@gmod/jbrowse
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JBrowse - client-side genome browser
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<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Blog · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="A fast, embeddable genome browser built with HTML5 and JavaScript"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Blog · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/index.html"/><meta property="og:description" content="A fast, embeddable genome browser built with HTML5 and JavaScript"/><meta name="twitter:card" content="summary"/><link rel="shortcut icon" href="/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css"/><link rel="alternate" type="application/atom+xml" href="https://jbrowse.org/blog/atom.xml" title="JBrowse Blog ATOM Feed"/><link rel="alternate" type="application/rss+xml" href="https://jbrowse.org/blog/feed.xml" title="JBrowse Blog RSS Feed"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><link rel="stylesheet" href="/css/main.css"/></head><body class="blog"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/"><h2 class="headerTitle">JBrowse</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive siteNavItemActive"><a href="/blog" target="_self">Blog</a></li><li class=""><a href="/docs/installation.html" target="_self">Documentation</a></li><li class=""><a href="/en/demos.html" target="_self">Demos</a></li><li class=""><a href="/en/developers.html" target="_self">Developers</a></li><li class=""><a href="/en/contact.html" target="_self">Contact</a></li><li class=""><a href="/en/references.html" target="_self">References</a></li><li class=""><a href="/en/help.html" target="_self">Help</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="container docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><i></i></div><h2><i>›</i><span>All Blog Posts</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">All Blog Posts</h3><ul><li class="navListItem"><a class="navItem" href="/blog/2019/07/11/jbrowse-1-16-6.html">JBrowse 1.16.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/06/12/jbrowse-1-16-5.html">JBrowse 1.16.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/04/10/jbrowse-1-16-4.html">JBrowse 1.16.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/02/20/jbrowse-1-16-3.html">JBrowse 1.16.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/01/31/jbrowse-1-16-2.html">JBrowse 1.16.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/12/27/jbrowse-1-16-1.html">JBrowse 1.16.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/12/13/jbrowse-1-16-0.html">JBrowse 1.16.0 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/10/05/jbrowse-1-15-4.html">JBrowse 1.15.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/08/29/jbrowse-1-15-3.html">JBrowse 1.15.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/08/16/jbrowse-1.15.2-maintenance-release-index.html">JBrowse 1.15.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/08/01/jbrowse-1-15-1-index.html">JBrowse 1.15.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/07/19/jbrowse-1-15-0-release-index.html">JBrowse 1.15.0 release - CRAM support, CSI indexes, and on the desktop!</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/06/04/jbrowse-1-14-2-index.html">JBrowse 1.14.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/05/02/jbrowse-1-14-1-maintenance-release-index.html">JBrowse 1.14.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/04/18/jbrowse-1-14-0-release-index.html">JBrowse 1.14.0 release - iframe-less embedding, BigBed support</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/03/28/jbrowse-1-13-1-maintenance-release-index.html">JBrowse 1.13.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/03/15/jbrowse-1-13-0-release-index.html">JBrowse 1.13.0 release - now with webpack!</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/02/28/jbrowse-1-12-5-maintenance-release-index.html">JBrowse 1.12.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/02/14/jbrowse-1-12-4-maintenance-release-index.html">JBrowse 1.12.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2017/05/02/jbrowse-1-12-3-index.html">JBrowse-1.12.3: Maintenance Release</a></li><li class="navListItem"><a class="navItem" href="/blog/2016/06/03/gsoc-students-do-cool-jbrowse-projects-index.html">GSoC Students Do Cool JBrowse Projects</a></li><li class="navListItem"><a class="navItem" href="/blog/2016/03/01/jbrowse-1-12-1-index.html">JBrowse-1.12.1: Maintenance Release</a></li><li class="navListItem"><a class="navItem" href="/blog/2016/02/25/state-of-the-browser-2016-index.html">State of the Browser, 2016</a></li><li class="navListItem"><a class="navItem" href="/blog/2015/12/17/jbrowse-1-12-0-index.html">JBrowse-1.12.0: Open new genome from FASTA, in-line refseqs, NeatFeatures, Desktop</a></li><li class="navListItem"><a class="navItem" href="/blog/2015/02/12/jbrowse-1-11-6-index.html">JBrowse-1.11.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/09/04/jbrowse-1-11-5-index.html">JBrowse-1.11.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/05/14/jbrowse-1-11-4-maintenance-release-index.html">JBrowse-1.11.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/03/07/jbrowse-1-11-3-index.html">JBrowse 1.11.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/02/12/tutorial-exploring-structural-variation-index.html">Tutorial: exploring structural variation using JBrowse, from the tomato 150+ re-seq project</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/02/10/jbrowse-1-11-2-index.html">JBrowse 1.11.