Berkeley Drosophila Transcription Network Project


Berkeley Quantitative Genome Browser

Synopsis

Here one can find early releases of the Berkeley Quantitative Genome Browser, sometimes known as "bbrowse", "bbrowser" or "BQGB".

BQGB duplicates much of the annotation display functionality typical of a genome browser but with an emphasis on custom and quantitative data such as that produced in high throughput sequencing and genome-wide association studies. The application runs locally on a user's desktop or laptop computer, avoiding the slow back-and-forth of web based genome browsers. BQGB expects data files to be local to the application process and in a file format such as GFF, BED, SGR, WIG, FASTA or any column delimited format that provides sequence and base pair position locations. This topography should generally be faster than that of a central remote database plus web based browser when working with many custom files, ie. downloading a single reference annotation to one's local machine is quicker than uploading hundreds of custom data files to a remote server!

Browsing needs are varied and no one visualization tool should be expected to provide insight into the diverse phenomena of molecular genetics, from highly localized SNPs, to near and far cis-regulatory elements, to distant trans relationships that may even span highly diverged species. Beyond the visualizations packaged with BQGB, the application provides an open-source API intended to ease the on-going development work that addresses the evolving visualization and exploration needs of molecular genetic inquiry.

BQGB runs on Linux, OSX and MS Windows. Development is done on a Linux platform. It is written in C++ using the GCC compiler and libraries. Additionally, BQGB makes extensive use of Nokia's Qt libraries (formerly Trolltech's Qt libraries). OSX and MS Window's users who choose to use the pre-compiled binaries provided below should not need to install Qt. However, one must have Qt installed to compile BQGB. The open source version of Qt can be obtained from Nokia's website.

The code releases are simply organized by date. The current release is "bleeding edge", ie. sometimes widgets visible in the GUI are not yet connected to functions and known and still unknown bugs certainly exist. All the same, the development process is iterative and every release is meant to be honest, ie. nothing is posted with known errors in data representation.


Documentation

Looking for more information?

Otherwise, please feel free to send questions, bug reports and suggestions (contact info in download).

Here's a screenshot of a recent release.


Download

Date Source Code* OSX Binary MS Windows Binary Comments
28 May, 2009 Get it Get it Get it
  • updated GCC and Qt libraries
  • added support for WIG format

The Mac univerals build was done using Qt 4.5 and gcc 4.0.1. The Win32 build used Qt 4.4.3 and gcc 4.3.2. This may cause some problems. Best bet is almost always to build from source code using the libraries listed at the bottom of this page.

    MD5 checksums (source, mac, win32 downloads)
  • ea44691e5430e2817035a80256183de2
  • a7efd0ca5e4e276f1c8f10de8bddf971
  • 2b5ad965eca8f2f3d4da9bfb6c2be597
30 April, 2009 Get it Get it Get it

The Bar and Line graph type- which shows alt transcripts, exons, CDS and similar types of relationships for GFF files- is back up. While the type displays as a single track, the strands occupy separate tiers in the track (unlike other graph types where strands have their own tracks).

A new graph type, Sequence, provides sequence, if available, when zoomed-in adequately. To slightly more distant zooms, the Sequence graph type can also provide either per word GC content or per word % purines; at still further zoom-out, nothing is shown. Word lengths and display options are controlled, as with other graphs, via the Track Appearance tool. Double click to activate a track for modification.

Fixed several bugs related to keyboard focus. Reminder, a selected graph (highlighted by a double mouse click), can be vertically stretched/compressed or restacked via the +/- and shift + up/down arrow keys respectively and panned or zoomed with the arrow keys. The graphs must have keyboard focus however.

    MD5 checksums (source, mac, win32 downloads)
  • 9d3207143829b2daffab06c20b001525
  • e93129d9fd385c5ce0b8e3b387c8473c
  • 1b9e883e618bad62f39f92eb33ec01aa
12 March, 2009 Get it N/A N/A

File preferences have undergone considerable change most noticeable in the Preferences dialog window. The idea of "Reference Annotation" and "Reference Sequence" are gone. In its place, one can set preferences for any file the may be using. With this release, not all shown in that dialog is working (next release hopefully); below is a list of new features and which are working:

  • Select files for which to set preferences that will be saved between application executions (in preference's xml file) -- working
  • Set file to be automatically opened when browser starts-up -- working
  • Set a list of filter terms by which to limit a file read, ie. if the file contains "gene", "exon" and "CDS" and one only wants to view "CDS" then one can limit the read into memory of only "CDS"; bear in mind that with really large files every record still needs to be examined as to whether it's in or out... so pre-filtering (with grep, awk, etc...) regularly used files is still faster -- working
  • Set a default graph type for the file -- not working yet
  • Set record relationships -- not working yet

The old Bar-and-line graphs are temporarily disabled since the record relationship functionality is currently being transititioned. Finally, the thread/file closing related crash causing bug still seems to be around. One may never see it, but if one cycles open and closes of the same file quickly, it'll probably rear its annoying head, beware.

    MD5 checksums (source, mac, win32 downloads)
  • 5483ab9ec65809fde6dc9da74605d0ef

* Builds are currently using the following library versions:

Library Version Start Date
Qt 4.5 1 May 2009
GCC (g++/glibc) 4.4.0 1 May 2009

If one chooses to build from source code, it's recommended that the required libraries match those above or earlier. Qt, particularly, seems behaviorly sensitive to release number.