ff88988351f96cd386fdc8647a818c2ab68bf72d
mspeir
  Fri Apr 15 14:37:01 2016 -0700
Adding announcement for snp146 for hg19 and hg38, slight edits to 3-primate announcement, edited dates on staged lens patents announcement, refs #16777

diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index 937c460..d029ef9 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -1,231 +1,247 @@
 <!-- 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" 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
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           target=_blank>blog</a> for posts about Genome Browser tools, features, projects and more.
           </p>
 
     <!-- start news -->
 <!-- Staged for later release
   <hr>
-  <font color="#006666" size="4"><b>7 Apr 2016
+  <font color="#006666" size="4"><b>20 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 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>
+  <p>
+  <font color="#006666" size="4"><b> 15 April 2016 -
+  dbSNP 146 Available for hg19 and hg38</b></font>
+  <p>
+  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, available on the two most
+  recent human assemblies GRCh37/hg19 and GRCh38/hg38.
+  NCBI's dbSNP database is a collection of &quot;simple nucleotide
+  polymorphisms&quot; (SNPs), which are a class of genetic variations
+  that include single nucleotide polymorphisms and small
+  insertions/deletions (indels). This immense database contains over
+  150 million such SNPs that cover the human genome.
+  </p>
+
+  <p>
+  There are four SNP tracks available as part of this release.
+  One is a track containing all mappings of reference SNPs
+  to the human assembly, labeled &quot;All SNPs (146)&quot;.
+  The other three tracks are subsets of this track
+  and show interesting and easily defined subsets of dbSNP:
+  </p>
+
+  <ul>
+  <li>Common SNPs (146): uniquely mapped variants that appear
+  in at least 1% of the population or are 100% non-reference.</li>
+  <li>Flagged SNPs (146): uniquely mapped variants, excluding
+  Common SNPs, that have been flagged by dbSNP as
+  "clinically associated".</li>
+  <li>Mult. SNPs (146): variants that have been mapped to more
+  than one genomic location. This track has been shrinking over
+  the course of the last few releases as dbSNP now excludes most
+  SNPs whose flanking sequences map to multiple locations in
+  the genome.</li>
+  </ul>
+
+  <p>
+  By default, only the Common SNPs (146) are visible;
+  other tracks must be made visible using the track controls.
+  You will find the other SNPs (146) tracks on both
+  of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group.
+  </p>
+  <p>
+  The tracks were produced at UCSC by Angie Hinrichs and
+  Matthew Speir. We'd like to thank the dbSNP group at
+  NCBI for providing access to these data.
+  </p>
 
-<!-- Staged for upcoming release
   <hr>
   <a name="041516"></a>
   <p>
   <font color="#006666" size="4"><b> 15 April 2016 -
   Three New Assemblies Now Available in the Genome Browser</b></font>
   <p>
   A Genome Browser is now available for the gorilla (<em>Gorilla gorilla gorilla</em>)
-  assembly released Dec 2014 by the Wellcome Trust Sanger Institute. 
+  assembly released December 2014 by the Wellcome Trust Sanger Institute. 
   For more information and statistics about this assembly, see the NCBI assembly record
   for <a href="http://www.ncbi.nlm.nih.gov/assembly/503571" target="_blank">gorGor4</a>.  
-  There are 40,730 scaffolds with a total size of 3,063,362,754 bases.
+  There are 25 complete chromosomes alongside 40,667 scaffolds with a total size of
+  3,063,362,754 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/gorGor4/">FTP server</a> or the
   <a href="http://hgdownload.soe.ucsc.edu/downloads.html#gorilla">Downloads</a> page.
   Please observe the <a href="credits.html#gorilla_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#gorilla_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 rhesus monkey (<em>Macaca mulatta</em>)
-  assembly released Nov 2015 by the 
+  assembly released November 2015 by the 
   <A HREF="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-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/2715158" target="_blank"> Mmul_8.0.1</a>.  
-There are 286,263 scaffolds with a total size of 3,236,224,332 bases.
+  There are 23 complete chromosomes alongside 284,705 scaffolds with a total size of
+  3,236,224,332 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/rheMac8/">FTP server</a> or the
   <a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus">Downloads</a> page.
   Please observe the <a href="credits.html#rhesus_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#rhesus_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 crab-eating macaque (<em>Ornithorhynchus anatinus</em>)
-  assembly released February 2007 by the 
+  A Genome Browser is now available for the crab-eating macaque (<em>Macaca fascicularis</em>)
+  assembly released June 2013 by the 
   <A HREF="http://genome.wustl.edu/genomes/detail/macaca-fascicularis/"
   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/704988" TARGET="_blank">
-Macaca_fascicularis_5.0</A> in the NCBI Assembly database. There are 
-7,625 scaffolds with a total size of 2,946,843,737 bases.
+  <A HREF="http://www.ncbi.nlm.nih.gov/assembly/704988"
+  TARGET="_blank">Macaca_fascicularis_5.0</A> in the NCBI Assembly database. There are 
+  22 complete chromosomes alongside 7,579 scaffolds with a total size of 2,946,843,737 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/macFas5/">FTP server</a> or the
   <a href="http://hgdownload.soe.ucsc.edu/downloads.html#crab-eating_macaque">Downloads</a> page.
   Please observe the <a href="credits.html#crab-eating_macaque_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#crab-eating_macaque_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>4 Apr 2016
   - New video shows how to obtain sequence or coordinates for exons. </b></font>
   <p>
   We have released a new <A HREF =
   "http://genome.ucsc.edu/training/vids/index.html#vid08" TARGET =
   _BLANK>video</A> to our YouTube channel.  This newest installment in our effort
   to share the capabilities of the Genome Browser shows how to
   use the Table Browser to obtain either the sequences or the coordinates for
   exons in the genes from a chosen region of the genome.
   </p>
 