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/01/07/jbrowse-1-11-1-index.html">JBrowse 1.11.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/12/19/jbrowse-1-11-0-index.html">JBrowse 1.11.0: hierarchical track selector, easier configuration, summary mode</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/12/10/jbrowse-1-10-12-index.html">JBrowse 1.10.12 maintenance release (please upgrade!)</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/12/03/jbrowse-1-10-11-index.html">JBrowse 1.10.11 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/11/21/jbrowse-1-10-10-index.html">JBrowse 1.10.10 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/11/08/jbrowse-1-10-9-index.html">JBrowse 1.10.9 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/25/jbrowse-1-10-8-index.html">JBrowse 1.10.8 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/15/jbrowse-1-10-7-index.html">JBrowse 1.10.7 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/07/jbrowse-1-10-6-index.html">JBrowse 1.10.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/03/jbrowse-1-10-5-index.html">JBrowse 1.10.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/09/23/jbrowse-1-10-4-index.html">JBrowse 1.10.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/09/04/jbrowse-1-10-3-index.html">JBrowse 1.10.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/08/15/jbrowse-1-10-2-index.html">JBrowse 1.10.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/08/06/jbrowse-1-10-1-maintenance-release-index.html">JBrowse 1.10.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/07/30/jbrowse-1-10-0-index.html">JBrowse 1.10.0: Combination tracks, better feature tracks, more glyphs, SPARQL support, and track pinning!</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/07/05/jbrowse-1-9-8-index.html">JBrowse 1.9.8 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/07/02/about-jbrowse-version-numbers-index.html">About JBrowse version numbers</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/06/25/jbrowse-1-9-7-maintenance-release-index.html">JBrowse 1.9.7 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/06/18/jbrowse-1-9-6-maintenance-release-index.html">JBrowse 1.9.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/06/12/jbrowse-1-9-5-index.html">JBrowse 1.9.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/05/22/jbrowse-1-9-4-index.html">JBrowse 1.9.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/05/09/jbrowse-1-9-3-index.html">JBrowse 1.9.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/05/02/jbrowse-1-9-2-index.html">JBrowse 1.9.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/04/25/jbrowse-1-9-1-index.html">JBrowse 1.9.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/04/16/jbrowse-1-9-0-index.html">JBrowse 1.9.0: VCF support, dataset switching, wiggle track dynamic scaling, REST backend</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/02/12/jbrowse-1-8-1-bugfix-release-index.html">JBrowse 1.8.1 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/01/31/jbrowse-1-8-0-index.html">JBrowse 1.8.0: opens local files, new BAM track types, new plugin system</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/01/10/jbrowse-1-7-6-bugfix-release-index.html">JBrowse 1.7.6 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/12/12/jbrowse-1-7-5-bugfix-release-index.html">JBrowse 1.7.5 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/12/06/jbrowse-1-7-4-bugfix-release-index.html">JBrowse 1.7.4 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/28/jbrowse-1-7-3-bugfix-release-index.html">JBrowse 1.7.3 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/09/jbrowse-1-7-2-bugfix-release-index.html">JBrowse 1.7.2 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/07/jbrowse-1-7-1-bugfix-release-index.html">JBrowse 1.7.1 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/05/jbrowse-1-7-0-index.html">JBrowse 1.7.0, now with data export, direct BAM display, and much more</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/10/26/jbrowse-1-6-5-bugfix-release-index.html">JBrowse 1.6.5 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/10/16/jbrowse-1-6-4-bugfix-release-index.html">JBrowse 1.6.4 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/09/28/jbrowse-1-6-3-bugfix-release-index.html">JBrowse 1.6.3 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/09/10/jbrowse-1-6-2-bugfix-release-index.html">JBrowse 1.6.2 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/09/07/rbuels-and-jbrowse-at-the-semantic-web-biohackathon-2012-index.html">@rbuels and JBrowse at the Semantic Web BioHackathon 2012</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/08/28/jbrowse-1-6-1-bugfix-release-index.html">JBrowse 1.6.1 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/08/25/jbrowse-1-6-0-released-includes-feature-descriptions-and-more-index.html">JBrowse 1.6.0 released, includes feature descriptions and more!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/08/13/jbrowse-1-5-0-released-includes-direct-bigwig-access-index.html">JBrowse 1.5.0 released, includes direct BigWig access!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/07/12/jbrowse-1-4-2-released-index.html">JBrowse 1.4.2 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/07/10/jbrowse-1-4-1-released-index.html">JBrowse 1.4.1 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/06/14/jbrowse-1-4-0-released-includes-faceted-track-selection-index.html">JBrowse 1.4.0 released, includes faceted track selection!