74149ccee6df5eec6902c16529577a6930fd6a3a Merge parents bd47b2b 254c5f3 ann Sun Apr 3 17:58:12 2016 -0700 trying to fix merge conflict diff --cc src/hg/htdocs/indexNews.bak.html index 0000000,0000000..f59f02c new file mode 100755 --- /dev/null +++ src/hg/htdocs/indexNews.bak.html @@@ -1,0 -1,0 +1,221 @@@ ++<!-- 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>4 Apr 2016 ++ - New video shows how to obtain sequence or coordinates for exons. </b></font> ++ <p> ++ We have released a new <A HREF = ++ "http://genome.ucsc.edu/training/vids/index.html#vid08" TARGET = ++ _BLANK>video</A> to our YouTube channel. This newest installment in our effort ++ to share the capabilities of the Genome Browser shows how to ++ use the Table Browser to obtain either the sequences or the coordinates for ++ exons in the genes from a chosen region of the genome. ++ </p> ++ ++ <p> ++ We also want to take this opportuinty to remind you that we offer ++ on-site <A HREF = "http://genome.ucsc.edu/training/index.html" TARGET = ++ _BLANK>workshops</A> to help you and your colleagues make the most out ++ of the Genome Browser. ++ </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 February 2013 by the C. elegans Sequencing Consortium ++ (C. elegans Sequencing Consortium version WBcel235, UCSC version ce11). ++ 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>. ++ There are 7 complete chromosomes 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="goldenPath/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="goldenPath/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> (MPI-EVA version AptMan0, ++ UCSC version aptMan1). ++ 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="goldenPath/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="goldenPath/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> ++ ++<!-- start archives --> ++<!--staged for future release ++ <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>. ++ ++ <font color="#006666" size="4"><b>4 Apr 2016 ++ - New video shows how to obtain sequence or coordinates for exons. </b></font> ++ <a href="goldenPath/newsarch.html#040416">Read more</a>. ++ </p> ++ ++ <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> ++ ++ <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> ++ ++--> ++ ++ </TD><TD WIDTH=15> ++ </TD></TR></TABLE> ++ <BR></TD></TR></TABLE> ++</TD></TR></TABLE>