41c99d987a7c1f61d6152b0c5d2d500d9a03d650 jcasper Fri Jun 26 15:31:58 2015 -0700 Adding announcement of Bonobo release, refs #8231 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8469d3e..637c900 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,141 +1,139 @@ <!-- 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> 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 @GenomeBrowser on Twitter" alt="Follow @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 --> <hr> <p> + <font face="courier" size="3"><b>26 June 2015 - + New Bonobo (panPan1) Assembly Now Available in the Genome Browser</b></font> + <p> + We are pleased to announce the release of a Genome Browser for the May 2012 + assembly of bonobo, <em>Pan paniscus</em> (Max-Planck Institute panpan1, UCSC + version panPan1). The assembly was provided by the + <a href="http://www.eva.mpg.de/" + target="_blank">Max-Planck Institute for Evolutionary Anthropology</a>. + There are 10,867 scaffolds with a total size of 2,869,190,071 bases. + </p> + <p> + Bulk downloads of the sequence and annotation data are available via the Genome + Browser + <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/panPan1/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#bonobo">Downloads</a> + page. These data have + <a href="goldenPath/credits.html#bonobo_credits">specific conditions for use</a>. + The bonobo (panPan1) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + <a href="goldenPath/credits.html#bonobo_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 June 2015 - Data Integrator</b></font> <p>Have you ever wished that the Table Browser could associate your custom track items with some other track, while retaining the item names from both? We have released a new tool that can do just that, and more: the Data Integrator. </p> <p>Using the Data Integrator you can select up to five tracks, including custom tracks and hub tracks, and output tab-separated text that contains all the fields from both the first track and the overlapping items from the other track(s). If you need only a subset of the fields from your selected tracks, the Data Integrator allows you to choose which fields to include in the output. You can also query your current Genome Browser position, search for positions of items such as genes, SNPs, etc. by name, query over a set of up to 1000 positions, and even retrieve genome-wide data (subject to data size). The Data Integrator output can be viewed in your web browser window or downloaded to an optionally gzip-compressed file. Look for "Data Integrator" in the Genome Browser Tools menu (top blue bar) if you'd like to try it out. </p> </p> <p>For more information about the Data Integrator's capabilities and usage, see the user's guide: <a href="http://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html" >http://genome.ucsc.edu/goldenPath/help/hgIntegratorHelp.html</a>. As always, we welcome questions and feedback on our public mailing list: <a href="mailto:genome@soe.ucsc.edu" >genome@soe.ucsc.edu</a> <!-- above address is genome at soe.ucsc.edu --> </p> <p>Thanks to Angie Hinrichs and Matthew Speir for all of their work on this feature. </p> <hr> - <p> - <font face="courier" size="3"><b>28 May 2015 - - New UCSC Genes Track Released for GRCm38/mm10</b></font> - <p> - We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 - mouse Genome Browser. The new release has 63,244 total transcripts, compared with 61,642 - in the previous version. The total number of canonical genes has increased from 32,408 - to 32,958. Comparing the new gene set with the previous version: - <ul> - <li>59,119 transcripts did not change between versions.</li> - <li>55 transcripts were not carried forward to the new version.</li> - <li>2,308 transcripts are "compatible" with those in the previous set, meaning - that the two transcripts show consistent splicing. In most cases, the old and new - transcripts differ in the lengths of their UTRs.</li> - <li>160 transcripts overlap with those in the previous set, but do not show consistent - splicing (i.e., they contain overlapping introns with differing splice sites).</li> - </ul> - </p> - <p> - More details about the new UCSC Genes track can be found on the - <a href="/cgi-bin/hgTrackUi?db=mm10&g=knownGene">UCSC Genes track - description page</a>. - </p> - - <p> - Many thanks to Brian Raney and Matthew Speir for their work on this track! - </p> - - <hr> <!-- start archives --> <!-- + <font face="courier" size="3"><b>26 June 2015 - + New Bonobo (panPan1) Assembly Now Available in the Genome Browser</b>: + </font> + We are pleased to announce the release of a Genome Browser for the May 2012 + assembly of bonobo, <em>Pan paniscus</em> (Max-Planck Institute panpan1, UCSC + version panPan1). + <a href="goldenPath/newsarch.html#062615">Read more</a>. + <font face="courier" size="3"><b>12 June 2015 - Data Integrator</b>: </font> Have you ever wished that the Table Browser could associate your custom track items with some other track, while retaining the item names from both? We have released a new tool that can do just that, and more: the Data Integrator. <a href="goldenPath/newsarch.html#061215">Read more</a>. </p> +--> <p> <font face="courier" size="3"><b>28 May 2015 - New UCSC Genes Track Released for GRCm38/mm10</b>: </font> We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. <a href="goldenPath/newsarch.html#052815">Read more</a>. </p> ---> + <p> <font face="courier" size="3"><b>15 May 2015 - Work for Us! New Job Openings on the UCSC Genome Browser Project</b>: </font> The UCSC Genome Browser project team is looking for two talented people to join our engineering staff based in Santa Cruz, CA. <a href="goldenPath/newsarch.html#051515">Read more</a>. </p> - - <p> - <font face="courier" size="3"><b>08 April 2015 - - bigGenePred Format Now Supported in the Genome Browser</b>: </font> - We are pleased to announce that the UCSC Genome Browser now supports data in - bigGenePred format. - <a href="goldenPath/newsarch.html#040815">Read more</a>. - </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>