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/05/07/poliovirus-xrate-demo-by-oscar-westesson-index.html">Poliovirus / XRate demo by Oscar Westesson</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/04/19/jbrowse-1-3-1-released-index.html">JBrowse 1.3.1 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/04/13/jbrowse-1-3-0-index.html">JBrowse 1.3.0, a major release!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/03/25/jbrowse-1-2-2-released-index.html">JBrowse 1.2.2 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/03/22/hg19-tarball-updated-to-jbrowse-1-2-1-index.html">hg19 tarball updated to JBrowse 1.2.1</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/03/16/jbrowse-in-google-summer-of-code-2012-2-index.html">JBrowse in Google Summer of Code 2012</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/01/13/new-jbrowse-lead-developer-index.html">New JBrowse Lead Developer</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/09/16/dna-sequencing-on-your-iphone-theres-an-app-for-that-index.html">DNA sequencing on your iPhone? There's an app for that</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/09/15/jbrowse-conference-call-index.html">JBrowse conference call</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/08/03/summer-2011-update-index.html">Summer 2011 update</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/04/06/jbrowse-is-hiring-index.html">JBrowse is hiring!</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/03/17/jbrowse-1-2-1-released-index.html">JBrowse 1.2.1 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/02/17/jbrowse-1-2-released-index.html">JBrowse 1.2 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/12/18/touch-the-genome-index.html">Touch the genome</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/11/24/hg19-tarball-updated-index.html">hg19 tarball updated</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/11/11/data-mini-release-hg19-annotation-tarball-index.html">JBrowse tarball for hg19 human genome data</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/10/11/personal-genomics-website-using-jbrowse-index.html">Personal genomics website using JBrowse</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/10/11/jbrowse-website-moved-to-amazon-cloud-index.html">JBrowse website moved to Amazon cloud</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/09/09/jbrowse-1-1-release-index.html">JBrowse 1.1 release</a></li></ul></div></div></section></div><script>
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</script></nav></div><div class="container mainContainer postContainer blogContainer"><div class="wrapper"><div class="posts"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/08/25/jbrowse-1-6-0-released-includes-feature-descriptions-and-more-index.html">JBrowse 1.6.0 released, includes feature descriptions and more!</a></h1><p class="post-meta">August 25, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm very pleased to announce the release of JBrowse 1.6.0! This release is not quite as major as the previous two releases, but there are still some nice things added.</p>
<p>As usual, this release comes in two flavors: the "minimal" release (<a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=14">JBrowse-1.6.0-min.zip</a> - 2.8M) that includes only the software and documentation necessary to format your own data and run the browser, and the "full" release (<a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=13">JBrowse-1.6.0-min.zip</a>- 27.2M) that includes the developers' test suite, more sample data files, and developer documentation. Here is the full list of new improvements in 1.6.0:</p>
<ul>
<li><p>Added <code>description</code> capabilities to HTML-based features, similar to
GBrowse's descriptions. If zoomed in far enough (as defined by
<code>style.descriptionScale</code>), adds a second line of text below the
feature's label that shows the content's of the featur's <code>Note</code> or
<code>description</code> attribute (issue #67).</p></li>
<li><p>Give prepare-refseqs.pl the capability to load reference sequences
from embedded FASTA sections in GFF3 files (issue #128).</p></li>
<li><p>Configuration files can now recursively <code>include</code> eachother, and
<code>tracks</code> sections are merged intelligently.</p></li>
<li><p>Made sequence tracks not disappear when zoomed out too far to see
base pairs. Instead, sequence tracks simply display lines
suggesting that DNA would be visible at higher
magnification. (issue #124).</p></li>
<li><p>Double-clicking track labels in the simple track selector now turns
the track on (issue #123).</p></li>
<li><p>Fixed bug in BigWig tracks that use the "scale": "log" option: did
not render properly when the wiggle data included 0's. This was due
to the fact that the origin was being mapped to Infinity. Thanks to
the <a href="http://www.mocklerlab.org/">Mockler Lab</a> for the fix! (issue #127).</p></li>
<li><p>Fixed bug in NCList binary search code in which zero-length
features at node boundaries would not be found (fix by Ed Lee).</p></li>
<li><p>Fixed bug in which dragging the scroll bar on the simple track
selector can sometimes cause a drag-and-drop to erroneously begin
(issue #89).</p></li>
<li><p>Fixed some bugs in the layout of HTML-based features in which
features in different blocks would overlap in some circumstances.
