@gmod/jbrowse
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JBrowse - client-side genome browser
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<!DOCTYPE html><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 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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/2016/06/03/gsoc-students-do-cool-jbrowse-projects-index.html">GSoC Students Do Cool JBrowse Projects</a></h1><p class="post-meta">June 3, 2016</p><div class="authorBlock"></div></header><article class="post-content"><div><span><div>I'm pleased to introduce two Google Summer of Code students who are working actively on Jbrowse projects:</div>
<div>
<h1><a class="anchor" aria-hidden="true" id="span-style-font-size-small-pubudu-dodangoda-span-span-style-font-size-small-is-working-on-a-social-commenting-extension-for-gene-features-span"></a><a href="#span-style-font-size-small-pubudu-dodangoda-span-span-style-font-size-small-is-working-on-a-social-commenting-extension-for-gene-features-span" 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><span style="font-size: small;">Pubudu Dodangoda</span></strong> <span style="font-size: small;">is working on a social commenting extension for gene features.</span></h1>
</div>
<div>
<h1><a class="anchor" aria-hidden="true" id="span-style-font-size-small-saksham-saxena-span-span-style-font-size-large-span-span-style-font-size-small-is-working-a-module-to-manage-synthetic-chromosomes-through-github-span"></a><a href="#span-style-font-size-small-saksham-saxena-span-span-style-font-size-large-span-span-style-font-size-small-is-working-a-module-to-manage-synthetic-chromosomes-through-github-span" 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><span style="font-size: small;">Saksham Saxena</span></strong><span style="font-size: large;"> </span><span style="font-size: small;">is working a module to manage synthetic chromosomes through GitHub.</span></h1>
</div>
<div>**Pubudu** is a student of Department of Computer Science and Engineering, Faculty of Engineering, University of Moratuwa. He is planning to continue studies in the areas of Web app/service development primarily with technologies such as JS, ES2015, AngularJs, ReactJs, NodeJs etc, Human Computer Interaction(HCI), machine learning, Bioinformatics and c<wbr />oncurrent programming.</div>
<div></div>
<div>Pubudu plays table tennis and enjoys music during his free times. He used to do some photoshop work some time back but kind of stopped it due to the workload of final year project and all. He was also a teaching assistant for 'communication skills' module during the last semester and worked as an intern at WSO2 last year.</div>
<div></div>
<div>Github - [https://github.com/pupudu](https://github.com/pupudu)</div>
<div>LinkedIn - [https://lk.linkedin.com/in/<wbr />pupudu](https://lk.linkedin.com/in/pupudu)</div>
<div></div>
<div></div>
<div>**Saksham** is attending Delhi Technological University, pursuing Bachelor's of Technology in Engineering Physics. Presently in third year.</div>
<div>
Saksham is an audiophile, science, technology and philosophy indulgent who drives to live, and is an occasional poet.
<p>GitHub: <a href="https://github.com/sakshamsaxena">https://github.com/<wbr />sakshamsaxena</a>,
LinkedIn: <a href="https://www.linkedin.com/in/saxenasaksham">https://www.<wbr />linkedin.com/in/saxenasaksham</a>
Blog/Tumblr: <a href="http://sakshamsaxena.in/">sakshamsaxena.in</a></div></p>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2016/03/01/jbrowse-1-12-1-index.html">JBrowse-1.12.1: Maintenance Release</a></h1><p class="post-meta">March 1, 2016</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>We are happy to announce JBrowse 1.12.1 release! This is a maintenance release.</p>
<ul>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.1.zip">JBrowse-1.12.1.zip</a> - 4.9M
file SHA1 bb917733f768744d703ab7b17b1f80040c055a78</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.1-dev.zip">JBrowse-1.12.1-dev.zip</a> - 26M
file SHA1 737851bf52c0d537eb1c54b5a4b6a12d6736d2f0</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.1-desktop-osx.zip">JBrowse-1.12.1-desktop-osx.zip</a> - 49M (OSX)
file SHA1 d766afe66ccb6eb754d1d329c097a447435d108b</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.1-desktop-win.zip">JBrowse-1.12.1-desktop-win.zip</a> - 49M (Windows)
file SHA1 22613a35ff5eab9d4f9e151f6a153297fe21cb2d</li>
<li><a href="https://hub.docker.com/r/jbrowse/gmod-jbrowse/">Docker Image</a></li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" 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>Minor improvements</h2>
<ul>
<li>Update Dojo to 1.8.10</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="bug-fixes"></a><a href="#bug-fixes" 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>Bug fixes</h2>
<ul>
<li>Fix RegexSearch plugin and NeatCanvasFeatures plugin - search track
loading failure (issue #676)</li>
