JBrowse in Google Summer of Code 2012

Great news!  JBrowse has been accepted to Google Summer of Code 2012 under the Genome Informatics umbrella organization.  Many thanks to Reactome’s Robin Haw for shepherding the Genome Informatics organization through the application process!

Are you a college undergraduate interested in working on JBrowse this summer?  You should consider applying to Google Summer of Code to fund you for the summer!  The student application deadline is April 6, 2012.

Relevant links

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New JBrowse Lead Developer

We’re excited to report that Robert Buels has joined the JBrowse team as lead developer, effective January 10, 2012. He succeeds Mitch Skinner, who created JBrowse in its modern form and more recently been working with the JBrowse “sister project”, WebApollo.

Rob has been active in open-source bioinformatics for many years, contributing to a long list of projects such as GBrowse, BioPerl, Chado, Bio::Chado::Schema, Catalyst, and DBIx::Class. Before joining JBrowse, Rob was employed as Engineering Lead at the Sol Genomics Network, a clade-oriented database for plants centered on the Solanaceae family.

As JBrowse lead developer, Rob is responsible for the project’s technical strategy, architecture, planning, and coordination, as well as a large part of the implementation. In the coming months, he intends to focus on helping JBrowse mature as a project: solidifying its development infrastructure and incorporating new features and contributions from developers around the world.

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“DNA sequencing on your iPhone? There’s an app for that”

Courtesy of Dave Clements: JBrowse appears (and gets a laugh, for some reason) at 8:41 in this TED talk (“Welcome to the genomic revolution” by Richard Resnick).

In other news, we are happy to report that JBrowse has had its R01 funding support from NHGRI renewed for three years. This enables a whole lot of exciting stuff. We will post further developments here in the coming weeks.

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JBrowse conference call

The first JBrowse developers’ conference call will be held on Monday Sept 19 at 2pm Pacific time. We intend for this to be a monthly event. Call details are below; we hope you will join in.

The main agenda topics for this first call will be:

  1. Introductions; quick survey of projects built on, or with, JBrowse
  2. JBrowse funding situation
  3. JBrowse software developments
  4. JBrowse and Web-Apollo
  5. Any other business

Please email Ian if there is anything you’d like to have on the agenda.

Call details:

  • Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
  • Enter access code 4867508#
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Summer 2011 update

Over the summer the JBrowse project has been very capably assisted by two student interns. In Toronto, Natalie Fox has been working on extending the JBrowse user interface and feature set, while in Berkeley, Stephen Cummings has been documenting the existing server-side API. You can track their efforts via the links above, which lead to the GMOD wiki (the new home of JBrowse documentation).

The debt ceiling and budget kerfuffles seem to have delayed things in Bethesda somewhat, with the ripple effect of delaying our process of hiring someone to fill the JBrowse lead developer position, but we hope that will all be resolved soon (watch this space). In the meantime, check out the progress that Natalie has made with faceted browsing and hierarchical track organization — it is really exciting, and in fact seems quite obviously crucial, as genome databases naturally progress to having hundreds and even thousands of experimental annotation tracks.

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JBrowse is hiring!

The lead developer on the JBrowse team is moving on to pastures new: Mitch Skinner has accepted an offer to work at an exciting new medical genomics startup (which will, for the moment, remain nameless, but keep an eye out for their launch sometime in the next year).

Mitch hopes to continue contributing to JBrowse, but this also leaves an open position in the core team. Accordingly, we are now hiring.

Full details of the position can be found at http://biowiki.org/JBrowseJob.

Update: the position has been filled.  Many thanks to all the applicants!

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JBrowse 1.2.1 released

JBrowse 1.2.1 is a maintenance release that fixes some bugs that were reported in 1.2.  Get it here:

http://jbrowse.org/releases/jbrowse-1.2.1.zip

Release Notes:

version 1.2.1, March 2011

Fixed bugs in release 1.2:

  • problems with BED handling reported by Gregg Helt and Brenton Graveley
  • performance regression reported by Chris Childers
  • incorrect handling of names in ucsc-to-json.pl
  • wig2png slowdown reported by Brenton Graveley
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JBrowse 1.2 released

New JBrowse release!  This is version 1.2, which makes the server-side scripts much more scalable, includes a script for importing UCSC database dumps into JBrowse, and integrates Juan Aguilar’s touch code for the iPad/iPhone.  Code is here:

http://jbrowse.org/releases/jbrowse-1.2.zip

Release Notes:

version 1.2, Febrary 2011

These notes document changes since release 1.1 in September 2010.
(Release Notes for 1.1 are here.)

Most of the work in this release went into making JBrowse handle large
amounts of feature data
better.  Before, the amount of memory used
when processing BAM files was more than 10 times the size of the file;
now, the amount of memory required is fixed.

Other new features in this release:

  • Import of UCSC database dumps. A ucsc-to-json.pl script is now provided for taking database dumps from UCSC and creating a JBrowse instance using them.  The “genePred” and “bed” track types are currently supported; “psl” tracks are not yet supported.
  • Touch. Juan Aguilar’s code for using JBrowse on an iOS device (iPhone, iPod touch, iPad) is now integrated.  As of the current release, users wanting to use JBrowse on those devices have to navigate to a separate HTML page (touch.html) rather than the default index.html; i.e. the code does not currently detect touchscreen devices automatically.
  • Bug fixes. A number of bugs have also been fixed, including one that restricted the placement of the “data” directory, and a bug in wiggle rendering that caused spurious peaks or troughs at tile boundaries.

Known issues/limitations with this release:

  • Some additional CPAN modules are now required:

PerlIO::gzip
Heap::Simple
Devel::Size

  • 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. We apologize for the inconvenience of this, but it is inevitable sometimes; we do aim to minimize the number of releases which are backwardly-incompatible in this way.
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Touch the genome

Thanks to some great work by Juan Aguilar, JBrowse now runs on the iPad. Working with Lincoln Stein, Juan hooked up JBrowse to the iOS JavaScript touch/gesture callbacks.

The result is very cool indeed. Click here to see it in action (um, using an iPad, naturally; if you have an iPhone, it will still work, but the screen is a bit small to do anything meaningful).

Alternatively, you can watch it here:

This code should (fingers crossed) make it into the next release. It’s still “alpha” at the moment, but several people have asked for JBrowse on the iPad, and we do hate to disappoint.

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hg19 tarball updated

Chris Tandiono reported a bug in the hg19 tarball, and supplied a script to fix the problem.  The tarball has now been updated with the fix; you can download the new version here:

http://jbrowse.org/releases/hg19mini-2.tar.gz

The bug prevented name/id searching from working; with the fixed tarball, searches work again.

Update: a newer hg19 tarball has been released, you should use that one.

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