Under the hood, replaced the contour-based layout engine with a
simpler, not-much-slower implementation that is more correct in the
general case (issue #122).</p></li>
<li><p>Fixed a bug with vertical centering of strand arrows and other
sub-elements of HTML-based features.</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/08/13/jbrowse-1-5-0-released-includes-direct-bigwig-access-index.html">JBrowse 1.5.0 released, includes direct BigWig access!</a></h1><p class="post-meta">August 13, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm very pleased to announce the release of JBrowse 1.5.0! There are three headline features in this release. First, we've integrated a <strong>direct-access BigWig data backend</strong>, adapted from the <a href="http://www.biodalliance.org/">Dalliance Genome Explorer</a> that can read wiggle data directly from compressed <a href="http://genome.ucsc.edu/goldenPath/help/bigWig.html">BigWig files</a> stored on your web server. Second, there is now a beautiful, full-featured canvas-based <strong><code>Wiggle</code> track type</strong>. Third, we have a very powerful new click system that allows JBrowse administrators complete flexibility in configuring what happens when a user left- or right-clicks a feature in an HTML-based feature track, including <strong>right-click context menus</strong>.</p>
<p>A demonstration of JBrowse 1.5.0 showing a test BigWig-based wiggle track (alongside an old-style image-based wiggle track for comparison) can be seen <a href="http://jbrowse.org/code/JBrowse-1.5.0-full/index.html?loc=ctgA%3A6481..27220&tracks=DNA%2Cvolvox_microarray.bw%2Cvolvox_microarray.wig&data=sample_data%2Fjson%2Fvolvox">here</a>, and a whole-genome RNA-seq profile of tomato, with corresponding gene models, can be seen <a href="/genomes/tomato/">here</a>.</p>
<p>As usual, this release comes in two flavors: the "minimal" release (<a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=12">JBrowse-1.5.0-min.zip</a> - 2.8M) that includes only the software and documentation necessary to format your own data and run the browser, and the "full" release (<a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=11">JBrowse-1.5.0-min.zip</a> - 27.2M) that includes the developers' test suite, more sample data files, and developer documentation.</p>
<p>Here is the full list of new improvements in 1.5.0:</p>
<ul>
<li><p>Added a direct-access storage driver for BigWig data files, based
on code from the Dalliance Genome Explorer by Thomas Down. BigWig
file access is supported now by the current versions of all major
browsers except Internet Explorer (which is expected to work when
version 10 is released along with Windows 8).</p></li>
<li><p>Added a <code>canvas</code>-based wiggle track implementation for quantitative
data that, when used with the new BigWig storage backend, removes
the need to pre-generate rendered images of wiggle data. Its
display is also highly configurable, with configuration options
modeled on the GBrowse <code>wiggle_xyplot</code> glyph type
(i.e. <code>Bio::Graphics::Glyph::wiggle_xyplot</code>).</p></li>
<li><p>Added highly configurable behavior for left-clicking and
right-clicking features in HTML-based feature tracks. If a
<code>menuTemplate</code> option is specified in the track configuration,
right-clicking a feature brings up a context menu, the items in
which can be configured to do nearly anything, but that are easy to
configure for the very common use case of wanting to display
content from a certain URL. Feature left-clicks are also
configurable using the same mechanism. Thanks to Alexie
Papanicolaou and Temi Varghese for the initial implementation of
context menus.</p></li>
<li><p>Improved the default HTML feature left-click dialog box. It is now
both prettier, and more comprehensive, displaying all available
data for the feature.</p></li>
<li><p>Added a small helper script, <code>add-track-json.pl</code> that developers
and advanced users can use to programmatically add a block of track
configuration JSON to an existing JBrowse configuration file.</p></li>
<li><p>Improved / fixed vertical alignment of sub-elements of HTML
features, including subfeatures and the arrowheads that show
strand. All elements in a feature are now vertically centered by
