4713b6785bf375410b1e6a1d769a05c727113f8e mspeir Fri Dec 12 10:32:15 2014 -0800 Adding announcement for dm6 release, refd #40449 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8c8b6ed..2af5764 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -26,151 +26,111 @@ <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>12 December 2014 - + New <i>D. melanogaster</i> (dm6) Assembly Now Available in the Genome Browser</b></font> + <p> + We are pleased to announce the release of a Genome Browser for the August 2014 assembly + of <i>Drosophila melanogaster</i> (BDGP Release 6, UCSC version dm6). This updated <i>D. + melanogaster</i> assembly was provided by the <a href="http://www.fruitfly.org/" + target="_blank">Berkeley Drosophila Genome Project</a> (BDGP). Please see + <a href="http://flybase.org/static_pages/feature/previous/articles/2014_07/FB2014_04.html" + target="_blank">this announcement</a> on the FlyBase website for more details about this + updated <i>D. melanogaster</i> assembly. + <p> + Bulk downloads of the sequence and annotation data are available via the Genome + Browser + <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6/">FTP server</a> + or the + <a href="http://hgdownload.cse.ucsc.edu/downloads.html#fruitfly">Downloads</a> + page. These data have + <a href="/goldenPath/credits.html#dm_credits">specific conditions for use</a>. + The <i>D. melanogaster</i> (dm6) browser annotation tracks were generated by UCSC and + collaborators worldwide. See the + <a href="/goldenPath/credits.html#dm_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>29 October 2014 - Genome Browser in a Box (GBiB)</b></font> <p> Sometimes you just want to keep your genomics data to yourself. Have you ever hesitated when uploading your data set into the UCSC Genome Browser? If so, you'll be happy to know that we have created a stand-alone personal version: Genome Browser in a Box (GBiB). If you have sensitive genomics data that you would like to view securely on your own laptop in the context of the UCSC Genome Browser, GBiB is for you. <p> GBiB is an easy-to-install personal copy of the Genome Browser that comes preloaded with the most popular annotation tracks for human. It is highly configurable — you can access or download other annotation tracks of interest, or view any of the other 90+ organisms featured in the public Genome Browser. GBiB runs inside of Oracle's free VirtualBox virtual machine. It has the same core functionality as the UCSC Genome Browser, but keeps your data private and local to your own computer. <p> GBiB is free for non-commercial use by non-profit organizations, academic institutions, and for personal use. Commercial use requires purchase of a license with setup fee and annual payment. Download or purchase GBiB in our secure online <a href="https://genome-store.ucsc.edu/">store</a>. <p> You can read more about GBiB on our <a href="http://genome.ucsc.edu/blog/genome-browser-in-a-box-gbib-origins/"> blog</a>, or in the <a href="/goldenPath/help/gbib.html"> help doc</a>. - <p> - <hr> - <font face="courier" size="3"><b>20 October 2014 - - dbSNP 141 Available for hg19 and hg38</b></font> - <p> - We are pleased to announce the release of four tracks derived from NCBI - <a href="http://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a> Build 141 - data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. - The new tracks contain additional annotation data not included in previous dbSNP - tracks, with corresponding coloring and filtering options in the Genome Browser. - </p> - <p> - There are three SNP tracks available for the GRCh37/hg19 assembly. One is a track - containing all mappings of reference SNPs to the human assembly, labeled - "All SNPs (141)". The other two tracks are subsets of this track and show - interesting and easily defined subsets of dbSNP: - </p> - <ul> - <li>Common SNPs (141): uniquely mapped variants that appear in at least 1% - of the population or are 100% non-reference - <li>Flagged SNPs (141): uniquely mapped variants, excluding Common SNPs, - that have been flagged by dbSNP as "clinically associated" - </ul> - <p> - Unlike previous dbSNP releases for GRCh37/hg19, Build 141 does not include - mappings to alternate haplotype sequences. In addition, variants that map to - multiple genomic locations (e.g. to different chromosomes, or more than one - position on the same chromosome) have been removed. - </p> - <p> - This release also marks the first set of dbSNP data available for the newest - human assembly, GRCh38/hg38. In addition to the three tracks described for - hg19, there is one additional track available for hg38: - <ul> - <li>Mult. SNPs (141): variants that have been mapped to more than one genomic location - </ul> - <p> - By default, only the Common SNPs (141) are visible; other tracks must be - made visible using the track controls. You will find the other SNPs (141) tracks on - both of GRCh37/hg19 and GRCh38/hg38 browsers in the "Variation" group. - </p> - <p> - The tracks were produced at UCSC by Angie Hinrichs and Matthew Speir. We'd like - to thank the dbSNP group at NCBI for providing access to these data. - </p> <hr> - <font face="courier" size="3"><b>07 October 2014 - - Introducing the UCSC Genome Browser Blog</b> - </font> + <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>: </font> + <p> - We're excited to introduce a new - <a href="http://genome.ucsc.edu/blog" target="_blank">blog</a> that will feature posts by - Genome Browser staff and guests. On the blog we'll be publishing in-depth information about - UCSC Genome Browser features, tools, projects and related topics that we hope people will - find both useful and interesting. We just published our inaugural post written by Jim Kent, - the UCSC Genome Browser Architect and PI, on the - <a href="http://genome.ucsc.edu/blog/2014-ebola-epidemic/" - target="_blank">2014 Ebola Epidemic</a>. + <font face="courier" size="3"><b>12 December 2014 - + New <i>D. melanogaster</i> (dm6) Assembly Now Available in the Genome Browser</b>: </font> + We are pleased to announce the release of a Genome Browser for the August 2014 assembly + of <i>Drosophila melanogaster</i> (BDGP Release 6, UCSC version dm6). + <a href="goldenPath/newsarch.html#121214">Read more</a>. </p> + <p> - If you have a suggestion for a blog post topic, please let us know via our - <a href="/cgi-bin/hgUserSuggestion">suggestion box</a>. - </p> + <font face="courier" size="3"><b>29 October 2014 - + Genome Browser in a Box (GBiB)</b>: </font> + GBiB is an easy-to-install personal copy of the Genome Browser that comes + preloaded with the most popular annotation tracks for human. + <a href="goldenPath/newsarch.html#102914">Read more</a>. + </p> --> - <hr> - <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b>: </font> + <!-- start archives --> <p> <font face="courier" size="3"><b>20 October 2014 - dbSNP 141 Available for hg19 and hg38</b>: </font> We are pleased to announce the release of four tracks derived from NCBI <a href="http://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a> Build 141 data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. <a href="goldenPath/newsarch.html#102014">Read more</a>. </p> <p> <font face="courier" size="3"><b>07 October 2014 - Introducing the UCSC Genome Browser Blog</b>: </font> We're excited to introduce a new <a href="http://genome.ucsc.edu/blog" target="_blank">blog</a> that will feature posts by Genome Browser staff and guests. <a href="goldenPath/newsarch.html#100714">Read more</a>. - </p> --> - - <!-- start archives --> - <p> - <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). - <a href="goldenPath/newsarch.html#093014">Read more</a>. - </p> - - <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> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>