<li>Fix compat_121.html to access /css directory</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2016/02/25/state-of-the-browser-2016-index.html">State of the Browser, 2016</a></h1><p class="post-meta">February 25, 2016</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>It's been a while since we posted on here<a href="#asterisk">*</a>, and while the JBrowse-o-sphere has not been silent (there's been plenty of chatter on the <a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax">gmod-ajax</a> mailing list and the GitHub <a href="https://github.com/gmod/jbrowse/issues">issues tracker,</a> for example) we think it's high time for an update on the main site.</p>
<p>In part, this update is triggered by the (near-)completion of a state-of-the-JBrowse paper, which should be published soon. That paper describes what's been happening in JBrowse over the past few years, code-wise. You can get a sense of that from the <a href="https://github.com/GMOD/jbrowse/blob/master/release-notes.txt">release notes</a>. The (complementary) goal of this blog post is to give some idea of the direction we're headed in.</p>
<h3><a class="anchor" aria-hidden="true" id="kicking-the-perl-habit"></a><a href="#kicking-the-perl-habit" 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>Kicking the Perl Habit</h3>
<p>JBrowse was the spiritual child of <a href="http://gmod.org/wiki/GBrowse">GBrowse</a>, and GBrowse was built on the good ship Perl. Sadly, those days belong to a glorious past that has not yet been resurrected in the name of vintage kitsch. Speaking as a hacker who still dreams in Perl (and sometimes talks to myself in Perl while riding the train) I'm <span style="text-decoration: underline;">proud</span> to be a national monument and I'd be happy to share my memories of the 80's with you... but even I have to admit that I teach Python to my undergrads these days. They need jobs.</p>
<p>The ancient Perl timbers that support JBrowse are showing their age; and that's why we've been adding more and more features that allow the JBrowse client to leave its BioPerl exoskeleton behind. Most of that exoskeleton is oriented toward slurping data out of object relational databases like <a href="http://gmod.org/wiki/Chado_-_Getting_Started">Chado</a>, or from flatfiles, so as to generate JBrowse-specific JSON-based index files (using <a href="http://www.ncbi.nlm.nih.gov/pubmed/17234640">Nested Containment Lists</a>) that allow the client to do fast range queries on feature sets.</p>
<p>Fans of Chado need not worry: the JBrowse distribution will keep that functionality around, but the Perl part is less fundamental: the JavaScript client can load many file formats natively now, and can make use of other (more standard) indices, like <a href="http://www.htslib.org/doc/tabix.html">tabix</a> and <a href="http://www.htslib.org/doc/samtools.html">faidx</a> in SAMTools.</p>
<p>A direct benefit of this is that it's possible to use JBrowse like a desktop browser, opening local files directly; either by firing up a web browser and pointing it at a JBrowse instance, or by using the new <a href="http://jbrowse.org/jbrowse-1-12-0/">desktop version</a> of JBrowse (built using <a href="http://electron.atom.io/">Electron</a>). The reduced dependency on JBrowse-specific indexing scripts also makes it conceptually a little simpler to feed data to a JBrowse instance from a server.</p>
<h3><a class="anchor" aria-hidden="true" id="repos-man"></a><a href="#repos-man" 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>Repos, Man</h3>
<p>Several plugins have been developed for JBrowse and Apollo (indeed, Apollo itself is also a plugin) and there are more on the way, both from our team and from third parties. To help admins find cool plugins, we are developing a plugin repository which will allow developers to register their plugins at jbrowse.org.</p>
<p>We are also close to publishing a registry of publicly accessible JBrowse instances. Over the past year, our analytics suggest that there are at least 2,600 active JBrowse hosts out there. Keeping a central, accessible list of active instances will help model organism databases and other small genome projects become more "discoverable".</p>
<h3><a class="anchor" aria-hidden="true" id="fresh-tracks"></a><a href="#fresh-tracks" 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>Fresh Tracks</h3>
<p>We're constantly adding new kinds of track, and there are several in the pipeline. The latest release has <a href="http://jbrowse.org/jbrowse-1-12-0/">NeatFeatures</a>, which finally brings intron hat cartoons to JBrowse.</p>
<p>Mitch Skinner, the visionary and pragmatist who was the first full-time lead dev of JBrowse, once said that <em>"HTML can draw any shape you want, as long as it's a rectangle"</em>. Well, that may have been true back in the day, but <a href="http://www.w3counter.com/globalstats.php">97% of web users</a> now have Canvas support (and 99.9% of JBrowse users), and we feel comfortable drawing some diagonal lines.</p>