default.</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/07/12/jbrowse-1-4-2-released-index.html">JBrowse 1.4.2 released</a></h1><p class="post-meta">July 12, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.4.2 has been released, containing some small fixes for issues in the <a href="http://jbrowse.org/jbrowse-1-4-1-released/" title="JBrowse 1.4.1 released">1.4.1 release</a>.</p>
<ul>
<li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=2" title="download JBrowse-1.4.2-min.zip">JBrowse-1.4.2-min.zip</a> - 2.6M</p></li>
<li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=1" title="download JBrowse-1.4.2-full.zip">JBrowse-1.4.2-full.zip</a> - 5.5M
Changes in this release:</p></li>
<li><p>Restore support for histScale, subfeatureScale, and labelScale in <code>--clientConfig</code> command-line options and track configuration JSON. Thanks to Hernán Bondino for pointing this out.</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/07/10/jbrowse-1-4-1-released-index.html">JBrowse 1.4.1 released</a></h1><p class="post-meta">July 10, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.4.1 has been released, containing some small fixes for issues in the <a href="http://jbrowse.org/jbrowse-1-4-0-released-includes-faceted-track-selection/" title="JBrowse 1.4.0 released, includes faceted track selection!">1.4.0 release</a>.</p>
<ul>
<li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=4" title="download JBrowse-1.4.1-min.zip">JBrowse-1.4.1-min.zip</a> - 2.6M</p></li>
<li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=3" title="download JBrowse-1.4.1-full.zip">JBrowse-1.4.1-full.zip</a> - 5.5M
Changes in this release:</p></li>
<li><p>Made displayColumns option for the faceted track selector
case-insensitive, and interpret a column name of "Name" as meaning
the track's key.</p></li>
<li><p><code>bam-to-json.pl</code> now filters out alignments that are not at least
two nucleotides in length. Thanks to Tristan Lubinski for
assistance.</p></li>
<li><p>Introduced limits on the sizes of cookies that can be set,
preventing '400 bad request' errors (issue #113).</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/06/14/jbrowse-1-4-0-released-includes-faceted-track-selection-index.html">JBrowse 1.4.0 released, includes faceted track selection!</a></h1><p class="post-meta">June 14, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.4.0 has been released! There are two headline features in this release: a new, extremely powerful <strong>faceted track selector</strong> that makes it easy for users to search through hundreds or thousands of tracks based on their metadata, and much better support for <strong>large numbers of reference sequences</strong>, enabled by retiring the old reference sequence dropdown selector in favor of adding a new find-as-you-type feature to the location box.</p>
<p>A <a href="/code/JBrowse-1.4.0-full/index.html?data=sample_data/json/modencode" title="view faceted track selector demo">demonstration of the faceted track selector</a> can be seen <a href="/code/JBrowse-1.4.0-full/index.html?data=sample_data/json/modencode">here</a>. This contains a snapshot of the modENCODE track metadata taken from <a href="http://data.modencode.org">http://data.modencode.org</a>. Note that the track data and reference sequences in this track selection demo are not real: the reference sequences and wiggle data are all just copies of the volvox wiggle test track from the JBrowse test suite.</p>
<p>As is becoming the norm, this release comes in two flavors: the "minimal" release (<a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=6" title="download JBrowse-1.4.0-min.zip">JBrowse-1.4.0-min.zip</a> - 2.6M) that includes only the software and documentation necessary to format your own data and run the browser, and the "full" release (<a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=5" title="download JBrowse-1.4.0-full.zip">JBrowse-1.4.0-full.zip</a> - 5.5M) that includes the developers' test suite, more sample data files, and developer documentation.</p>
<p>There have been lots of improvements over the 1.3 series:</p>
<ul>
<li>Added a full-featured** faceted track selector** for users that have
many (hundreds or thousands) of tracks. This can be turned on by
