b11d3ec41119d59fbc0c4dbeb5090d7b8926bb4a donnak Fri Jan 27 16:06:25 2012 -0800 Archived some items. Changed some links to not open new window. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 4516034..8fd76e4 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -23,138 +23,62 @@ 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 --> <!-- Wallaby Assembly release --> <FONT FACE="courier" SIZE="3"><B>23 January 2012 - Wallaby Browser Available</B></FONT> <P> We have released a Genome Browser for the September 2009 genome assembly of the Tammar Wallaby, <em>Macropus eugenii</em> (TWGS version Meug_1.1, UCSC version macEug2). This assembly, which has been sequenced to 2X coverage, was produced by the Tammar Wallaby Genome Sequencing Consortium, a collaboration between the Baylor College of Medicine - <a href="http://www.hgsc.bcm.tmc.edu/project-species-m-Wallaby.hgsc" target="_blank"> - Human Genome Sequencing Center</a> and the - <a href="http://www.agrf.org.au/default.aspx" target="_blank">Australian Genome Research Facility</a>. + <a href="http://www.hgsc.bcm.tmc.edu/project-species-m-Wallaby.hgsc" + target="_blank"> Human Genome Sequencing Center</a> and the + <a href="http://www.agrf.org.au/default.aspx" + target="_blank">Australian Genome Research Facility</a>. <P> Bulk downloads of the sequence and annotation data are available via the Genome Browser - <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/" target="_blank">FTP server</A> + <A HREF="ftp://hgdownload.cse.ucsc.edu/goldenPath/macEug2/">FTP server</A> or the - <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#wallaby" target="_blank">Downloads</A> + <A HREF="http://hgdownload.cse.ucsc.edu/downloads.html#wallaby">Downloads</A> page. These data have - <A HREF="goldenPath/credits.html#wallaby_use" target="_blank">specific + <A HREF="goldenPath/credits.html#wallaby_use">specific conditions for use</A>. <P> We'd like to thank the Tammar Wallaby Genome Sequencing Consortium for providing this assembly. The wallaby Genome Browser and annotation tracks were produced by Chin Li and Luvina Guruvadoo. See the - <A HREF="goldenPath/credits.html#wallaby_credits" target="_blank">Credits</A> + <A HREF="goldenPath/credits.html#wallaby_credits">Credits</A> page for a detailed list of the organizations and individuals who contributed to this release. <P> + <HR> + + <!-- start archives --> <FONT FACE="courier" SIZE="3"><B>3 January 2012 - Roadmap Epigenomics Now Available through Data Hub at Washington - University</B></FONT> - <P> + University: </B></FONT> We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our - Data Hub function. The Roadmap Epigenomics Project is part - of The NIH Common Fund's <a href="https://commonfund.nih.gov/epigenomics/" - target="_blank">Epigenomics Program</a>. - It was launched with the goal of producing a public resource - of human epigenomic data to catalyze basic biology - and disease-oriented research. The Consortium leverages - experimental pipelines built around next-generation sequencing - technologies to map DNA methylation, histone modifications, - chromatin accessibility and small RNA transcripts in stem - cells and primary ex vivo tissues selected to represent the - normal counterparts of tissues and organ systems frequently - involved in human disease. The Consortium expects to deliver - a collection of normal epigenomes that will provide a framework - or reference for comparison and integration within a broad - array of future studies. - <P> - All data were produced and processed by the - <a href="http://www.roadmapepigenomics.org/" target="_blank"> - Roadmap Epigenomics Mapping Consortium</a>, and will be periodically - updated. Genome Browser tracks were constructed and hosted by - <a href="http://vizhub.wustl.edu/" - target="_blank">VizHub</a> at Washington University in St. Louis. - Tracks are available at UCSC Genome Browser via the Data Hub - function, or follow this - <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl= - http://vizhub.wustl.edu/VizHub/RoadmapRelease4.txt" target="_blank">link</a>. - The Roadmap Epigenomics Mapping Consortium is responsible for - the quality of the data. + Data Hub function. + <A HREF="goldenPath/newsarch.html#030112">Read more</A>. <P> <FONT FACE="courier" SIZE="3"><B>19 December 2011 - Variant - Call Format (VCF) Now Supported in Genome Browser</B></FONT> - <P> + Call Format (VCF) Now Supported in Genome Browser: </B></FONT> We are pleased to announce that the UCSC Genome Browser - now supports Variant Call Format (VCF). VCF is a flexible - and extendable line-oriented text format developed by the - 1000 Genomes Project for releases of single nucleotide variants, - indels, copy number variants and structural variants discovered - by the project. Similar to bigBed, bigWig and BAM, the Browser - transfers only the portions of VCF files necessary to display - viewed regions, making VCF a fast and attractive option for - large data sets. VCF files will need to be compressed and - indexed using the tabix package available from - <a href="http://samtools.sourceforge.net/" - target="_blank">SAMtools</a>. This new format is available - for use in custom tracks and data hubs. For more information - about VCF and tabix, please see our <a href="goldenPath/help/vcf.html" - target="_blank">VCF Track Format help page</a>.</P> - <P> - <HR> - - <!-- start archives --> - <!-- bosTau6 Assembly Release --> - <FONT FACE="courier" SIZE="3"><B>7 November 2011 - UMD Cow - Assembly Now Available in Genome Browser:</B></FONT> - 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. - <A HREF="goldenPath/newsarch.html#071111">Read more</A>. - </P> - - - <!-- 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>. + now supports Variant Call Format (VCF). + <A HREF="goldenPath/newsarch.html#191211">Read more</A>. </P> - - <!-- New javascript features --> - <P> - <FONT FACE="courier" SIZE="3"><B>8 September 2011 - -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. - <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. - <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>