1d58a54a7f6539f1b77db01b0e505a72ae1f6ee4 donnak Wed Nov 16 08:15:56 2011 -0800 Added UMD cow announcement, archived some news items, fixed some typos etc. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8537181..4610bef 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -14,128 +14,96 @@ </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="https://lists.soe.ucsc.edu/mailman/listinfo/genome-announce" TARGET=_blank>genome-announce</A> mailing list.</P> <!-- start news --> - - - <!-- sacCer3 Assembly Release --> + <FONT FACE="courier" SIZE="3"><B>7 November 2011 - UMD Cow + Assembly Now Available in Genome Browser</B></FONT> <P> - <FONT FACE="courier" SIZE="3"><B>10 October 2011 - Updated Yeast Browser Released</B></FONT> - <p>We are happy to announce an updated Yeast Genome Browser for - <i>Saccharomyces cerevisiae</i>, sacCer3. The April 2011 <em>Saccharomyces cerevisiae</em> - genome assembly (<i>Saccharomyces cerevisiae</i> S288c assembly from Saccharomyces Genome - Database (GCA_000146055.2)) was produced by the <A HREF="http://www.yeastgenome.org/" - taget="_blank"><em>Saccharomyces</em> Genome Database (SGD™)</A> project.</p> - + In response to the many requests from the bovine research + community, we now offer the University of Maryland (UMD) + <em>Bos taurus</em> assembly in the Genome Browser, in + addition to the assemblies produced by the Baylor College + of Medicine Human Genome Sequencing Center. The UMD v3.1 + assembly (Nov. 2009, UCSC bosTau6) was produced by the + <A HREF="http://www.cbcb.umd.edu/" TARGET=_blank>UMD Center + for Bioinformatics and Computational + Biology</A> (CBCB) in College Park, MD. </P> + <P> + The UMD 3.1 assembly is based on reads downloaded from + the NCBI Trace Archive, most of which were sequenced by + the Baylor College of Medicine. UMD reports that they were + able to apply several assembly improvement techniques + to produce an assembly that is substantially more accurate + and complete than alternative versions, as evaluated using + independent metrics. Based on UMD statistics, this + assembly provides more genome coverage, closes + thousands of gaps, corrects many erroneous inversions, + deletions, and translocations, and fixes thousands of + single-nucleotide errors. For more information, see + Zimina AV <em>et al</em>, + <A HREF="http://genomebiology.com/2009/10/4/R42" + TARGET=_blank>A whole-genome assembly of the domestic + cow, Bos taurus</A>, <em>Genome Biol.</em>2009;10(4) and + the UMD CBCB + <A HREF="http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml">Bos taurus assembly</A> web page.</P> <P> - Chromosomes available in this assembly: chrI, chrII, chrIII, chrIV ... etc ... chrXVI, - and chrM. See also: <A HREF="http://www.yeastgenome.org/cache/genomeSnapshot.html" - TARGET="_blank">SGD™ genome snapshot/overview</A>. + Downloads of the UMD bovine data and annotations may be + obtained from the UCSC Genome Browser + <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/">FTP server</A> + or <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#cow">Downloads</A> page. </P> - <P> - Downloads of the yeast data and annotations may be obtained from the UCSC - Genome Browser <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/" - TARGET=_blank>FTP server</A> or - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#yeast" - TARGET=_blank>Downloads</A> page. - The <EM>S. cerevisiae</EM> annotation tracks were generated by - UCSC and collaborators worldwide. - - <p> - We'd like to thank the Saccharomyces Genome - Database (SGD™). The <i>S. cerevisiae</i> Genome Browser and annotation tracks were produced by - Hiram Clawson, Greg Roe, and Steve Heitner. See the <A HREF="goldenPath/credits.html#yeast_credits" - >Credits</A> page for a detailed list of the organizations and individuals who - contributed to this release. - </p> - + We'd like to thank the UMD CBCB for providing this genome + assembly. The UMD Cow Genome Browser and annotation tracks + were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg + Roe, Steve Heitner, and Donna Karolchik. 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> + <P> <HR> - - - + <!-- start archives --> + <!-- sacCer3 Assembly Release --> + <FONT FACE="courier" SIZE="3"><B>10 October 2011 - Updated Yeast Browser Released: </B></FONT> + We are happy to announce the release of an updated browser + for the <em>Saccharomyces cerevisiae</em> yeast genome. + <A HREF="goldenPath/newsarch.html#101011">Read more</A>. + </P> <!-- New javascript features --> <P> <FONT FACE="courier" SIZE="3"><B>8 September 2011 - -New Navigation and Display Features </B></FONT> - <P> +New Navigation and Display Features: </B></FONT> We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window. - <P> - <B>Automatic image resizing:</B> The first time the annotation - track window is displayed, or after the Genome Browser has - been reset, the size of the track window is now set by - default to the width that best fits your Internet browser - window. If you subsequently resize your browser window, - you can automatically adjust the annotation track image - size to the new width by clicking the <em>resize</em> button - under the track image. The default width can still be - manually overridden on the Track Configuration page. - <P> - <B>Scrolling left or right in the track window:</B> You can now - scroll (pan) horizontally through the tracks image by clicking - on the image, dragging the cursor to the left or right, - then releasing the mouse button. The view may be scrolled - by up to one image width. - <P> - <B>Improved drag-zoom navigation:</B> The browser's - "drag-and-zoom" feature lets you quickly zoom to a - specific region of interest on the annotation tracks image. - To define the region you wish to zoom to, depress the shift - key, click-and-hold - the mouse button on one edge of the desired zoom area - (which can be anywhere in the tracks window), - drag the mouse right or left to highlight the - selection area, then release the mouse button. - The annotation tracks image will automatically zoom to - the new region. The Genome Browser still supports the - earlier implementation of this feature, which restricted - the click-drag to the Base Position track area of the image, - but did not require the shift key to be pressed. - <P> - <B>Reordering groups of tracks:</B> - You can now vertically reposition an entire group of - associated tracks in the tracks image (such as all the - displayed subtracks in a composite track) by clicking and - holding the gray bar to the left of the tracks, - dragging the group to the new position, then releasing - the mouse button. To move a single track up or down, click - and hold the mouse button on the side label, drag the - highlighted track to the new position, then release the - mouse button. - <P> - If you haven't yet tried the browser's right-click - menu for quick access to frequently used track - configuration features and functionality, read more - <A HREF="goldenPath/newsarch.html#011011">here</A>. - <HR> + <A HREF="goldenPath/newsarch.html#090811">Read more</A>. <!-- data hubs release --> <P> <FONT FACE="courier" SIZE="3"><B>18 August 2011 - New Feature: Track Data Hubs: </B></FONT> - We are pleased to announce a new feature in the UCSC Genome Browser: Track Data Hubs. Track hubs are web-accessible directories of genomic data - that can be viewed on the UCSC Genome Browser alongside native annotation - tracks. + We are pleased to announce a new feature in the UCSC Genome + Browser: Track Data Hubs. Track hubs are web-accessible + directories of genomic data that can be viewed on the UCSC + Genome Browser alongside native annotation tracks. <A HREF="goldenPath/newsarch.html#081811">Read more</A>. </P> ==> <a href="goldenPath/newsarch.html">News Archives</a> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>