setting the <code>trackSelectorType</code> config variable to "Faceted". See
the JBrowse wiki for more documentation on how to use faceted track
selection. (issue #95)</li>
<li>Removed the dropdown selector for reference sequences in favor of
making the <strong>location box auto-complete reference sequence and</strong>
** feature names<strong>. This makes JBrowse much more <strong>scalable to large</strong>
** numbers of reference sequences</strong>. (fixes issues #3, #60, and #101)</li>
<li>Added a <strong>vertical-scrolling marker</strong> on the right side of the track
pane, making it much easier to discern the vertical position of the
track display. (issue #93).</li>
<li>biodb-to-json.pl and flatfile-to-json.pl now <strong>load all available</strong>
** feature data**: all attributes of features are now encoded in the
JSON and are available for use by feature callbacks. (issue #72)</li>
<li><strong>Feature labels now do not scroll off screen</strong> if any part of the
feature is still visible (fixes issue #62).</li>
<li>Added jbrowse_conf.json, a default JSON-format configuration file,
to the JBrowse root directory. Makes it <strong>easier to get started</strong>
** with more advanced JBrowse configuration**.</li>
<li>JBrowse instances now <strong>report anonymous usage statistics</strong> to the JBrowse developers. This data is very important to the JBrowse project,
since it is used to make the case to grant agencies for continuing
to fund JBrowse development. No research data is transmitted, the
data collected is limited to standard Google Analytics, along with
a count of how many tracks the JBrowse instance has, how many
reference sequences are present, their average length, and what
types of tracks (wiggle, feature, etc) are present. Users can
disable usage statistics by setting "suppressUsageStatistics: true"
in the JBrowse configuration.</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/05/07/poliovirus-xrate-demo-by-oscar-westesson-index.html">Poliovirus / XRate demo by Oscar Westesson</a></h1><p class="post-meta">May 7, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>Oscar Westesson has contributed a nice demonstration of using JBrowse 1.2.1 to display and compare performance of four different XRate grammars on the poliovirus genome.</p>
<p><a href="/genomes/westesson_polio_xrate/index.html">View demo</a>
<a href="/genomes/westesson_polio_xrate.zip" title="Download">Download .zip</a> (35M)</p>
<p>Thanks Oscar!</p>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/04/19/jbrowse-1-3-1-released-index.html">JBrowse 1.3.1 released</a></h1><p class="post-meta">April 19, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.3.1 has been released, this is a minor release with fixes for some bugs found in 1.3.0.</p>
<dl><dt>[JBrowse-1.3.1-min.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=7 "download JBrowse 1.3.1 - min") - 2.0MB</dt><dd>Includes all that is needed for running JBrowse and formatting your own data.</dd><dt>[JBrowse-1.3.1-full.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=8 "download JBrowse 1.3.1 - full") - 4.7MB</dt><dd>Includes developer API documentation, developer test suites, additional sample data</dd></dl>
<h3><a class="anchor" aria-hidden="true" id="changes-in-this-release"></a><a href="#changes-in-this-release" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a><strong>Changes in this release</strong></h3>
<ul>
<li><p>Fixed memory-management bug that caused way too much RAM to be used
by FeatureTrack loading (flatfile, bam, and biodb-to-json.pl) when
loading with very large numbers of reference sequences. Big thanks
to Tristan Lubinski for help in isolating this.</p></li>
<li><p>Fixed some bugs in BAM support section of setup.sh autosetup
script, thanks to Tristan Lubinski for help in isolating this as
well.</p></li>
<li><p>Added an example document with an iframe running JBrowse in
embedded mode in docs/examples/embedded_mode.html</p></li>
<li><p>flatfile-to-json.pl now loads the 'score' attribute of features in the
JSON.</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/04/13/jbrowse-1-3-0-index.html">JBrowse 1.3.0, a major release!</a></h1><p class="post-meta">April 13, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse version 1.3.0 has arrived!</p>
