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ann
  Sun Apr 3 17:58:12 2016 -0700
trying to fix merge conflict

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++<!-- News Section ============================================- -->  
++<TABLE style="background-color:#888888; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px">
++    <TR><TD>        
++    <TABLE style="background-color:#fffee8; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px">
++        <TR><TD>        
++        <TABLE style="background-color:#D9E4F8; background-image: url('images/hr.gif'); width: 100%; border: 0px">
++            <TR><TD>
++            <!--cheap trick to get background on row to be continuous-->
++            <TABLE CELLPADDING=0 CELLSPACING=0 WIDTH="100%">
++                <TR><TD ALIGN="left">
++                 <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>
++                 <a title="Genome Browser Facebook page"
++                 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>
++            </TD></TR></TABLE>
++        </TD></TR></TABLE>
++        <TABLE style="background-color:#fffee8; width: 100%; padding: 0px">
++          <TR><TH HEIGHT=3></TH></TR>
++          <TR><TD WIDTH=10></TD>
++          <TD>
++          <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>
++
++    <!-- 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>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>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 February 2013 by the C. elegans Sequencing Consortium
++  (C. elegans Sequencing Consortium version WBcel235, UCSC version ce11).
++  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>.
++  There are 7 complete chromosomes 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="goldenPath/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="goldenPath/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> (MPI-EVA version AptMan0,
++  UCSC version aptMan1).
++  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="goldenPath/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="goldenPath/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>
++
++<!-- start archives -->
++<!--staged for future release
++	<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>.
++
++	<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>
++
++	<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>
++
++-->
++
++            </TD><TD WIDTH=15>
++         </TD></TR></TABLE>
++    <BR></TD></TR></TABLE>
++</TD></TR></TABLE>