@gmod/jbrowse
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JBrowse - client-side genome browser
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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 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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 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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 navListItemActive"><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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<p><a href="http://jbrowse.org/releases/jbrowse-1.1.zip">http://jbrowse.org/releases/jbrowse-1.1.zip</a></p>
<p>Release notes and screenshots below the fold.</p>
<p><span id="more-56"></span><strong>JBrowse release notes, version 1.1, September 2010.</strong></p>
<p>These notes document JBrowse developments in the period from July 2009 (online publication of the first JBrowse paper in Genome Research, the de facto "version 1.0") up to September 2010 (the first in a planned series of quarterly releases).</p>
<p>New features in this release:</p>
<ul>
<li><a href="bam-screenshot.png"><img src="http://jbrowse.org/wordpress/wp-content/uploads/2010/09/bam-screenshot.png" alt=""> </a>Scalability. JBrowse can now handle very large data tracks, including human EST/SNP tracks, or tracks of next-gen sequence reads. Large datasets are broken into smaller chunks, so there is no loading delay for big tracks.</li>
<li><a href="arc-screenshot.png"><img src="http://jbrowse.org/wordpress/wp-content/uploads/2010/09/arc-screenshot.png" alt=""></a>Extensibility. A Perl module (ImageTrackRenderer.pm) for creating user-drawn image tracks is now available, based on the CPAN GD.pm module. An example program is provided, draw-basepair-track.pl, that uses this module to draw arcs over a sequence representing the base-pairing interactions of RNA secondary structure.</li>
<li>Bug fixes. Numerous display glitches have been fixed, including issues with wide-screen monitors and long mostly-offscreen features.</li>
</ul>
<p>Known issues/limitations with this release:</p>
<ul>
<li>No JSON-level backward compatibility. If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server. This means wiping your jbrowse/data directory and re-running all server scripts (flatfile-to-json, biodb-to-json, wig-to-json, etc.) to regenerate your data from the original FASTA/GFF/BED/WIG files.</li>
<li>Next-gen sequence display is currently restricted to the co-ordinates of the outermost region to which a single read is mapped. There is no support (yet) for displaying pairing between reads, sequences of reads, alignment of read to reference sequence (e.g. splicing), or mismatches between read and reference.</li>
<li>Processing SAM/BAM next-gen sequence files takes a lot of memory (about 500 megabytes per million features).</li>
<li>Numerical (as opposed to comparative) readout of the data in Wiggle tracks, e.g. via a y-axis label or mouseover popup, is still unsupported.</li>
</ul>
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