<p>We have a long list of improvements in this release, some of which have been a long time coming. It's full speed ahead from here: more major new features are just around the corner!</p>
<p>This release comes in two flavors: the "minimal" release (<a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=9" title="download JBrowse-1.3.0-min.zip">JBrowse-1.3.0-min.zip</a> - 2.0M) that includes only the software and documentation necessary to format your own data and run the browser, and the "full" release (<a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=10" title="download JBrowse-1.3.0-full.zip">JBrowse-1.3.0-full.zip</a> - 4.7M) that includes the developers' test suite, more sample data files, and developer documentation.</p>
<p>One important note about browser support: as of this 1.3.0 release, JBrowse no longer supports Microsoft Internet Explorer 6.</p>
<p>And now, the <strong>Big List of New Features!</strong></p>
<ul>
<li>Added support for** "rubberband" dynamic zooming**, in which users can
click and drag to select a region to zoom to. Dragging on any
scale bar, or shift-dragging on the main track pane, triggers a
dynamic zoom.</li>
<li>Correcting a long-standing oversight, wiggle data tracks and
feature histograms now have <strong>numerical y-axis scales</strong> that show the
numerical values of the data.</li>
<li>Server-side data-formatting scripts now support a** --compress option**
to compress (gzip) feature and sequence data to <strong>conserve server</strong>
** disk space**. Using this option requires some web server
configuration. Under Apache, AllowOverride FileInfo (or
AllowOverride All) must be set for the JBrowse data directories in
order to use the included .htaccess files, and mod_headers and
mod_setenvif must be installed and enabled. Under nginx a
configuration snippet like the following should be included in the
configuration:</li>
</ul>
<pre> location ~* "\.(json'txt)z$" {
add_header Content-Encoding gzip;
gzip off;
types { application/json jsonz; }
}</pre>
<ul>
<li>flatfile-to-json.pl: now much <strong>faster and more memory-efficient</strong>,
especially for GFF3 files. Remember that '###' directives are very
important to have in large GFF3 files! Also removed nonfunctional
--extraData switch.</li>
<li>Added ability to <strong>turn off some JBrowse UI panels via URL arguments</strong>
to the default index.html, or via arguments to the Browser
constructor itself. Can dynamically turn off the navigation box,
the overview panel, and the track list, respectively. When all of
these are off, and if run in an iframe, JBrowse is running in an
<strong>"embedded mode"</strong> that looks similar to the output of GBrowse's
gbrowse_img script, with the exception that the view in this case
is a fully functioning, scrollable and zoomable JBrowse. See the
GMOD wiki (<a href="http://gmod.org/wiki/JBrowse">http://gmod.org/wiki/JBrowse</a>) for more on how to set up
embedded mode. Thanks to Julie Moon, a co-op student working at
OICR, for this work!</li>
<li><strong>Improved graphical look and feel</strong>.</li>
<li>Browser support for this release:</li>
</ul>
<table>
<tbody>
<tr>
<td>Google Chrome 18</td>
<td>perfect</td>
</tr>
<tr>
<td>Google Chrome 17</td>
<td>perfect</td>
</tr>
<tr>
<td>Mozilla Firefox 11.0</td>
<td>perfect</td>
</tr>
<tr>
<td>Mozilla Firefox 10.1</td>
<td>perfect</td>
</tr>
<tr>
<td>Mozilla Firefox 10.0.2</td>
<td>perfect</td>
</tr>
<tr>
<td>Mozilla Firefox 3.6.28</td>
<td>nonfunctional</td>
</tr>
<tr>
<td>Apple Safari 5.1.5 (Lion)</td>
<td>perfect</td>
</tr>
<tr>
<td>Microsoft Internet Explorer 9</td>
<td>good</td>
</tr>
<tr>
<td>Microsoft Internet Explorer 8</td>
<td>good</td>
</tr>
<tr>
<td>Microsoft Internet Explorer 7</td>
<td>minor problems</td>
</tr>
<tr>
<td>Microsoft Internet Explorer 6</td>
<td>not tested</td>
</tr>
<tr>
<td>KDE Konqueror 4.7.4</td>
<td>nonfunctional</td>
</tr>
<tr>
<td>KDE Konqueror 4.5.5</td>
<td>nonfunctional</td>
</tr>
<tr>
<td>Opera (all versions)</td>
<td>not tested</td>
</tr>
</tbody>
</table>
<ul>
<li>Added an <strong>automated-setup script, setup.sh</strong>, that tries to install
Perl prerequisites, format Volvox example data, and install Wiggle
and BAM support (fetching samtools from SVN if necessary)