<p>We're also working on SVG-based tracks that remove some of the ancient legacy limitations imposed on track classes, and can play nicely with <a href="https://d3js.org/">d3</a> for some truly cool viz. Watch for new SVG-based tracks for visualizing population-level variation in the near future.</p>
<h3><a class="anchor" aria-hidden="true" id="tips-for-the-server"></a><a href="#tips-for-the-server" 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>Tips for the Server</h3>
<p>JBrowse can be described as a <a href="https://davidwalsh.name/introduction-static-site-generators">static site generator</a>: after running the indexing tools, you don't need to execute any code on the server. Just serve up the indices to the client as static files, and you're set. This has some important benefits, notably for performance (it relieves the processing burden on the server and makes distributed servers much easier) and security (e.g. you can in principle use a super-secure webserver like <a href="https://cr.yp.to/publicfile.html">publicfile</a>). However, it's also limiting for some applications.</p>
<p>There's nothing stopping admins from setting up JBrowse as part of a larger dynamic web application, and there are plenty of hooks in the JavaScript code that allow developers to interface to dynamic code. However, up until this point, a systematic "recommended" way to write dynamic JBrowse apps has been lacking.</p>
<p>That's going to change soon: JBrowse is finally growing a server-side. Although, in keeping with our general philosophy about how to do things on the bioinformatics web, our approach to this will be minimal -- and compatible with a wide range of different back-ends.</p>
<p>We're going to begin with basic infrastructure that most server applications will need: specifically, <a href="https://en.wikipedia.org/wiki/Publish%E2%80%93subscribe_pattern">pub-sub</a> messaging for notifying the client of updates. We then want to build some analysis capabilities into JBrowse -- or, more precisely, hook JBrowse up to existing analysis engines. Everyone's favorite workflow manager <a href="https://usegalaxy.org/">Galaxy</a> will be top of the list. As usual (and this is something we view as a good sign), the community has gotten there before us: <a href="https://github.com/erasche">Eric Rasche</a>, who also built an excellent Docker image for JBrowse, has developed a <a href="https://github.com/galaxyproject/tools-iuc/pull/507">JBrowse Galaxy tool</a>, which we will certainly be hoping to build on.</p>
<p>We recognize that there are other web-based job control shells apart from Galaxy, and some (e.g. <a href="http://www.iplantcollaborative.org/">iPlant</a>) are already working with JBrowse. Our current plan is to write a (thin) abstraction layer that allows JBrowse to talk to Galaxy or other web shells for job control.</p>
<h3><a class="anchor" aria-hidden="true" id="dashes-and-mashes"></a><a href="#dashes-and-mashes" 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>Dashes and Mashes</h3>
<p>We think a big part of the future of JBrowse is in building rich, integrated bioinformatics web apps of which the genome browser is just one component. The kind of thing that used to be called a <a href="https://en.wikipedia.org/wiki/Mashup_%28web_application_hybrid%29">mashup</a> but now (rather more professionally and stylishly) is known as a <a href="https://www.pinterest.com/explore/dashboard-design/">dashboard.</a></p>
<p>OK, technically mashups and dashboards are different: a mashup combines visualizations of multiple data sources, while a dashboard combines multiple controls in a single interface. Bioinformatics web apps, though, typically do both.</p>
<p>Some examples of what one might do with this sort of hybrid:</p>
<ul>
<li>a phylogeography dashboard, combining genome/popgen views with geographical views (e.g. Google Maps)</li>
<li>a systems biology dashboard, combining genome view with gene network/ontology browsers, allowing visualization of RNA-seq experiments at pathway level (e.g. using <a href="http://js.cytoscape.org/">Cytoscape</a>) as well as the reference-aligned reads</li>
<li>a molecular evolution dashboard, with integrated browsing of phylogenetic gene trees and multiple sequence alignments (e.g. using <a href="https://biojs.net">BioJS</a> components), alongside species trees and syntenic relationships between genomes
And so on... now, to be clear, lots of people are dreaming about, or doing, <a href="http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-397">things</a> <a href="http://www.nature.com/nmeth/journal/v11/n9/abs/nmeth.3038.html">like</a> <a href="https://biojsnet.herokuapp.com/">this</a>. We want to make JBrowse play well with those efforts, and with future dashboards/mashups in the same vein. Some critical steps are required.</li>
</ul>
