efd9891d11d4d23f109ab09baddd1d69e4b139d8 jcasper Mon Apr 4 14:22:59 2016 -0700 Fixed broken links diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index d5f2cf0..3c0a3ec 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,280 +1,280 @@ <!-- 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> <p> </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="images/joke04012016.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>. <p> <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> <p> <font color="#006666" size="4"><b>1 Apr 2016 - Going Back to Our Roots</b></font> <a href="goldenPath/newsarch.html#040116">Read more</a>. </p> <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> --> <p> <font color="#006666" size="4"><b> 10 February 2016 - Two New Assemblies Now Available in the Genome Browser</b></font> - <a href="goldenPath/newsarch.html/#021016">Read more</a>. + <a href="goldenPath/newsarch.html#021016">Read more</a>. </p> <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>. + <a href="goldenPath/newsarch.html#012016">Read more</a>. </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>