21635cdb9d8d23fe98692522adf6916dfcb2c364 jcasper Thu Sep 10 16:44:05 2015 -0700 Removing release tags related to 100-way and pushing announcement, refs #14560 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 6479d23..7cbee33 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -27,120 +27,95 @@ <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 color="#006666" size="4"><b>10 September 2015 — + 100 Species Conservation Track now available on GRCh38/hg38 </b></font> + </p> + <p> + We are pleased to announce the release of a new Conservation track based on the human + (GRCh38/hg38) assembly. This track shows multiple alignments of 100 vertebrate species and + measurements of evolutionary conservation using two methods (phastCons and phyloP) from the + PHAST package for all species. The multiple alignments were generated using multiz and other + tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. + Conserved elements identified by phastCons are also displayed in this track. For more + details, visit the + <a href="../cgi-bin/hgTrackUi?db=hg38&g=cons100way">track description page</a>. + </p> + <p> + We would like to thank Hiram Clawson and Jonathan Casper for their efforts in creating this track. + </p> + + <hr> + <p> <font color="#006666" size="4"><b>12 August 2015 — New blog post: How to share your UCSC screenthoughts </b></font> </p> <p> Do you want to save your UCSC Browser screenthoughts, or share them with a colleague, or make a slide for a talk, or publish them in a paper? Saving the state of your screen can take two forms: static or dynamic. You can snap and save a picture of the screen, or you can share a link to an active Genome Browser. We talk about both approaches <A HREF = "http://genome.ucsc.edu/blog/how-to-share-your-ucsc-screenthoughts/" TARGET = _BLANK>here</A> and discuss some of the advantages and pitfalls of each. </p> <hr> - <p> - <font color="#006666" size="4"><b>29 June 2015 — - GENCODE Genes Now the Default Gene Set on the Human (GRCh38/hg38) Assembly</b></font> - <p> - In a move towards standardizing on a common gene set within the bioinformatics - community, UCSC has made the decision to adopt the GENCODE set of gene models - as our default gene set on the human genome assembly. Today we have released - the GENCODE v22 comprehensive gene set as our default gene set on human - genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set - generated by UCSC. To facilitate this transition, the new gene set employs - the same familiar UCSC Genes schema, using nearly all the same table names - and fields that have appeared in earlier versions of the UCSC set. - </p> - <p> - By default, the browser displays only the transcripts tagged as "basic" by the - GENCODE Consortium. These may be found in the track labeled "GENCODE Basic" in - the Genes and Gene Predictions track group. However, all the transcripts in the - GENCODE comprehensive set are present in the tables, and may be viewed by - adjusting the track configuration settings for the All GENCODE super-track. - The most recent version of the UCSC-generated genes can still be accessed in - the track "Old UCSC Genes". - </p> - <p> - The new release has 195,178 total transcripts, compared with 104,178 in the - previous version. The total number of canonical genes has increased from - 48,424 to 49,534. Comparing the new gene set with the previous version: - </p> - <ul> - <li>9,459 transcripts did not change.</li> - <li>22,088 transcripts were not carried forward to the new version.</li> - <li>43,681 transcripts are "compatible" with those in the previous set, - meaning that the two transcripts show consistent splicing. In most cases, - the old and new transcripts differ in the lengths of their UTRs.</li> - <li>28,950 transcripts overlap with those in the previous set, but do not - show consistent splicing (i.e., they contain overlapping introns with - differing splice sites)</li> - </ul> - <p> - More details about the new GENCODE Basic track can be found on the - <a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene"> - GENCODE Basic track description page</a>. - </p> - - <hr> <!-- start archives --> <!-- - <hr> <p> - <font color="#006666" size="4"><b>12 August 2015 — - New blog post: How to share your UCSC screenthoughts. </b></font> + <font color="#006666" size="4"><b>10 September 2015 — + 100 Species Conservation Track now available on GRCh38/hg38 </b>: + </font> + We are pleased to announce the release of a new Conservation track based on the human + (GRCh38/hg38) assembly. + <a href="goldenPath/newsarch.html#091015">Read more</a>. + </p> + <p> + <font color="#006666" size="4"><b>12 August 2015 — + New blog post: How to share your UCSC screenthoughts. </b>: + </font> We talk about saving static images and dynamic Browser sessions in a new <A HREF = "">blog</A> post, and discuss some of the advantages and pitfalls of each. <a href="goldenPath/newsarch.html#081215">Read more</a>. </p> +--> <p> <font color="#006666" size="4"><b>29 June 2015 — GENCODE Genes Now Default Gene Set on the Human (GRCh38/hg38) Assembly</b>: </font> In a move towards standardizing on a common gene set within the bioinformatics community, UCSC has made the decision to adopt the GENCODE set of gene models as our default gene set on the human genome assembly. <a href="goldenPath/newsarch.html#062915">Read more</a>. </p> ---> <p> <font color="#006666" size="4"><b>26 June 2015 — New Bonobo (panPan1) Assembly Now Available in the Genome Browser</b>: </font> We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, <em>Pan paniscus</em> (Max-Planck Institute panpan1, UCSC version panPan1). <a href="goldenPath/newsarch.html#062615">Read more</a>. </p> - <font color="#006666" size="4"><b>12 June 2015 — - Data Integrator</b>: </font> - Have you ever wished that the Table Browser could associate your custom track items - with some other track, while retaining the item names from both? We have released a - new tool that can do just that, and more: the Data Integrator. - <a href="goldenPath/newsarch.html#061215">Read more</a>. - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>