924657687100e3490cecd17c5a0295458fa95e87 brianlee Wed Nov 25 13:43:42 2015 -0800 Adding news announcement about external tools refs #16308 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index de15a4d..16de7a6 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,153 +1,117 @@ <!-- News Section ============================================- --> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"> <TR><TD> <TABLE BGCOLOR="#fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"> <TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="images/hr.gif" WIDTH="100%" BORDER=0> <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 BGCOLOR="#fffee8" WIDTH="100%" CELLPADDING=0> <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 --> <hr> <p> - <font color="#006666" size="4"><b>3 November 2015 — - We are pleased to announce new quick links for the Browser's top menu bar!</b></font> + <font color="#006666" size="4"><b>25 November 2015 — + New "View - In External Tools" Menu Sends Data to Prediction Websites!</b></font> <p> - The "Genomes" menu now features direct links to jump to browsing the human (hg38 and hg19) - and mouse (mm10 and mm9) assemblies! These links also preserve location information, such - as a favorite gene's location, allowing users to quickly compare available annotation - tracks between two assemblies. + Do you often get the current sequence with "View - DNA" just to copy + and paste it into another website? With the new menu "View - In External Tools" + you can now send the current region to remote tools with two clicks. </p> <p> - The "Genome Browser" menu now features a "Configure" link to quickly set visibilities for - all tracks on the currently browsed assembly and a "Reset All User Settings" option that will - remove all external hubs and custom tracks data while resetting the entire browser to default - visibilities and the hg38 assembly. - </p> - <hr> - + For example, when browsing hg38 and zoomed in on the start of a gene like ABO at + <a href="/cgi-bin/hgTracks?db=hg38&position=chr9%3A133255000-133255555" + target="_blank">chr9:133,255,000-133,255,555</a>, + click the View menu and select "In External Tools", + or simply type the keyboard shortcut "s" then "t", + to send the region to a list of different prediction tools.</p> <p> - <font color="#006666" size="4"><b>23 September 2015 — - New keyboard shortcuts on the Genome Browser!</b></font> - <p> - We are excited to announce the addition of keyboard shortcuts to navigate - the Genome Browser display! It's now possible to zoom in and out, navigate left - and right, hide all tracks, configure the browser display and much more using - only your keyboard. Use the "?" key to view the entire list of shortcuts. - Happy browsing! - </p> + Some of the available tools (not available for all assemblies or all zoom levels) + are primer design and restriction enzyme predictions (Primer3Plus, Primer-BLAST, + NEBCutter), mRNA and protein predictions (RegRNA 2, Riboswitches, RNAfold, PFAM), + cis-regulatory predictions (Promoter 2, RSAT Metazoa), and CRISPR/Cas9 predictions + (CRISPOR, CHOPCHOP), as well as links to view the region at NCBI or Ensembl. + You can suggest other tools via our + <a href="/cgi-bin/hgUserSuggestion">Suggestion Box</a>.</p> <p> Credit goes to Max Haeussler for implementing this new feature. </p> <hr> + <!-- start archives --> +<!--staged for future release <p> - <font color="#006666" size="4"><b>14 September 2015 — - Human Genome Browser default changed to GRCh38/hg38 </b></font> - </p> + <font color="#006666" size="4"><b>25 November 2015 — + New "View - In External Tools" Menu Sends Data to Prediction Websites!</b></font> <p> - In conjunction with the release of the new 100-species Conservation track on the - hg38/GRCh38 human assembly, we have now changed the default human browser on our - website from hg19 to hg38. This should not affect your current browsing sessions; - if you were last looking at the hg19 (or older) browser, the Genome Browser will - continue to display that assembly for you when you start it up. There are circumstances, - however, in which the selected assembly can switch to the newer version. For instance, - the assembly will switch to hg38 if you reset your browser defaults. If you find - yourself in a situation where some of your favorite browser tracks have "disappeared", - you may want to check that you're viewing the right assembly. - </p> - <p> - We will continue our efforts to expand the annotation track set on the hg38 browser - to include many of the tracks present on previous human assemblies. In cases where - it makes sense, data may be simply "lifted" from hg19 using migration tools. - In many instances, however, we must rely on our data providers to generate new versions - of their data on the latest assembly. We will publish these data sets as they become available. + Do you often get the current sequence with "View - DNA" just to copy + and paste it into another website? With the new menu "View - In External Tools" + you can now send the current region to remote tools with two clicks. </p> + <a href="goldenPath/newsarch.html#112515">Read more</a>. +--> <p> - For a summary of the new features in the GRCh38 assembly, see the - <a href="goldenPath/newsarch.html#030614">overview</a> we published in March 2014. + <font color="#006666" size="4"><b>3 November 2015 — + New quick links for the Genome Browser's top menu bar </b>:</font> + The "Genomes" menu now features direct links to jump to browsing the human + (hg38 and hg19) and mouse (mm10 and mm9) assemblies! + <a href="goldenPath/newsarch.html#110315">Read more</a>. </p> - <hr> - - <!-- start archives --> -<!-- <p> - <font color="#006666" size="4"><b>3 November 2015 — - We are pleased to announce new quick links for the Browser's top menu bar!</b></font> - The "Genomes" menu now features direct links to jump to browsing the human (hg38 and hg19) - and mouse (mm10 and mm9) assemblies! The "Genome Browser" menu now features a "Configure" - link to quickly set visibilities for all tracks on the currently browsed assembly and a "Reset - All User Settings" option. - <a href="goldenPath/newsarch.html#110315">Read more</a>. + <font color="#006666" size="4"><b>23 September 2015 — + New keyboard shortcuts on the Genome Browser </b>:</font> + It's now possible to zoom in and out, navigate left + and right, hide all tracks, configure the browser display and much more using + only your keyboard. Use the "?" key to view the entire list of shortcuts. + <a href="goldenPath/newsarch.html#092315">Read more</a>. </p> <p> <font color="#006666" size="4"><b>14 September 2015 — Human Genome Browser default changed to GRCh38/hg38 </b>:</font> In conjunction with the release of the new 100-species Conservation track on the hg38/GRCh38 human assembly, we have changed the default human browser on our website from hg19 to hg38. <a href="goldenPath/newsarch.html#091415">Read more</a>. </p> ---> + <p> <font color="#006666" size="4"><b>10 September 2015 — 100 Species Conservation Track now available on GRCh38/hg38 </b>: </font> We are pleased to announce the release of a new Conservation track based on the human (GRCh38/hg38) assembly. <a href="goldenPath/newsarch.html#091015">Read more</a>. </p> - - <p> - <font color="#006666" size="4"><b>12 August 2015 — - New blog post: How to share your UCSC screenthoughts</b>: - </font> - We talk about saving static images and dynamic Browser sessions in a new - <A HREF = "">blog</A> post, - and discuss some of the advantages and pitfalls of each. - <a href="goldenPath/newsarch.html#081215">Read more</a>. - </p> - - <p> - <font color="#006666" size="4"><b>29 June 2015 — - GENCODE Genes Now Default Gene Set on the Human (GRCh38/hg38) Assembly</b>: - </font> - In a move towards standardizing on a common gene set within the bioinformatics - community, UCSC has made the decision to adopt the GENCODE set of gene models - as our default gene set on the human genome assembly. - <a href="goldenPath/newsarch.html#062915">Read more</a>. - </p> </TD><TD WIDTH=15> </TD></TR></TABLE> <BR></TD></TR></TABLE> </TD></TR></TABLE>