88735c9a958cfd813bb1a6621c77a415b881758d
mspeir
  Mon Mar 21 14:52:49 2016 -0700
Fixing links to credits page in ce11 and aptMan1 announcement, refs #15209 #16029

diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index 77dd133..3ac947f 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -1,216 +1,216 @@
 <!-- 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>
                  <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>
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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. 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>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
+  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="credits.html#ce_credits">Credits</a> page for a detailed list of the
+  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>.
   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
+  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="credits.html#brown_kiwi_credits">Credits</a> page for a detailed list of the
+  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>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>
 
 -->
         <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>
 
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