@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>JBrowse 1.3.0, a major release! · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="JBrowse version 1.3.0 has arrived!"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="JBrowse 1.3.0, a major release! · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/blog/2012/04/13/jbrowse-1-3-0-index.html"/><meta property="og:description" content="JBrowse version 1.3.0 has arrived!"/><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 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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 navListItemActive"><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="lonePost"><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><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>
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