automatically.</li>
<li>Navigating to JBrowse with missing or malformed configuration or
data will now bring up an error page with useful messages and links
to help documentation, instead of a blank white page.</li>
<li>JBrowse data directories now include an Apache .htaccess in their
root directory that, if mod_headers is installed and AllowOverride
FileInfo or AllowOverride All is enabled, will emit the proper <strong>HTTP</strong>
** headers to allow cross-origin XHR requests** for the data.</li>
<li>A new "Help" link in the upper right, or pressing "?" on the
keyboard, brings up a "JBrowse Help" dialog box with basic usage
information and links to more help information.</li>
<li>Arrowheads indicating strandedness are now drawn inside feature
boundaries.</li>
<li>Clicking on the overview bar or the main scale bar now centers the
view at the clicked position. In addition, while holding down
shift, clicking in the main track panel will also center the view
at that position.</li>
<li>Added bin/remove-track.pl,** a script to remove a track** from a
JBrowse data directory. Run bin/remove-track.pl -? to see its
documentation.</li>
<li>Added build instrumentation to support a JSDoc-based system of
<strong>developer API documentation</strong>. This documentation is still far from
complete.</li>
<li>Ian Davis contributed code to add a view of the <strong>reverse strand of</strong>
** the sequence in the DNA track**. Thanks Ian!</li>
<li>Fixed bug in which, for some sequence chunk sizes, the DNA bases
would display incorrectly.</li>
<li>Added <strong>minor gridlines</strong> to the main track view.</li>
<li>Fixed a long-standing off-by-one bug where the window could not be
scrolled to view the last base in the reference sequence.</li>
<li>Coordinates displayed in the <strong>user interface are now 1-based closed</strong>
** coordinates**, which are more familiar to most users. Previously,
the labels displayed interbase (i.e. 0-based half-open)
coordinates.</li>
<li><strong>NON-BACKWARDS-COMPATIBLE</strong> improvements to the JSON format used for
track configuration, feature data, and image data</li>
</ul>
<ul>
<li>initial support for a new hook system for greater
administrator-configurability of feature display</li>
<li>support for more than one level of subfeatures</li>
</ul>
<ul>
<li>Miscellaneous improvements and refactoring of data-formatting Perl
code.</li>
<li><strong>More detailed POD-based help documentation</strong> on all scripts</li>
<li>--tracklabel options to all scripts replaced with --trackLabel.</li>
<li>New suite of <strong>integration tests</strong>, and some unit tests, for
server-side Perl code.</li>
<li>Beginnings of a suite of <strong>Selenium-based integration tests</strong> for the
front-end JavaScript code.</li>
<li>Support for Apple touch-based devices merged into normal
index.html, so that the same link can be used regardless of the
browsing platform.</li>
<li>Bug fixed in which non-stranded features do not display properly
(a problem with the CSS styles).</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/03/25/jbrowse-1-2-2-released-index.html">JBrowse 1.2.2 released</a></h1><p class="post-meta">March 25, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>This is a minor bugfix release, containing fixes for display of unstranded features and a correction to the tutorial HTML file that incorrectly suggested using flatfile-to-json.pl to format feature data from a BAM file.</p>
<p>JBrowse 1.2.2 can be downloaded from <a href="http://jbrowse.org/releases/jbrowse-1.2.2.zip">http://jbrowse.org/releases/jbrowse-1.2.2.zip</a></p>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/03/22/hg19-tarball-updated-to-jbrowse-1-2-1-index.html">hg19 tarball updated to JBrowse 1.2.1</a></h1><p class="post-meta">March 22, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>A new tar.gz file is available, containing a copy of JBrowse 1.2.1 with Human hg19 data. Being based on a more recent version of JBrowse, it should work much better than the previous hg19 tarball releases. Enjoy!</p>
<p>The new file is here: <a href="http://jbrowse.org/releases/jbrowse-1.2.1-hg19mini.tar.gz">http://jbrowse.org/releases/jbrowse-1.2.1-hg19mini.tar.gz</a></p>
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