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.html index 293d527,860fa78..0000000 deleted file mode 100755,100755 --- src/hg/htdocs/indexNews.html +++ /dev/null @@@ -1,260 -1,225 +1,0 @@@ --<!-- 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>1 Apr 2016 - - Going Back to Our Roots</b></font> - <p> - For many years, the UCSC Genome Browser has provided a dynamic, cutting-edge - interface for - viewing genomic data. As time has gone by, however, it has become clear to us - that we - cannot keep this up. It is not fair to you, our users, that our interface - keeps changing, - and it has increasingly been a burden on us to keep up with emerging web - technologies. Today - that all changes, as we return you to the roots of the web: ASCII. - <p> - <center><img src="newLook.png" width="65%"></center> - <p> - We apologize again for subjecting you to so many changes over the years, and - hope that this - new, more consistent interface will find your approval. - <p> - In related news, we have also revised the interface for uploading custom - tracks. Rather than - forcing you to wrestle with inconvenient file formats for your data or attempt - to set up a web server, - we now provide the option of loading your data from a deck of ISO 6586:1980 - punch cards. Simply - punch your data onto a deck and mail the deck to us. Our staff of highly - trained specialists - will take care of loading track, and will inform you by mail when the process - is complete. Please - note that our current policy of expiring unused custom tracks remains in - effect; you must visit - your track within 72 hours of the postmark date. Regrettably, decks cannot be - returned. - <p> - Card decks may be addressed to:<br> - UCSC Genome Informatics Group<br> - Center for Biomolecular Science & Engineering<br> - CBSE, 501D Engineering II Building<br> - University of California, Santa Cruz<br> - 1156 High Street<br> - Santa Cruz, CA 95064 - <p> - This new file format is also an option for data output from the <a - href="/cgi-bin/hgTables">UCSC Table Browser</a>. - Simply select "mail card deck" from the "output format" menu, and then enter - your name and address on the subsequent - page. Please allow 4-6 weeks for delivery. - - <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>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> - - --> - <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> - - </TD><TD WIDTH=15> - </TD></TR></TABLE> - <BR></TD></TR></TABLE> - </TD></TR></TABLE> - <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> - - <p> - </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>