<p>First, on the UI side, JBrowse must play nicely inside a DIV or inside a jQuery element (this is in process), and must be 100% programmatically controllable via the JavaScript API (this is mostly true already).</p>
<p>Second, on the server side, some aspects of the basic infrastructure need to be fleshed out; for example, notifications of changes to the sequence and/or track sets. As noted above, this is very much a part of our plans.</p>
<h3><a class="anchor" aria-hidden="true" id="social-personal"></a><a href="#social-personal" 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>Social, Personal</h3>
<p>Like Mark Zuckerberg, we really just want to connect people. Some of the coolest applications that has been built with JBrowse are the collaborative ones for distributed and/or crowdsourced curation of genome features, like <a href="http://genomearchitect.org/">Apollo</a> and <a href="https://github.com/wurmlab/afra">Afra</a>. We're also very excited to make JBrowse work better with personal genomics sites like <a href="http://myvariant.info/">myvariant.info</a>.</p>
<p>We want to enable more stuff like this, and are offering several <a href="http://gmod.org/wiki/GSOC_Project_Ideas_2016">Google Summer of Code projects</a> this year. At least one of these is social in nature (developing a chat plugin for JBrowse) and another, offered by François Moreews and Thomas Darde, uses Docker to deploy personal JBrowse instances.</p>
<h3><a class="anchor" aria-hidden="true" id="that-s-all-for-now"></a><a href="#that-s-all-for-now" 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>That's All For Now</h3>
<p>Watch this space for more updates!</p>
<p>~Ian</p>
<p><strong>Updated 2/25:</strong> There are a lot of issues still on the GitHub tracker that we plan to get to but I haven't mentioned here. James Gilbert on Twitter <a href="https://twitter.com/jgrgilbert/status/702766473605988352">asked</a> about flipping the view to the reverse strand, which is issue <a href="https://github.com/GMOD/jbrowse/issues/170">#170</a> on GitHub. Rest assured that just because I didn't necessarily mention every last one of them here, that doesn't mean we've forgotten about them. We do still plan to get to those issues and to keep upgrading and refining the UI.</p>
<p><a name="asterisk"></a>* OK, there was the <a href="http://jbrowse.org/jbrowse-1-12-0/" title="JBrowse-1.12.0: Open new genome from FASTA, in-line refseqs, NeatFeatures, Desktop">1.12 release</a>, but you know. A while since we just pontificated for the hell of it.</p>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a 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></h1><p class="post-meta">December 17, 2015</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>We are happy to announce JBrowse 1.12.0 release! This new release includes some exciting new features including the ability to load new genomes from FASTA and indexed FASTA formats; in-line refseqs, and server-free desktop applications for Windows and OSX (based on Electron). New plugins beautifully enhances feature rendering with intron hats and gradients in both HTML and canvas tracks, provide URL links to call up tracks by category URL, among others. Improvements include the ability to load custom histograms for tracks loaded from flatfile-to-json.pl; a new wiggle track option scoreType: 'avgValue', which helps preserve continuity when zooming in on certain tracks like GC-content; and the ability to specify the set of startCodons and stopCodons in the config. In addition, several bugs have been addressed.</p>
<ul>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.0.zip">JBrowse-1.12.0.zip</a> - 4.9M
file SHA1 c74adeb9840ae5c9348e59a9054fa93cf68d0402</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.0-dev.zip">JBrowse-1.12.0-dev.zip</a> - 26M
file SHA1 55c8fa8aa843813ea24a71e1e905c6af80b6db7a</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.0-desktop-osx.zip">JBrowse-1.12.0-desktop-osx.zip</a> - 49M (OSX)
file SHA1 219ae48753c2dc57f341bfed1458ad1f194d3c9f</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.0-desktop-win.zip">JBrowse-1.12.0-desktop-win.zip</a> - 49M (Windows)
file SHA1 4e3d2098cd6b352caac1b0234a290540ba0ff9a1</li>
<li><a href="https://hub.docker.com/r/jbrowse/gmod-jbrowse/">Docker Image</a></li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="new-features"></a><a href="#new-features" 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>New features</h2>
<ul>
<li>Added ability to open a new genome in FASTA format from the browser. Also supports indexed FASTA. Thanks to Bradford Powell for the original indexed FASTA contribution (<a href="https://github.com/gmod/jbrowse/issues/495">issue #495</a>, <a href="https://github.com/gmod/jbrowse/issues/647">issue #647</a>).</li>
<li>Support for inline reference sequence configurations.</li>
