7c66f8b3fdf123b9dd3423c45cd54b29ecfd66a7
kuhn
  Sat Mar 5 15:35:35 2011 -0800
added announcement for color-scheme change in DGV and DECIPHER
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                           <FONT SIZE="4"><A NAME="TOC"></A><B>&nbsp; News</B></FONT></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="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" 
                     TARGET=_blank>genome-announce</A> mailing list.</P>
 
                     <!-- start news -->
 		    <P>
-                    <FONT FACE="courier" SIZE="3"><B>1 March 2011 -
-Updated Chimpanzee Browser Released</B></FONT>
+                    <FONT FACE="courier" SIZE="3"><B>04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs</B></FONT>
+		    </P>
+		    <P>
+		    Consensus was reached on color standards to represent CNV loss (red) 
+		    and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA 
+		    during the 1st annual ISCA Scientific Conference.
+		    </P>
+		    <P>
+		    At the recent ISCA Scientific Conference in Atlanta, GA, Nigel Carter, 
+		    representing DECIPHER, made a plea for a standardized color scheme for 
+		    representation of CNV loss (deletion) or gain (duplication). Discussions 
+		    in person and by email with leaders of major CNV/genomic databases (including 
+		    DGV, dbVar, ISCA, and the UCSC Genome Browser) resulted in the recommendation 
+		    to utilize red to represent loss/deletion (consistent with the original 
+		    convention for CGH on metaphase chromosomes) and blue to represent 
+		    gain/duplication (avoiding green which is difficult for color-blind 
+		    individuals to discriminate from red).
+		    </P>
+		    <P>
+		    Announcememnt reprinted from the website for the International Standards for
+		    Cytogenomic Arrays (<A HREF = "http://iscaconsortium.org" TARGET = _BLANK>ISCA</A>) 
+		    Consortium.  The UCSC Genome Browser is now conforming to this standard for the 
+		    DECIPHER and DGV (which was released today) tracks on human assemblies and on 
+		    any future tracks derived from dbVar.
+		    </P>
+		    <P>
+		    Thanks to Nigel Carter, Steve Scherer, Deanna Church, Angie Hinrichs, Fan Hsu,
+		    Pauline Fujita and Robert Kuhn.
+		    </P>
+
+		    <HR>
+		    <P>
+                    <FONT FACE="courier" SIZE="3"><B>01 March 2011 - Updated Chimpanzee Browser Released</B></FONT></P>
 		    <P>
 		    We are happy to announce the release of a Genome Browser for
 		    the latest release of the chimpanzee (<em>Pan 
 		    troglodytes</em>) genome. The Oct. 2010 assembly -- CGSC 
 		    v2.1.3, UCSC version panTro3 -- was produced by the 
 		    <A HREF="http://genome.wustl.edu/genome.cgi?GENOME=Pan%20troglodytes&SECTION=collaborators"
 		    TARGET=_BLANK>Chimpanzee Sequencing and Analysis 
 		    Consortium</A>.</P>
 		    <P>
 		    This assembly covers about 97 percent of the genome and is 
 		    based on 6X sequence coverage. It comprises 192,898 contigs 
 		    with an N50 length of 44 kb and 33,990 supercontigs with an
 		    N50 length of 8.4 Mb.  
 		    Improvements introduced with the 2.1.3 assembly include the 
 		    addition of over 300,000 finishing reads and the merging in 
 		    of 640 finished BACS. Approximately 49,000 additional merges
 		    were made in this assembly as compared with the 2.1 
 		    assembly.
 		    <P>
 		    The whole genome shotgun data were derived primarily from 
 		    the donor Clint, a captive-born male chimpanzee from the 
 		    Yerkes Primate Research Center in Atlanta, GA, USA. 
 		    The sequence data were assembled and organized by the 
 		    Washington University Genome Center. The underlying whole 
 		    genome shotgun data were generated at the Washington 
 		    University School of Medicine and the Broad Institute. 
 		    For detailed information about the assembly 
 		    process, see the sequencing and analysis discussion in the 
 		    <A HREF="http://www.ncbi.nlm.nih.gov/nuccore/AACZ00000000"
 		    TARGET=_blank>GenBank accession record</A>.
 		    </P>
 		    <P>
 		    Bulk downloads of the sequence and annotation data are 
 		    available via the Genome Browser 
 		    <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/">FTP
 		    server</A> or the 
 		    <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#chimp">Downloads</A> 
 		    page. The complete set of sequence reads is available at the
 
 		    <A HREF="http://www.ncbi.nlm.nih.gov/Traces" 
 		    TARGET=_blank>NCBI trace archive</A>. These data have 
 		    <A HREF="goldenPath/credits.html#chimp_use">specific
 		    conditions for use</A>.</P>
 		    <P>
 		    We'd like to thank the International Chimpanzee 
 		    Sequencing and Analysis Consortium, Washington 
 		    University at St. Louis School of Medicine Genome Sequencing
 		    Center, and the Broad Institute for providing this assembly.
 		    We'd also like to acknowledge the UCSC team who worked on 
 		    this release: Hiram Clawson, Greg Roe, and Donna Karolchik. 
 		    The chimpanzee browser annotation tracks were generated by 
 		    UCSC and collaborators worldwide. </P>
 		    <P>
 		    <HR>
+
                     <FONT FACE="courier" SIZE="3"><B>19 January 2011 -
 Browser Released for Zebrafish Zv9 Assembly: </B></FONT>
                     The most recent zebrafish assembly -- Zv9 (UCSC version
                     danRer7, Jul. 2010) -- is now available in the UCSC
                     Genome Browser. 
 		    <A HREF="goldenPath/newsarch.html#011911">Read more</A>.
 		    <P>
                     <FONT FACE="courier" SIZE="3"><B>10 January 2011 - Introducing Genome Browser Right-click Navigation: </B></FONT>
 		    Several of the common display and navigation operations 
 		    offered on the Genome Browser tracks page may now be quickly
 		    accessed by right-clicking on a feature on the tracks image 
 		    and selecting an option from the displayed menu. 
 		    <A HREF="goldenPath/newsarch.html#011011">Read more</A>.
 		    <P>
                     <FONT FACE="courier" SIZE="3"><B>2 December 2010 -
-Searching for Tracks Just Got Easier! </B></FONT>
+Searching for Tracks Just Got Easier! </B></FONT> </P>
 		    With our latest Genome Browser release, we've introduced a 
 		    new track search feature that will help you to quickly and 
 		    easily find and display specific annotation data sets. The 
 		    search feature is available via the "track search" button 
 		    on the browser gateway and tracks display pages.
 		    <A HREF="goldenPath/newsarch.html#120210">Read more</A>.
 		    </P>
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