brown_kiwi_credits">Credits</a> page for a detailed list of the
+  organizations and individuals who contributed to this release.
+  </p>
+
   <hr>
   <font color="#006666" size="4"><b>8 Mar 2016
   - Combine Multiple Regions of the Genome Browser into a Single Visualization!</b></font>
   <p>
   Have you ever wished you could remove all of the intronic or intergenic regions from the
   Genome Browser display? Have you ever dreamed of being able to visualize multiple
   far-flung regions of a genome? Well, now you can with the new &quot;multi-region&quot; option
   in the Genome Browser!
   </p>
 
   <p>
   The multi-region modes provide four different ways to manipulate the display.
   First, we have an &quot;exon-only&quot; mode that allows you to
   remove all of the intergenic and intronic sequences from the display, leaving you with
   only the exonic regions. Next, there is the &quot;gene-only&quot; mode allowing you to remove only
   the intergenic regions from the display, leaving the genes with exons and introns intact.
   Then there is the &quot;custom regions&quot; mode that allows you to use a remote BED file to
   specify the regions you are interested in viewing alongside each other. Lastly, for human
   assemblies hg17 and newer, there is the &quot;alternative haplotype&quot; mode that allows you to
   view a haplotype sequence inserted into its position in the reference genome.
   </p>
 
   <p>
   To access these exciting, new multi-region modes, first select your organism and assembly
   of interest and navigate to the Genome Browser visualization. Below the tracks display,
   there is a button labeled &quot;multi-region&quot;. Clicking this button will bring up
   a configuration box for the different multi-region modes. For example:
   </p>
 
   <p>
   <img style="border: 1px solid black; display: block;"
                 src="images/MultiRegionButton.png">
   </p>
 
   <p>
   From this pop-up, you will be able to switch between the different modes or exit these
   multi-region modes if desired. For instance:
   </p>
 
   <p>
   <img style="border: 1px solid black; display: block;"
                 src="images/MultiRegionConfigurationWindow.png">
   </p>
 
   <p>
   Additionally, you can enter the &quot;Exon-only&quot; mode by typing the keyboard shortcut
   &quot;e&quot; then &quot;v&quot;. You can exit any of the multi-region modes and return to the
   default Genome Browser display by typing the keyboard shortcut &quot;d&quot; then &quot;v&quot;.
   </p>
 
   <p>
   For more information about each individual multi-region mode, please see the
   <a href="goldenPath/help/multiRegionHelp.html">User Guide</a>.
   </p>
 
   <p>
   Thank you to Galt Barber, Matthew Speir, and the entire UCSC Genome Browser quality assurance team for
   all of their efforts in creating these exciting new display modes.
   </p>
 
   <hr>
-<p>
-  <font color="#006666" size="4"><b> 10 February 2016 -
-  Two New Assemblies Now Available in the Genome Browser</b></font>
-  <p>
-  A Genome Browser is now available for the mouse lemur (<em>Microcebus murinus</em>)
-  assembly released May 2015 by the
-<A HREF="http://www.broadinstitute.org/scientific-community/science/projects/mammals-models/29-mammals-project"
-TARGET="_blank">The Broad Institute</A> and the
-<A HREF="https://www.hgsc.bcm.edu/non-human-primates/mouse-lemur-genome-project"
-TARGET="_blank">Baylor College of Medicine Human Genome Sequencing Center</A>.
-  For more information and statistics about this assembly, see the NCBI assembly record
-  for <a href="http://www.ncbi.nlm.nih.gov/assembly/329621" target="_blank"> Mmur_2.0</a>.
-There are 10,311 scaffolds with a total size of 2,438,804,424 bases.
-  </p>
 
+<!-- start archives -->
+<!--staged for future release
 	<p>
-  Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
-  <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/micMur2/">FTP server</a> or the
-  <a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse_lemur">Downloads</a> page.
-  Please observe the <a href="./goldenPath/credits.html#mouse_lemur_use">conditions for use</a> when
-  accessing and using these data sets.  The annotation tracks for this browser were
-  generated by UCSC and collaborators worldwide.  See the <a
-  href="./goldenPath/credits.html#mouse_lemur_credits">Credits</a> page for a detailed list of the
-  organizations and individuals who contributed to this release.
-  </p>
-  ---
-  <p>
-  A Genome Browser is now available for the platypus (<em>Ornithorhynchus anatinus</em>)
-  assembly released February 2007 by the
-<A HREF="http://genome.wustl.edu/genomes/detail/ornithorhynchus-anatinus/"
-TARGET=_blank>Genome Sequencing Center at Washington University, St. Louis</A>.
-For more information about this assembly, see
-<A HREF="http://www.ncbi.nlm.nih.gov/assembly/237598/" TARGET="_blank">
-Ornithorhynchus_anatinus-5.0.1</A> in the NCBI Assembly database. There are
-201,525 scaffolds with a total size of 1,996,826,513 bases.
-  </p>
+	<font color="#006666" size="4"><b>16 Mar 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#031616">Read more</a>.
 
-  <p>
-  Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser
-  <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ornAna2/">FTP server</a> or the
-  <a href="http://hgdownload.soe.ucsc.edu/downloads.html#platypus">Downloads</a> page.
-  Please observe the <a href="./goldenPath/credits.html#platypus_use">conditions for use</a> when
-  accessing and using these data sets.  The annotation tracks for this browser were
-  generated by UCSC and collaborators worldwide.  See the <a
-  href="./goldenPath/credits.html#platypus_credits">Credits</a> page for a detailed list of the
-  organizations and individuals who contributed to this release.
+	<font color="#006666" size="4"><b>21 Mar 2016
+	- Genome Browsers for <i>C. elegans</i> and Brown Kiwi Now Available.</b></font>
+	<a href="goldenPath/newsarch.html#030816">Read more</a>.
 	</p>
-<hr>
-
-<!-- start archives -->
-<!--staged for future release
 
 	<p>
 	<font color="#006666" size="4"><b>8 Mar 2016
 	- Combine Multiple Regions of the Genome Browser into a Single Visualization!</b></font>
 	<a href="goldenPath/newsarch.html#030816">Read more</a>.
         </p>
 
+-->
         <p>
         <font color="#006666" size="4"><b> 10 February 2016 -
         Two New Assemblies Now Available in the Genome Browser</b>: </font>
         Genome Browsers are now available for the mouse lemur 
 	(<em>Microcebus murinus</em>)
         and platypus (<i>Ornithorhynchus anatinus</i>) assemblies.
 	<a href="goldenPath/newsarch.html#021016">Read more</a>. 
         </p>
 
--->
 	<font color="#006666" size="4"><b>20 Jan 2016 &mdash;
 	dbSNP 142 Available for mm10</b></font>
         <a href="goldenPath/newsarch.html#012016">Read more</a>.
         </p>
-        <p>
-        <font color="#006666" size="4"><b>08 January 2016 &mdash; 
-        dbSNP 144 Available for hg19 and hg38 </font></b>
-        <a href="goldenPath/newsarch.html#010816">Read more</a>.
-        </p>
 
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