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 @@ -24,30 +24,106 @@ <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 @@ -85,97 +161,56 @@ "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>