f000807b5b934fa0f543419ce52e7d282c5d2168 mspeir Tue Mar 8 15:15:17 2016 -0800 Adding announcement for Multi-region feature, refs #12242 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 3a2890d..daefda1 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,155 +1,181 @@ <!-- News Section ============================================- --> <TABLE style="background-color:#888888; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px"> <TR><TD> <TABLE style="background-color:#fffee8; width: 100%; border-width: 0px; border-spacing: 0px; padding: 0px"> <TR><TD> <TABLE style="background-color:#D9E4F8; background-image: url('images/hr.gif'); width: 100%; border: 0px"> <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 style="background-color:#fffee8; width: 100%; padding: 0px"> <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> + <font color="#006666" size="4"><b>8 Mar 2016 + - Combine Multiple Regions of the Genome Browser into a Single Visualization!</b></font> + <p> + Have ever wished you could remove all of the intronic or intergenic regions from the + Genome Browser display? Have you ever dreamed of being able to visualize multiple + far-flung regions of a genome? Well, now you can with the new "multi-region" option + in the Genome Browser! + </p> + + <p> + The multi-region modes provide four different ways to manipulate the display. + First, we have an "exon-only" mode that allows you to + remove all of the intergenic and intronic sequences from the display, leaving you with + only the exonic regions. Next, there is the "gene-only" mode allowing you to remove only + the intergenic regions from the display, leaving the genes with exons and introns intact. + Then there is the "custom regions" mode that allows you to use a remote BED file to + specify the regions you are interested in viewing alongside each other. Lastly, for human + assemblies hg17 and newer, there is the "alternative haplotype" mode that allows you to + view a haplotype sequence inserted into its position in the reference genome. + </p> + + <p> + To access these exciting, new multi-region modes, first select your organism and assembly + of interest and navigate to the Genome Browser visualization. Below the tracks display, + there is a button labeled "multi-region". Clicking this button will bring up + a configuration box for the different multi-region modes. For example: + </p> + + <p> + <img style="border: 1px solid black; display: block;" + src="images/MultiRegionButton.png"> + </p> + + <p> + From this pop-up, you will be able to switch between the different modes or exit these + multi-region modes if desired. For instance: + </p> + + <p> + <img style="border: 1px solid black; display: block;" + src="images/MultiRegionConfigurationWindow.png"> + </p> + + <p> + Additionally, you can enter the "Exon-only" mode by typing the keyboard shortcut + "e" then "v". You can exit any of the multi-region modes and return to the + default Genome Browser display by typing the keyboard shortcut "d" then "v". + </p> + + <p> + For more information about each individual multi-region mode, please see the + <a href="goldenPath/help/multiRegionHelp.html">User Guide</a>. + </p> + + <p> + Thank you to Galt Barber, Matthew Speir, and the entire UCSC Genome Browser quality assurance team for + all of their efforts in creating these exciting new display modes. + </p> + + <hr> <p> <font color="#006666" size="4"><b> 10 February 2016 - Two New Assemblies Now Available in the Genome Browser</b></font> <p> A Genome Browser is now available for the mouse lemur (<em>Microcebus murinus</em>) assembly released May 2015 by the <A HREF="http://www.broadinstitute.org/scientific-community/science/projects/mammals-models/29-mammals-project" TARGET="_blank">The Broad Institute</A> and the <A HREF="https://www.hgsc.bcm.edu/non-human-primates/mouse-lemur-genome-project" TARGET="_blank">Baylor College of Medicine Human Genome Sequencing Center</A>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="http://www.ncbi.nlm.nih.gov/assembly/329621" target="_blank"> Mmur_2.0</a>. There are 10,311 scaffolds with a total size of 2,438,804,424 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/micMur2/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse_lemur">Downloads</a> page. Please observe the <a href="./goldenPath/credits.html#mouse_lemur_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="./goldenPath/credits.html#mouse_lemur_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 platypus (<em>Ornithorhynchus anatinus</em>) assembly released February 2007 by the <A HREF="http://genome.wustl.edu/genomes/detail/ornithorhynchus-anatinus/" TARGET=_blank>Genome Sequencing Center at Washington University, St. Louis</A>. For more information about this assembly, see <A HREF="http://www.ncbi.nlm.nih.gov/assembly/237598/" TARGET="_blank"> Ornithorhynchus_anatinus-5.0.1</A> in the NCBI Assembly database. There are 201,525 scaffolds with a total size of 1,996,826,513 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/ornAna2/">FTP server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#platypus">Downloads</a> page. Please observe the <a href="./goldenPath/credits.html#platypus_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="./goldenPath/credits.html#platypus_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> - <hr> - <font color="#006666" size="4"><b>20 Jan 2016 - - dbSNP 142 Available for mm10</b></font> - <p> - Data from dbSNP build 142 is now available for the most recent mouse - assembly (mm10/GRCm38). As was the case for previous annotations - based on dbSNP data, there are three tracks in this release. - One is a track containing all mappings of reference SNPs to the - mouse assembly, labeled "All SNPs (142)". The other two tracks - are subsets of this track and show different 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 - <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. The other - tracks can be made visible using the track controls. - These three SNPs (142) tracks can be found on the Mouse Dec. - 2011 (mm10/GRCm38) browser in the "Variation and Repeats" group. - </p> - Thank you to the <a href="http://www.ncbi.nlm.nih.gov/SNP/"> - dbSNP</a> group at NCBI for making these data publicly available. - The tracks were produced at UCSC by Brian Raney, Angie Hinrichs - and Matthew Speir. - </p> -<hr> <!-- start archives --> <!--staged for future release <p> - <font color="#006666" size="4"><b> 10 February 2016 - - Two New Assemblies Now Available in the Genome Browser</b></font> + <font color="#006666" size="4"><b>8 Mar 2016 + - Combine Multiple Regions of the Genome Browser into a Single Visualization!</b></font> + <a href="goldenPath/newsarch.html#030816">Read more</a>. + </p> + <p> + <font color="#006666" size="4"><b> 10 February 2016 - + Two New Assemblies Now Available in the Genome Browser</b>: </font> Genome Browsers are now available for the mouse lemur (<em>Microcebus murinus</em>) and platypus (<i>Ornithorhynchus anatinus</i>) assemblies. <a href="goldenPath/newsarch.html#021016">Read more</a>. </p> +--> <font color="#006666" size="4"><b>20 Jan 2016 — dbSNP 142 Available for mm10</b></font> <a href="goldenPath/newsarch.html#012016">Read more</a>. </p> ---> <p> <font color="#006666" size="4"><b>08 January 2016 — dbSNP 144 Available for hg19 and hg38 </font></b> <a href="goldenPath/newsarch.html#010816">Read more</a>. </p> - <p> - <font color="#006666" size="4"><b> 21 December 2015 - - Two New Assemblies Now Available in the Genome Browser</b></font> - <p> - Genome Browsers are now available for the frog (<em>Xenopus tropicalis</em>) - and cat (<i>Felis catus</i>) assemblies. - <a href="goldenPath/newsarch.html#122115">Read more</a>. - </p> - </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>