Berkeley Drosophila Transcription Network Project

Berkeley Quantitative Genome Browser

Synopsis

Here one can find very early releases of the Berkeley Quantitative Genome Browser, sometimes known as "BBrowse", "BBrowser", "BQGB", "BQB" or just "BBQ".

BQGB duplicates much of the annotation display functionality typical of a genome browser but with an additional emphasis on quantitative data. The expectation is that the data is local to the application process and in one of the following file formats: GFF, SGR, FASTA or any column delimited format that provides sequence and base pair position locations.

Once data has been loaded into BQGB, it may be searched and filtered. The development goal is to also support a rich selection of mathematical transformations, graphical manipulation, visualization options and plug-in support for the addition of more complicated or esoteric tools than supported by the core functionality.

BQGB runs on Linux, OSX and MS Windows. Development is done on a Linux platform. It is written in C++ using g++ version 4.2.x and Gnu C/C++ libraries. Additionally, it makes extensive use of Trolltech's Qt version 4.3 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 Trolltech's website.

The code releases are simply organized by date. The current release is "bleeding edge", ie. a few 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. I try to make releases every two to four weeks, but admittedly, I'm not always successful in maintaining this rate.

Documentation

Looking for more information? A newly started online User Manual may be able to help. Also, please check the Helpful Hints Page-- at least I hope it's helpful! Legal stuff, like copyright and license, can be found with the source/applications downloads or on the License page. Otherwise, please feel free to send questions, bug reports and suggestions (contact info in download).

Download

Date Source Code OSX Binary MS Windows Binary Comments
30 October, 2008 Get it Get it Get it

This release focuses on bug fixes, a valuable feature in itself of course!

  • Fixed: Relations not getting seqeunce focus upon sequence focus changes
  • Fixed: Incorrect chromosome sequence showing when toggling between files with completely different sequence names (eg. fly and yeast) when both file types are open
  • Change: Hide/show sequence/files is now broken out into "hide" and "show", ie. two separate options to simplify expected results from the action... in otherwords, to stop some sequence from showing while others are hiding
  • Change: The seqeunce tracker tree now requires use of control (CTRL) key when selecting multiple sequences
  • Fixed: yet another strategy for clearing out the "spent readers" stack (back-end stuff... but previously a possible cause of crash in some rare configurations like when rapidly opening and closing files simultaneously)
  • Fixed: Crashes caused by toggling between Exon-Intron-Gene Notation and other graph types like Data Density
    MD5 checksums (source, mac, win32 downloads)
  • 0c0a097546e935ce61526fb43f87c22a
  • 57bde72c72f34ba43155637dd9e0f027
  • 187b1c4a8c84d2603ca47baa45448e8a
21 October, 2008 N/A N/A N/A

Sorry... I pulled this version after finding an annoying, recently introduced bug causing incorrect sequence to be displayed when mixing/matching relations. This one was a little too big to let fester; the bug is fixed and I'll make a new release in the next week with several additional improvements. Please see previous release instead or wait for next release last week of October.

Reference annotation display has been largely revamped. The default display will show gene (or similar) along with some user set relations such as exon or coding sequence along with an option to view alternate transcripts. The options are set in the Preferences and are currently tailored for GFF files containing ID/Parent sort of relationships within their attribute fields. This work introduced a more general mechanism to define 1:m relationships between data, which again, can be used at runtime for some gff files or extended within the application code as implementation rules become available and need dictates. Other changes include:

  • Support for FASTA sequence data appended to GFF files
  • Per the above change, file names are now associated more closely with their file type, because the file type now gives less indication of the type of data that might be contained therein
  • A number of changes to the threading mechanism, which from the user's point-of-view, affects changing reference files mid-read; hopefully, a better design overall
  • Arrow keys now control graph pan and zoom; shift + up/down arrow keys controls graph stack ordering of selected graphs
    MD5 checksums (source, mac, win32 downloads)
  • 2fa35d522edf513c8aafd860ebd03be2
  • 07bff21fbe26ecda73cfa73bb7b4492d
  • 82d9c9d9202655999d68dd85a40bf7f3
29 August, 2008 Get it Get it Get it

A bunch of small but important changes since last week:

  • Tool widgets are now forced to appear as tabs, though they are still allowed to float as well
  • Search functionality now defaults to search all available features... users may still specify features to limit the search scope
  • An annoying bug causing crashes (sometimes) when opening multiple files simultaneously has (hopefully) been corrected... this gnat seemed to involve both threads and signals, making it hard to track down; that it also seemed to involve a race condition means the test cases are pretty data specific. so, it seems fixed deductively and empirically, but could still be lurking!
  • A bug causing incorrect sequence data to show *after* focus changes has been corrected (sequence data with default focus immediately after opening a file showed fine)
  • Bug where program entered endless loop when failing to find a search term has been elimininated
    MD5 checksums (source, mac, win32 downloads)
  • 546e18639a1b56423da01b191170de62
  • 454ee13fef8cd1dd4bbbabe133d75011
  • 0aeb31926d0a2e8b667c66332f9aa066


Screenshot