Something we get asked for a lot is data releases: tarballs of JBrowse JSON pre-generated from widely-used datasets, ready for you to plonk on your webserver, unzip, and serve to the world (perhaps after adding your own tracks, or making other modifications).
Data releases are good because they make it even easier to deploy JBrowse on your website, while illustrating what we consider best practices in using the JBrowse setup scripts.
Doing this right takes time, but it didn’t seem fair in the meantime to deprive people of the JSON files we’ve generated to run our demos. Particularly the human genome demo — there have been several requests for the data files underpinning that.
So, without further ado, here is a tarball of the UCSC hg19 annotation tracks. At least, some of them: we’ve tried to keep this tarball small. It’s 62 megabytes compressed; 330 megabytes uncompressed; it has the smallest 27 annotation tracks, and in order to keep the size down, we didn’t include actual sequence (just the locations of features like genes).
This demo should not be considered a final-quality data release. Some things aren’t set up as nicely as we’d like; for example, the outgoing links from features. However, if you’re interested in exploring using JBrowse for human applications (e.g. like genomesunzipped), this might help get you started.
(Update 2010/11/23: a bug in the tarball has been fixed; the link above now points to the fixed version)
(Update 2012/3/22: updated again to point to hg19mini on JBrowse 1.2.1)
The folks over at genomesunzipped.org are trying an interesting experiment in personal genomics. A group of experts in fields related to personal genomics are analysing their own genomes (via 23andMe) and making all the results available online. Naturally they chose JBrowse as their genome browser 🙂
It will be very interesting to see how this experiment in transparency plays out, and what kinds of discussion it provokes. More here.
Update (9/24/2010): The jbrowse.org site has now been moved to the Amazon EC2 cloud. Most links and demos are back online, but some are still broken (the human genome demo is missing the large tracks (BAM, SNPs) and the Release 1.1 tarball is missing). Restorative maintenance is ongoing…
JBrowse release notes, version 1.1, September 2010.
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).
New features in this release:
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.
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.
Bug fixes. Numerous display glitches have been fixed, including issues with wide-screen monitors and long mostly-offscreen features.
Known issues/limitations with this release:
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.
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.
Processing SAM/BAM next-gen sequence files takes a lot of memory (about 500 megabytes per million features).
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.