f1b12be756db6fcc33cec8bd5a5a41b2c526ac4c steve Fri May 9 12:38:35 2014 -0700 Releasing criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190) diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index e013dfc..1cacbc3 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,124 +1,201 @@ <!-- 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 - + <font face="courier" size="3"><b> 09 May 2014 - + Three New Assemblies Now Available in the Genome Browser</b> + </font> + <p> + A Genome Browser is now available for the Chinese hamster (<em>Cricetulus griseus</em>) + assembly released July 2013 by the <a href="http://www.genomics.cn/en/index" + target="_blank">Beijing Genomics Institution-Shenzhen</a> + (BGI version C_griseus_v1.0, UCSC version criGri1). For more + information and statistics about this assembly, see the NCBI assembly record + for <a href="http://www.ncbi.nlm.nih.gov/assembly/40911" target="_blank"> + C_griseus_v1.0</a>. There are 52,711 scaffolds with a total size of 2,360,146,428 + 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/criGri1/">FTP server</a> or the + <a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_hamster">Downloads</a> page. + Please observe the <a href="goldenPath/credits.html#chinese_hamster_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#chinese_hamster_credits">Credits</a> page for a detailed list of the + organizations and individuals who contributed to this release. + </p> + --- + <p> + A Genome Browser is now available for the hedgehog (<em>Erinaceus europaeus</em>) + assembly released May 2012 by the <a href="http://www.broadinstitute.org/" + target="_blank">Broad Institute</a> + (Broad version EriEur2.0, UCSC version eriEur2). For more + information and statistics about this assembly, see the NCBI assembly record + for <a href="http://www.ncbi.nlm.nih.gov/assembly/426148" target="_blank"> + EriEur2.0</a>. There are 5,802 scaffolds with a total size of 2,715,720,925 + 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/eriEur2/">FTP server</a> or the + <a href="http://hgdownload.soe.ucsc.edu/downloads.html#hedgehog">Downloads</a> page. + Please observe the <a href="goldenPath/credits.html#hedgehog_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#hedgehog_credits">Credits</a> page for a detailed list of the + organizations and individuals who contributed to this release. + </p> + --- + <p> + A Genome Browser is now available for the zebra finch (<em>Taeniopygia guttata</em>) + assembly released February 2013 by <a href="http://genome.wustl.edu/genomes/detail/taeniopygia-guttata/" + target="_blank">The Genome Institute at Washington University</a> + (WUSTL version Taeniopygia_guttata-3.2.4, UCSC version taeGut2). For more + information and statistics about this assembly, see the NCBI assembly record + for <a href="http://www.ncbi.nlm.nih.gov/assembly/524908" target="_blank"> + Taeniopygia_guttata-3.2.4</a>. There are 37,096 scaffolds with a total size of 1,232,135,591 + 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 (Callorhinchus milii) + 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> <p> - <font face="courier" size="3"><b> 5 May 2014 - + <font face="courier" size="3"><b> 05 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> <!-- staged for archive use. NOTE: condense header line from .... </b></font><p> to </b></font>: - <font face="courier" size="3"><b> 8 May 2014 - + <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> + + <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 (Callorhinchus milii) + 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> - <font face="courier" size="3"><b> 5 May 2014 - + <font face="courier" size="3"><b> 05 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> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>