0374d744112f73043c95d7b58b28afb60a4db855 mspeir Tue May 27 16:27:04 2014 -0700 adding announcement for new Roadmap hub, refs #13023 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 0e2122f..8260ca4 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -16,30 +16,68 @@ <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> <p> + <font face="courier" size="3"><b> 27 May 2014 - + New Roadmap Epigenomics Integrative Analysis Hub now available</b> + </font> + </p> + + <p> + We are pleased to announce the addition of the + <a href="../cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt" + >Roadmap Epigenomics Integrative Analysis Hub</a> to our list of publicly available track hubs. + This new hub, produced by <a href="http://vizhub.wustl.edu/" target="blank">VizHub</a> at Washington + University in St. Louis (WUSTL), contains hundreds of tracks that cover the wide range of epigenomic data + available from the <a href="http://www.roadmapepigenomics.org/" target='blank'>Roadmap Epigenomics + Project</a>. This hub contains data from over 40 different assays carried out on over 250 different + cell and sample types. These assays include RNA-seq, MeDIP-seq, MRE-seq, methylC-seq, DNase + hypersensitivity, chromHMM segmentation, ChIP-seq, and more than 30 histone modifications. The data + contained in this hub is complementary to the ENCODE data available at UCSC and in the ENCODE + Integrative Analysis public hub. + </p> + + <p> + You can view more data produced by the Roadmap Epigenomics Project in their other publicly available + track hub, the Roadmap Epigenomics Data Complete Collection. You can use these two hubs together + to access all the available Roadmap Epigenomics Project data using the UCSC Genome Browser. To access + and view these hubs, navigate to the <a href="../cgi-bin/hgHubConnect">Track Hub gateway page</a> + and select both the Roadmap Epigenomics Integrative Analysis Hub and Roadmap Epigenomics Data + Complete Collection Hub from the Public Hubs list. + </p> + + <p> + Any queries about the data should be directed to + <A HREF="mailto:twang@genetics. +wustl. +edu">Ting Wang</A> from VizHub. +<!-- above address is twang at genetics.wustl.edu --> + </p> + + <hr> + <p> <font face="courier" size="3"><b> 15 May 2014 - New UCSC Gene Track Released for GRCh38/hg38</b> </font> <p> We're happy to announce the release of a new UCSC Genes track for the GRCh38/hg38 human Genome Browser. The new release has 104,178 transcripts, compared with 82,960 in the previous version on hg19. The total number of canonical genes has increased from 31,848 to 48,424. Comparing the new gene set with the previous version: </p> <ul> <li>69,691 transcripts did not change between versions.</li> <li>619 transcripts were not carried forward to the new version.</li> <li>8,879 transcripts are "compatible" with those in the previous set, @@ -118,87 +156,61 @@ bases. </p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/taeGut2/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebra_finch">Downloads</a> page. Please observe the <a href="goldenPath/credits.html#zebra_finch_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="goldenPath/credits.html#zebra_finch_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> 08 May 2014 - - New Elephant Shark (calMil1) Assembly Now Available in the Genome Browser</b> - </font> - <p> - A Genome Browser is now available for the elephant shark (<em>Callorhinchus milii</em>) - assembly released December 2013 by the <a href="http://www.imcb.a-star.edu.sg/" - target="_blank">Singapore Institute of Molecular and Cell Biology</a> - (IMCB version Callorhinchus_milii-6.1.3, UCSC version calMil1). For more - information and statistics about this assembly, see the NCBI assembly record - for <a href="http://www.ncbi.nlm.nih.gov/assembly/85971" target="_blank"> - Callorhinchus_milii-6.1.3</a>. There are 21,204 scaffolds with a total size of 974,498,586 - bases. - </p> - <p> - Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/calMil1/">FTP server</a> or the - <a href="http://hgdownload.soe.ucsc.edu/downloads.html#elephant_shark">Downloads</a> page. - Please observe the <a href="goldenPath/credits.html#elephant_shark_use">conditions for use</a> when - accessing and using these data sets. The annotation tracks for this browser were - generated by UCSC and collaborators woldwide. See the <a - href="goldenPath/credits.html#elephant_shark_credits">Credits</a> page for a detailed list of the - organizations and individuals who contributed to this release. - </p> - - <hr> <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b></font>: + <font face="courier" size="3"><b> 22 May 2014 - + New Roadmap Epigenomics Integrative Analysis Hub now available</b>:</font> + We are pleased to announce the addition of the + <a href="../cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt" + >Roadmap Epigenomics Integrative Analysis Hub</a> to our list of publicly available track hubs. + <a href="goldenPath/newsarch.html#052714">Read more</a> + <font face="courier" size="3"><b> 15 May 2014 - We're happy to announce the release of a new UCSC Genes track for the GRCh38/hg38 human Genome Browser. <a href="goldenPath/newsarch.html#051514">Read more</a> <font face="courier" size="3"><b> 09 May 2014 - Three New Assemblies Now Available in the Genome Browser</b>:</font> A Genome Browser is now available for the Chinese hamster (<em>Cricetulus griseus</em>), hedgehog (<em>Erinaceus europaeus</em>), and zebra finch (<em>Taeniopygia guttata</em>). <a href="goldenPath/newsarch.html#050914">Read more</a> + --> + <!-- start archives --> + + <p> <font face="courier" size="3"><b> 08 May 2014 - New Elephant Shark (calMil1) Assembly Now Available in the Genome Browser</b>:</font> A Genome Browser is now available for the elephant shark (<em>Callorhinchus milii</em>) assembly released December 2013 by the Singapore Institute of Molecular and Cell Biology. <a href="goldenPath/newsarch.html#050814">Read more</a> - --> - + </p> - <!-- start archives --> - <font face="courier" size="3"><b> 05 May 2014 - + <p> + <font face="courier" size="3"><b> 06 May 2014 - Introducing the new stacked overlay for multi-wiggle tracks</b>:</font> We are excited to announce the release of the new "stacked" overlay method for multi-wiggle tracks. <a href="goldenPath/newsarch.html#050614">Read more</a> </p> - <p> - <font face="courier" size="3"><b> 29 Apr 2014 - - 100-species Conservation track re-release</b>:</font> - We released the initial version of the 100-species Conservation track - for the hg19 human assembly in November 2013. Over the past few months, - we found a couple of inconsistencies and decided, for the integrity of - the data, that we should rerun the computation pipeline and re-release - the data. <a href="goldenPath/newsarch.html#042914">Read more</a> - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>