<li>Created stand-alone desktop version of JBrowse using the Electron platform for OSX, Windows (<a href="https://github.com/gmod/jbrowse/issues/647">issue #647</a>).</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="new-plugins"></a><a href="#new-plugins" 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>New plugins</h2>
<ul>
<li>NeatHTMLFeatures - Add the drawing of introns and gradient features to HTML tracks.</li>
<li>NeatCanvasFeatures - Add the drawing of introns and gradient features to Canvas tracks.</li>
<li>CategoryUrl - Implements a cat= URL option to display tracks for a given category (<a href="https://github.com/gmod/jbrowse/issues/618">issue #618</a>).</li>
<li>DebugEvents - a plugin to display global publish and milestone events on the debug console.</li>
<li>HideTrackLabels - Adds a toolbar button to toggle the display of track labels on and off (<a href="https://github.com/gmod/jbrowse/issues/614">issue #614</a>).</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" 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>Minor improvements</h2>
<ul>
<li>Added new menu format to support loading your own genome. The open genome option can be hidden via <code>hideGenomeOption</code> in config, and the classic menu style can be restored via <code>classicMenu</code> in config.</li>
<li>Added ability to load custom histograms for tracks loaded from <a href="http://flatfile-to-json.pl/">flatfile-to-json.pl</a> (i.e. override a pre-existing histogram store). See (<a href="https://github.com/gmod/jbrowse/issues/612">issue #612</a>).</li>
<li>Added these options to <a href="http://add-bw-track.pl/">add-bw-track.pl</a> --clip_marker_color , --bg_color , --height (<a href="https://github.com/gmod/jbrowse/issues/510">issue #510</a>).</li>
<li>Added an option for Wiggle tracks, scoreType: 'avgValue', which helps preserve continuity when zooming in on certain tracks like GC-content. It complements the scoreType: 'maxValue' introduced in 1.11.6. Thanks to Han Lin for the pull request (<a href="https://github.com/gmod/jbrowse/issues/504">issue #504</a>).</li>
<li>Clarify track filter box description and feature search box "placeholder" text. (<a href="https://github.com/gmod/jbrowse/issues/611">issue #611</a>)</li>
<li>Implement option to have a separate location box from search box (<a href="https://github.com/gmod/jbrowse/issues/611">issue #611</a>, <a href="https://github.com/gmod/jbrowse/issues/652">issue #652</a>).</li>
<li>Move CSS files into css folder.</li>
<li>Added ability to specify the set of startCodons and stopCodons in the config files. Thanks to Eric Rasche for the contribution (<a href="https://github.com/gmod/jbrowse/issues/657">issue #657</a>)!</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="bug-fixes"></a><a href="#bug-fixes" 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>Bug fixes</h2>
<ul>
<li>Add Travis-CI and jshint linting to build (<a href="https://github.com/gmod/jbrowse/issues/628">issue #628</a>).</li>
<li>Fixed a bug where the BAM popup boxes would display some incorrect info due to byte packing. Thanks to Thomas Downs for contributing the fix.</li>
<li>Fixed a bug where grid lines wouldn't render at some particular zoom levels (<a href="https://github.com/gmod/jbrowse/issues/514">issue #514</a>).</li>
<li>Fixed a bug where the user's --workdir parameter would be deleted which could have unintended side effects if the --workdir was pointing to important data, but this is uncommon (<a href="https://github.com/gmod/jbrowse/issues/563">issue #563</a>).</li>
<li>Allow falsey values to be used in browser.cookie.</li>
<li>Fix minor issue where sometimes the length field of refSeqs.json was missing.</li>
<li>Fix some issues that occurred when a reference sequence was named '0' (<a href="https://github.com/gmod/jbrowse/issues/662">issue #662</a>, <a href="https://github.com/gmod/jbrowse/issues/610">issue #610</a>).</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2015/02/12/jbrowse-1-11-6-index.html">JBrowse-1.11.6 maintenance release</a></h1><p class="post-meta">February 12, 2015</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm pleased to announce JBrowse 1.11.6 is now available! Everybody's feedback, bug reports, pull requests, and feature requests have been invaluable for making this happen. This release includes new UI options for easily setting "Log scale" on wiggle tracks and dynamically changing strandedness on RNA-seq according to multi-segment template flags and splice site (XS) flags. It also includes bug fixes for calculating SNP positions on certain flag combinations in BAM files and for reporting the correct genotypes on certain VCF tracks. Enjoy!</p>
<ul>
<li><a href="http://jbrowse.org/releases/JBrowse-1.11.6.zip">JBrowse-1.11.6.zip</a> - 4.9M
file SHA1 81dd4db6d0dcab261450dab1414e343e106ed6c4</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.11.6-dev.zip">JBrowse-1.11.6-dev.zip</a> - 26M
file SHA1 c6d6ff4f68fa3ae0180bdea9c7871f9a5a4dd1d7</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" aria-hidden="true" class="hash-link"><svg class="hash-l