fe44b184b47b963c2b481e88d8bb90a7504844d4 jcasper Thu May 8 14:45:31 2014 -0700 Added calMil1 release to the news, credits, etc. diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 8fda413..e013dfc 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,126 +1,124 @@ <!-- 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" alt="Follow GenomeBrowser on Twitter" style="vertical-align:text-bottom; margin-left: 15px;"></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.</P> <!-- start news --> <hr> <p> + <font face="courier" size="3"><b> 8 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 (Callorhinchus milii) + 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> + <p> <font face="courier" size="3"><b> 5 May 2014 - Introducing the new stacked overlay for multi-wiggle tracks</b></font> <p> We are excited to announce the release of the new stacked overlay method for multi-wiggle tracks. This new stacked overlay method displays each graph stacked on top of each other. </p> <img style="border: 2px solid black; margin-left:auto; margin-right:auto; display: block;" src="images/stackedMultiWig_screenshot.png" alt="Stacked screenshot"> <p> Navigate to the track settings for <A HREF="cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegMarkH3k27ac" >H3K27Ac Mark</A> on the human hg19 assembly to view this new stacked overlay method on a multi-wiggle track. On the track settings page, from the "Overlay method" drop-down menu select "stacked". Make sure that the display mode is not set to hide, and click submit. </p> <p> Credit for the implementation and testing of this new feature goes to Brian Raney and Matthew Speir. </p> - - <hr> - <p> - <font face="courier" size="3"><b> 29 Apr 2014 - - 100-species Conservation track re-release</b></font> - <p> - 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. The fixes required minimal changes, and resulted in a more - precise data set. We published the new version of the hg19 100-species - Conservation track on 15 April 2014. - </p> - <p> - Here are more details about the two fixes that we made: - </p> - <p> - 1. We tracked down the cause of some unusual gaps in the alignments to a - bug in the multiz program used in our alignment pipeline. The Penn State - Bioinformatics Group provided us with a fixed version of multiz that we - used to rerun the pipeline. - </p> - <p> - 2. We inadvertently used the pre-release assembly for one of the species - in the 100-way alignment: the panda. We replaced this assembly with the - correct version and verified that the data sets for all other species - were correct before rerunning the pipeline. - </p> <hr> <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b></font>: - <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> + <font face="courier" size="3"><b> 8 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 (Callorhinchus milii) + assembly released December 2013 by the Singapore Institute of Molecular + and Cell Biology. + <a href="goldenPath/newsarch.html#050814">Read more</a> <font face="courier" size="3"><b> 5 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> --> <!-- start archives --> + + <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> + <p> <font face="courier" size="3"><b>18 April 2014 - New Motif Displays and New Genome Segmentations from ENCODE</b></font>: The Browser's default displayed <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">Transcription Factor ChIP-seq track</a> updated to the latest release, enhanced with the display of Factorbook motifs. And the Browser added <a class="euro" href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgSegmentation">Genome Segmentations from ENCODE</a> tracks, which segment the genome into twenty-five states that were then grouped and colored to highlight predicted functional elements. <a href="goldenPath/newsarch.html#041814">Read more</a>. </p> - <p> - <font face="courier" size="3"><b>15 April 2014 - - New Minke Whale (balAcu1) Assembly Now Available in the - Genome Browser</b></font>: - A Genome Browser is now available for the minke whale - (Balaenoptera acutorostrata scammoni) assembly released - October 2013 by the Korea Ocean Research & Development Institute. - <a href="goldenPath/newsarch.html#041514">Read more</a>. - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>