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).

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

Date

Source Code*

OSX Binary

MS Windows Binary

Comments

28 May, 2009

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.

ea44691e5430e2817035a80256183de2
a7efd0ca5e4e276f1c8f10de8bddf971
2b5ad965eca8f2f3d4da9bfb6c2be597

30 April, 2009

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.

9d3207143829b2daffab06c20b001525
e93129d9fd385c5ce0b8e3b387c8473c
1b9e883e618bad62f39f92eb33ec01aa

12 March, 2009

Get it

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.

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.