bedca4fbd26ed7c4acf6c68841325e761b80c5fc mspeir Tue Sep 30 14:32:06 2014 -0700 Adding announcemnts and release info for eboVir3 release diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 556b02b..69deccc 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,117 +1,136 @@ <!-- 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.</P> <!-- start news --> <hr> + <font face="courier" size="3"><b>30 September 2014 - + Genome Browser for the Ebola Virus Now Available</b> + </font> + <p> + We are excited to announce the release of a Genome Browser for the June 2014 assembly + of Ebola Virus (Sierra Leone 2014 (G3683/KM034562.1), UCSC version eboVir3)! The sequence, + <a href="http://www.ncbi.nlm.nih.gov/nuccore/KM034561" target="_blank">KM034562</a> was + deposited into GenBank by the Pardis Sabeti lab at the Broad Intstitue. We have worked + closely with the Sabeti lab and other Ebola experts throughout the world to incorporate + annotations that will be useful to those studying Ebola. Annotation tracks included in this + intitial release include genes from <a href="http://www.ncbi.nlm.nih.gov/" + target="_blank">NCBI</a>, B- and T-cell epitopes from the <a href="http://www.iedb.org/" + target="_blank">IEDB</a>, structural annotiation from <a href="http://www.uniprot.org/" + target="_blank">UniProt</a> and a wealth of SNP data from the + <a href="http://www.ncbi.nlm.nih.gov/pubmed/25214632" target="_blank">2014 publication</a> + from the Sabeti lab. This initial release also contains a 160-way alignment of + 158 Ebola virus sequences from various African outbreaks, and 2 Marburg virus sequences. + You can find links to the Ebola virus Genome Browser and more information on the Ebola virus + itself on our <a href="/ebolaPortal/">Ebola Portal</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/eboVir3/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#ebola">Downloads</a> + page. These data have + <a href="../goldenPath/credits.html#ebola_use">specific conditions for use</a>. + The Ebola virus (eboVir3) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + <a href="../goldenPath/credits.html#ebola_credits">Credits</a> page for a detailed + list of the organizations and individuals who contributed to this release. + </p> + + <hr> <font face="courier" size="3"><b>23 September 2014 - Ensembl Regulatory Build Now Available in the Genome Browser</b> </font> <p> We are pleased to announce that data from the <a href="http://www.ensembl.org/info/genome/funcgen/regulatory_build.html" target="_blank">Ensembl Regulatory Build</a> is now available in the UCSC Genome Browser as a public track hub for both hg19 and hg38. This track hub contains promoters and their flanking regions, enhancers, and many other regulatory features predicted across a number of cell lines using annotated segmentation states. Click <a href="/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&hubUrl=http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt">here</a> to view this hub on the hg19 assembly, or click <a href="/cgi-bin/hgTracks?db=hg38&position=chr9%3A133252000-133280861&hubUrl=http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt">here</a> to view it on the hg38 assembly. </p> <p> We would like to thank our collaborators Daniel Zerbino, Steve Wilder, and Nathan Johnson from Ensembl and Kate Rosenbloom and Matthew Speir from UCSC for their efforts in bringing these resources to the UCSC Genome Browser. </p> - <hr> - <font face="courier" size="3"><b>04 September 2014 - - New ENCODE portal launched at <a href="https://www.encodeproject.org">www.encodeproject.org</a></b> - </font> + + <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>: </font> + <p> - The website for up-to-date information about the ENCODE project is no - longer hosted at <a href="ENCODE/index.html">genome.ucsc.edu/ENCODE</a>. - Those UCSC ENCODE pages now archive information and tools from the ENCODE - production and pilot phases (2003 to 2012) including live links to visualize and download data. - Please navigate to the new ENCODE portal for recent data releases. Along with the ability to use - faceted searching to explore all ENCODE data, the ENCODE portal provides visualization - in the UCSC Genome Browser via a "Visualize Data" link on assay pages when - processed data files are available. + <font face="courier" size="3"><b>30 September 2014 - + Genome Browser for the Ebola Virus Now Available</b>: </font> + We are excited to announce the release of a Genome Browser for the June 2014 assembly + of Ebola Virus (Sierra Leone 2014 (G3683/KM034562.1), UCSC version eboVir3). </p> - <hr> - - <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>: </font> <p> <font face="courier" size="3"><b>23 September 2014 - Ensembl Regulatory Build Now Available in the Genome Browser</b>: </font> We are pleased to announce that data from the <a href="http://www.ensembl.org/info/genome/funcgen/regulatory_build.html" target="_blank">Ensembl Regulatory Build</a> is now available in the UCSC Genome Browser as a public track hub for both hg19 and hg38. <a href="goldenPath/newsarch.html#092314">Read more</a>. </p> + --> + + <!-- start archives --> <p> <font face="courier" size="3"><b>04 September 2014 - New ENCODE portal launched at <a href="https://www.encodeproject.org">www.encodeproject.org</a></b>: </font> The website for up-to-date information about the ENCODE project is no longer hosted at <a href="ENCODE/index.html">genome.ucsc.edu/ENCODE</a>. <a href="goldenPath/newsarch.html#090414">Read more</a>. </p> - --> - - <!-- start archives --> <p> <font face="courier" size="3"><b>03 September 2014 - Data from the FaceBase Consortium Now Available in the Genome Browser</b>: </font> We are pleased to announce that much of the data from the <a href="https://www.facebase.org/" target"_blank">FaceBase Consortium</a> is now available in the UCSC Genome Browser as a public track hub. <a href="goldenPath/newsarch.html#090314">Read more</a>. </p> - <p> - <font face="courier" size="3"><b>30 July 2014 - - New Rat (rn6) Assembly Now Available in the Genome Browser</b>:</font> - We are excited to announce the release of a Genome Browser for the July 2014 assembly - of rat, <em>Rattus norvegicus</em> (RGSC Rnor_6.0, UCSC version rn6). - <a href="goldenPath/newsarch.html#073014">Read more</a>. - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>