JBrowse 1

JBrowse is hiring!

April 6, 2011

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 https://biowiki.org/JBrowseJob.

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

JBrowse 1.2.1 released

March 17, 2011

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

https://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

JBrowse 1.2 released

February 17, 2011

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:

https://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.

Touch the genome

December 18, 2010

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.

hg19 tarball updated

November 24, 2010

JBrowse tarball for hg19 human genome data

November 11, 2010

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)

Personal genomics website using JBrowse

October 11, 2010

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.

JBrowse website moved to Amazon cloud

October 11, 2010

The jbrowse.org website is now hosted by Amazon Web Services. The human genome demo has been regenerated using a new UCSC-to-JBrowse adaptor.

JBrowse 1.1 release

September 9, 2010

JBrowse version 1.1 is released! You can find the code here:

https://jbrowse.org/releases/jbrowse-1.1.zip

Release notes and screenshots below the fold.

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.
← Prev