   <p>
   We also want to take this opportuinty to remind you that we offer
   on-site <A HREF = "http://genome.ucsc.edu/training/index.html" TARGET =
   _BLANK>workshops</A> to help you and your colleagues make the most out
   of the Genome Browser.
   </p>
   <hr>
 
-  <font color="#006666" size="4"><b>1 Apr 2016
-  - Going Back to Our Roots</b></font>
-  <p>
-  For many years, the UCSC Genome Browser has provided a dynamic, cutting-edge interface for
-  viewing genomic data.  As time has gone by, however, it has become clear to us that we
-  cannot keep this up.  It is not fair to you, our users, that our interface keeps changing,
-  and it has increasingly been a burden on us to keep up with emerging web technologies.  Today
-  that all changes, as we return you to the roots of the web: ASCII.
-  <p>
-  <center><img src="images/joke04012016.png" width="65%"></center>
-  <p>
-  We apologize again for subjecting you to so many changes over the years, and hope that this
-  new, more consistent interface will find your approval.
-  <p>
-  In related news, we have also revised the interface for uploading custom tracks.  Rather than
-  forcing you to wrestle with inconvenient file formats for your data or attempt to set up a web server,
-  we now provide the option of loading your data from a deck of ISO 6586:1980 punch cards.  Simply
-  punch your data onto a deck and mail the deck to us.  Our staff of highly trained specialists
-  will take care of loading track, and will inform you by mail when the process is complete.  Please
-  note that our current policy of expiring unused custom tracks remains in effect; you must visit
-  your track within 72 hours of the postmark date.  Regrettably, decks cannot be returned.
-  <p>
-  Card decks may be addressed to:<br>
-  UCSC Genome Informatics Group<br>
-  Center for Biomolecular Science & Engineering<br>
-  CBSE, 501D Engineering II Building<br>
-  University of California, Santa Cruz<br>
-  1156 High Street<br>
-  Santa Cruz, CA 95064
-  <p>
-  This new file format is also an option for data output from the <a href="cgi-bin/hgTables">UCSC Table Browser</a>.
-  Simply select "mail card deck" from the "output format" menu, and then enter your name and address on the subsequent
-  page.  Please allow 4-6 weeks for delivery.
-  <hr>
-
 <!-- start archives -->
 <!--staged for future release
         <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">Read more</a>.
-	</p>
-	
-
-        <p>
-	<font color="#006666" size="4"><b>7 Apr 2016
+	<font color="#006666" size="4"><b>20 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#040716">Read more</a>.
+	<a href="goldenPath/newsarch.html#042016">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>
 	
 	<p>
 	<font color="#006666" size="4"><b>4 Apr 2016
         - New video shows how to obtain sequence or coordinates for exons. </b></font>
 	<a href="goldenPath/newsarch.html#040416">Read more</a>.
 	</p>
 
+-->
 	<p>
 	<font color="#006666" size="4"><b>1 Apr 2016
 	- Going Back to Our Roots!</b></font>
 	<a href="goldenPath/newsarch.html#040116">Read more</a>.
 	</p>
--->
+
 	<p>
 	<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>
 
-	<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>
-
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