5554a09d5cc142c5a01b4b4acc94f8900851ca9b
luvina
  Thu Jan 15 14:07:37 2015 -0800
added news announcement for CPTAC hub and PeptideAtlas track
diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html
index db4451a..47b19a0 100755
--- src/hg/htdocs/indexNews.html
+++ src/hg/htdocs/indexNews.html
@@ -1,133 +1,170 @@
 <!-- News Section ============================================- -->  
 <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1">
     <TR><TD>        
     <TABLE BGCOLOR="#fffee8" WIDTH="100%"  BORDER="0" CELLSPACING="0" CELLPADDING="0">
         <TR><TD>        
         <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0>
             <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 BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0>
           <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 -->
 
     <!-- staged announcemnt for YouTube 
 	<hr>
         <p>
         <font face="courier" size="3"><b>19 January 2015 - Genome Browser YouTube Channel</b></font>
 
         <p>We are pleased to announce the release of the UCSC Genome Browser
         <A HREF = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos">YouTube
         channel</A>.  The channel contains short videos showing
         how to use the Genome Browser and associated tools to solve selected problems.  The
         videos were produced by Robert Kuhn and Pauline Fujita, with assistance from Luvina
         Guruvadoo, Jonathan Casper and the rest of the Browser staff.
         </p>
 
         <p>See also the other materials on our <a href = "training/">training page</a>.
 
         </p>
     -->
 	<hr>
 	<p>
+	<font face="courier" size="3"><b>15 January 2015 - 
+	Proteomics Data Now Available in Genome Browser</b></font>
+	<p>
+	We are pleased to announce the release of proteomics data for the 
+	human hg19 assembly. Data from the National Cancer Institute’s (NCI) 
+	<a href="http://proteomics.cancer.gov/programs/cptacnetwork" target="_blank">
+	Clinical Proteomic Tumor Analysis Consortium (CPTAC)</a> is now available 
+	in the UCSC Genome Browser as a public track hub. This track hub 
+	contains peptides that were identified by CPTAC in their deep mass 
+	spectrometry based characterization of the proteome content of 
+	breast, colorectal and ovarian cancer biospecimens that were initially 
+	sequenced by <a href="http://cancergenome.nih.gov/" target="_blank">
+	The Cancer Genome Atlas</a>. This effort extends the 
+	accessibility of CPTAC data to more researchers and provides an 
+	additional level of analysis to assist the cancer biology community.
+	<p>
+	To access and view this hub, navigate to the 
+	<a href="http://genome.ucsc.edu/cgi-bin/hgHubConnect" target="_blank">
+	Track Hub gateway page</a> and select “CPTAC Hub v1” from the Public Hubs list. 
+	Please direct any queries to the Fenyo Lab at <a href="mailto:info@fenyolab.org">.
+	<p>
+	In addition, we have also released a <a href="http://www.peptideatlas.org/" target="_blank">
+	PeptideAtlas</a> track which displays peptide identifications from the 
+	<a href="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=433" target="_blank">
+	PeptideAtlas August 2014 (Build 433) Human build</a>. This build, based on 971 samples containing more than 420 
+	million spectra, identified over a million distinct peptides covering 
+	more than 15,000 canonical proteins. To read more about this track, 
+	please see the <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=peptideAtlas" target="_blank">
+	track description page</a>. Many thanks to Eric Deutsch, 
+	Zhi Sun, and the PeptideAtlas team at the Institute for Systems Biology, 
+	Seattle for providing this data.
+	</p>        
+
+
+
+	<hr>
+        <p>
         <font face="courier" size="3"><b>19 December 2014 -
         New Cow (bosTau8) Assembly Now Available in the Genome Browser</b></font>
         <p>
         We are pleased to announce the release of a Genome Browser for the June 2014 assembly
         of cow, <i>Bos taurus</i> (Bos_taurus_UMD 3.1.1, UCSC version bosTau8). This updated cow assembly was 
 	provided by the  <a href="http://www.cbcb.umd.edu/"
         target="_blank">UMD Center for Bioinformatics and Computational Biology</a> (CBCB). This
 	assembly is an update to the previous UMD 3.1 (bosTau6) assembly.  UMD 3.1 contained 
 	138 unlocalized contigs that were found to be contaminants. 
 	These have been suppressed in UMD 3.1.1.
         <p>
         Bulk downloads of the sequence and annotation data are available via the Genome
         Browser
         <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/">FTP server</a>
         or the
         <a href="http://hgdownload.cse.ucsc.edu/downloads.html#cow">Downloads</a>
         page. These data have
         <a href="/goldenPath/credits.html#cow_credits">specific conditions for use</a>.
         The cow browser annotation tracks were generated by UCSC and
         collaborators worldwide. See the
         <a href="/goldenPath/credits.html#cow_credits">Credits</a> page for a detailed
         list of the organizations and individuals who contributed to this release.
         </p>
 
 	<hr>
         <p>
         <font face="courier" size="3"><b>12 December 2014 -
         New <i>D. melanogaster</i> (dm6) Assembly Now Available in the Genome Browser</b></font>
         <p>
 	We are pleased to announce the release of a Genome Browser for the August 2014 assembly
         of <i>Drosophila melanogaster</i> (BDGP Release 6, UCSC version dm6). This updated <i>D.
 	melanogaster</i> assembly was provided by the  <a href="http://www.fruitfly.org/"
         target="_blank">Berkeley Drosophila Genome Project</a> (BDGP). Please see
 	<a href="http://flybase.org/static_pages/feature/previous/articles/2014_07/FB2014_04.html"
 	target="_blank">this announcement</a> on the FlyBase website for more details about this
 	updated <i>D. melanogaster</i> assembly.
 	<p>
 	Bulk downloads of the sequence and annotation data are available via the Genome
         Browser
         <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6/">FTP server</a>
         or the
         <a href="http://hgdownload.cse.ucsc.edu/downloads.html#fruitfly">Downloads</a>
         page. These data have
         <a href="/goldenPath/credits.html#dm_credits">specific conditions for use</a>.
         The <i>D. melanogaster</i> (dm6) browser annotation tracks were generated by UCSC and
         collaborators worldwide. See the
         <a href="/goldenPath/credits.html#dm_credits">Credits</a> page for a detailed
         list of the organizations and individuals who contributed to this release.
         </p>
 
 	<hr>
 
         <!-- start archives -->
 
  	<p>
         <font face="courier" size="3"><b>29 October 2014 -
         Genome Browser in a Box (GBiB)</b>:</font>
         Sometimes you just want to keep your genomics data to yourself. Have you ever
         hesitated when uploading your data set into the UCSC Genome Browser? If so,
         you'll be happy to know that we have created a stand-alone personal version:
         Genome Browser in a Box (GBiB). <a href="goldenPath/newsarch.html#102914">Read more</a>.
 
 	<p>
         <font face="courier" size="3"><b>20 October 2014 -
         dbSNP 141 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/" target="_blank">dbSNP</a> Build 141
         data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38.
         <a href="goldenPath/newsarch.html#102014">Read more</a>.
 	</p>
 
             </TD><TD WIDTH=15>
          </TD></TR></TABLE>
     <BR></TD></TR></TABLE>
 </TD></TR></TABLE>