13a3177e706f25defbc80a58e96ca0057d58b082 mspeir Mon Mar 21 14:38:33 2016 -0700 Adding announcement for ce11 and aptMan1. Staging announcement for Lens Patent track. refs #15209 #16029 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 733c8b4..77dd133 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,181 +1,216 @@ <!-- 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 --> + <!-- start news --> +<!-- Staged for later release + <hr> + <font color="#006666" size="4"><b>16 Mar 2016 + - Data from the Lens PatSeq Database Now Available</b></font> + <p> + We are pleased to announce the release of a set of tracks containing data from the + <a href="https://www.lens.org/" target="_blank">Lens</a> + PatSeq database in the UCSC Genome Browser. These tracks contain data from the + <a href="https://www.lens.org/lens/bio" target="_blank">PatSeq</a> + database mapped to the genome and then colored based on where the sequence appears in + the patent document. Details pages contain the patent titles with links to the patents in the + Lens database. The data from PatSeq is divided into two tracks, one includes those sequences + that were submitted in bulk patents containing 100 or more sequences and the other containing + all other sequences. These tracks are currently present on the human (hg19), mouse (mm10), + and Ebola virus (eboVir3) genomes. + </p> + + <p> + Thanks to our collaborators at the Lens, Osmat Jefferson and Deniz Koellhofer, for providing the + data and feedback on the visualization. Thank you to Max Haeussler and Matthew Speir, members of + the UCSC Genome Browser team, for their efforts in creating these tracks. + </p> +--> + <hr> + <font color="#006666" size="4"><b>21 Mar 2016 + - Genome Browsers for <i>C. elegans</i> and Brown Kiwi Now Available</b></font> + <p> + A Genome Browser is now available for the <em>Caenorhabditis elegans</em> + assembly released August 2014 by the C. elegans Sequencing Consortium, which is led by the + <a href="http://genome.wustl.edu/" + target="_blank">Genome Sequencing Center at Washington University, St. Louis</a> + and the <a href="http://www.sanger.ac.uk/" target="_blank">Wellcome Trust Sanger Institute</a>. + You can read more about their sequencing efforts + <a href=http://genome.wustl.edu/genomes/detail/caenorhabditis-elegans/ + target="_blank">here</a>. + For more information and statistics about this assembly, see the NCBI assembly record + for <a href="http://www.ncbi.nlm.nih.gov/assembly/554278" target="_blank">WBcel235</a>. Note + that the sequences in WBcel235 are identical to the sequence in WBcel245/ce11. This means + that WBcel245 only has different annotations, but is the exact same sequence as WBcel235. + There are 7 complete chromsomes with a total size of 100,286,401 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/ce11/">FTP server</a> or the + <a href="http://hgdownload.soe.ucsc.edu/downloads.html#c_elegans">Downloads</a> page. + Please observe the <a href="credits.html#ce_credits">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="credits.html#ce_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 brown kiwi (<em>Apteryx australis</em>) + assembly released June 2015 by the + <a href="http://www.eva.mpg.de/index.html" + target=_blank>Max-Plank Institute for Evolutionary Anthropology</a>. + For more information and statistics about this assembly, see + <a href="http://www.ncbi.nlm.nih.gov/assembly/GCF_001039765.1" + target="_blank">AptMant0</a> in the NCBI Assembly database. There are + 24,719 scaffolds with a total size of 1,523,986,457 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/aptMan1/">FTP server</a> or the + <a href="http://hgdownload.soe.ucsc.edu/downloads.html#brown_kiwi">Downloads</a> page. + Please observe the <a href="credits.html#brown_kiwi_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="credits.html#brown_kiwi_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>8 Mar 2016 - Combine Multiple Regions of the Genome Browser into a Single Visualization!</b></font> <p> Have you 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> +<!-- start archives --> +<!--staged for future release <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> + <font color="#006666" size="4"><b>16 Mar 2016 + - Data from the Lens PatSeq Database Now Available</b>: </font> + We are pleased to announce the release of a set of tracks containing data from the + <a href="https://www.lens.org/" target="_blank">Lens</a> + PatSeq database in the UCSC Genome Browser. + <a href="goldenPath/newsarch.html#031616">Read more</a>. - <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. + <font color="#006666" size="4"><b>21 Mar 2016 + - Genome Browsers for <i>C. elegans</i> and Brown Kiwi Now Available.</b></font> + <a href="goldenPath/newsarch.html#030816">Read more</a>. </p> -<hr> - -<!-- start archives --> -<!--staged for future release <p> <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> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>