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.
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.
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.
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.
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.
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.
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:
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:
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.