96d17c7705425cd776fcdba292c5f62a687daadc jcasper Thu Feb 12 10:54:13 2015 -0800 Adding notice of the retirement of snp135/137 to 142 release, refs #14189 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index a6ebe0f..ab1bac0 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,205 +1,213 @@ <!-- 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>11 February 2015 - dbSNP 142 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 142 data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. The new tracks contain a substantial amount of additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser. </p> <p> There are four SNP tracks available as part of this release. One is a track containing all mappings of reference SNPs to the human assembly, labeled "All SNPs (142)". The other three tracks are subsets of this track and show interesting and easily defined subsets of dbSNP: </p> <ul> <li>Common SNPs (142): uniquely mapped variants that appear in at least 1% of the population or are 100% non-reference <li>Flagged SNPs (142): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated" <li>Mult. SNPs (142): variants that have been mapped to more than one genomic location </ul> <p> By default, only the Common SNPs (142) are visible; other tracks must be made visible using the track controls. You will find the other SNPs (142) 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 Jonathan Casper. We'd like to thank the dbSNP group at NCBI for providing access to these data. </p> + <p> + As part of this release, we are also retiring the older dbSNP Build 135 and 137 + data from display on the GRCh37/hg19 human assembly. Those tracks will still be + available for viewing on our + <a href="http://genome-preview.soe.ucsc.edu" target="_blank">preview server</a>, + and the associated masked FASTA files will continue to be available on our + <a href="http://hgdownload.soe.ucsc.edu" target="_blank">download server</a>. + </p> <hr> <p> <font face="courier" size="3"><b>2 Febuary 2015 - Host a Genome Browser Workshop</b></font> <p> New timeslots are now available to host a Genome Browser workshop at your institution. Thanks to the funding support of NHGRI, we offer hands-on Genome Browser training onsite at your institution, tailored to your audience's level of expertise. </p> <p> For more information or to submit a request to host a workshop, please visit <a href="http://bit.ly/ucscTraining" target="_blank">our signup</a>. </p> <hr> <p> <font face="courier" size="3"><b>23 January 2015 - Genome Browser YouTube Channel</b></font> <p>We are pleased to announce the release of the UCSC Genome Browser <a href="http://bit.ly/genomebrowserYoutube" target=_blank">YouTube channel</a>. The channel contains short videos showing how to use the Genome Browser and associated tools to solve selected problems. The videos were produced by Robert Kuhn and Pauline Fujita, with assistance from Luvina Guruvadoo, Jonathan Casper, Matt Speir and the rest of the Browser staff. </p> <p>See also the other materials on our <a href="http://bit.ly/genomebrowserTraining">training page</a>. </p> <p>If you have any comments or questions - including requests for future video topics - please send them to our training group at: </p> <p> ucscgbtraining@soe. ucsc. edu <!-- above address is ucscgbtraining at soe ucsc edu --> </p> <hr> <p> <font face="courier" size="3"><b>15 January 2015 - Proteomics Data Now Available in Genome Browser</b></font> <p> We are pleased to announce the release of proteomics data for the human hg19 assembly. Data from the National Cancer Institute's (NCI) <a href="http://proteomics.cancer.gov/programs/cptacnetwork" target="_blank"> Clinical Proteomic Tumor Analysis Consortium (CPTAC)</a> is now available in the UCSC Genome Browser as a public track hub. This track hub contains peptides that were identified by CPTAC in their deep mass spectrometry based characterization of the proteome content of breast, colorectal and ovarian cancer biospecimens that were initially sequenced by <a href="http://cancergenome.nih.gov/" target="_blank"> The Cancer Genome Atlas</a>. This effort extends the accessibility of CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community. <p> To access and view this hub, navigate to the <a href="http://genome.ucsc.edu/cgi-bin/hgHubConnect" target="_blank"> Track Hub gateway page</a> and select "CPTAC Hub v1" from the Public Hubs list. Please direct any queries to the Fenyo Lab at <a href="mailto:info@fenyolab.org">info@fenyolab.org</a>. <p> In addition, we have also released a <a href="http://www.peptideatlas.org/" target="_blank"> PeptideAtlas</a> track which displays peptide identifications from the <a href="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=433" target="_blank"> PeptideAtlas August 2014 (Build 433) Human build</a>. This build, based on 971 samples containing more than 420 million spectra, identified over a million distinct peptides covering more than 15,000 canonical proteins. To read more about this track, please see the <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=peptideAtlas" target="_blank"> track description page</a>. Many thanks to Eric Deutsch, Zhi Sun, and the PeptideAtlas team at the Institute for Systems Biology, Seattle for providing this data. </p> <hr> <!-- start archives --> <!-- <p> <font face="courier" size="3"><b>11 February 2015 - dbSNP 142 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 142 data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. The new tracks contain a substantial amount of additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser. <a href="goldenPath/newsarch.html#021115">Read more</a>. </p> <p> <font face="courier" size="3"><b>2 Febuary 2015 - Host a Genome Browser Workshop</b>: </font> Host a Genome Browser workshop at your institution! Thanks to the funding support of NHGRI, we offer hands-on Genome Browser training onsite at your institution, tailored to your audience's level of expertise. <a href="goldenPath/newsarch.html#020215">Read more</a>. </p> <p> <font face="courier" size="3"><b>23 January 2015 - Genome Browser YouTube Channel</b>: </font> We are pleased to announce the release of the UCSC Genome Browser <a href="http://bit.ly/genomebrowserYoutube" target=_blank">YouTube channel</a>. The channel contains short videos showing how to use the Genome Browser and associated tools to solve selected problems. <a href="goldenPath/newsarch.html#012315">Read more</a>. </p> --> <p> <font face="courier" size="3"><b>15 January 2015 - Proteomics Data Now Available in Genome Browser</b>: </font> We are pleased to announce the release of proteomics data for the human hg19 assembly. Data from the National Cancer Institute's (NCI) <a href="http://proteomics.cancer.gov/programs/cptacnetwork" target="_blank"> Clinical Proteomic Tumor Analysis Consortium (CPTAC)</a> is now available in the UCSC Genome Browser as a public track hub. <a href="goldenPath/newsarch.html#011515">Read more</a>. </p> <p> <font face="courier" size="3"><b>19 December 2014 - New Cow (bosTau8) Assembly Now Available in the Genome Browser</b>: </font> We are pleased to announce the release of a Genome Browser for the June 2014 assembly of cow, <i>Bos taurus</i> (Bos_taurus_UMD 3.1.1, UCSC version bosTau8). <a href="goldenPath/newsarch.html#121914">Read more</a>. </p> <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> 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>. </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>