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.
A full fledge user manual and developers guide is forthcoming. For now, there is the Helpful Hints Page-- at least I hope it's helpful! Otherwise, please feel free to send questions, bug reports and suggestions (contact info in download). Legal stuff, like copyright and license, can be found with the source/applications downloads or on the License page.
| Date | Source Code | OSX Binary | MS Windows Binary | Comments |
|---|---|---|---|---|
| 21 August, 2008 | Get it | Get it | Get it |
This release includes a new graph type, data density. Data density is a sort of histogram showing how much data falls in a given stretch of base pairs by way of opacity (heat map). More generally, with the addition of the data density graph type, a much more general way of handling graphs has been modeled. Users may now toggle between graph types for a given data set and developers may add graph specific controls to the tool windows. The framework for adding new visualizations has been improved via a GraphFactory class. Additionally, bqgb now has better warnings when encountering unparsable data during file reads. This accompanied code improvements to the reading thread mechanisms.
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| 21 July, 2008 | Get it | Get it | Get it |
This release focuses on feature info. This includes the addition of an info tool window where, when applicable, a feature's attributes and, if sequence data is available, sequence may be viewed by left clicking on the feature. When multiple features overlap in a given track, meta-data for all pertinent features should be displayed. A separate tab in the info window shows file information such as comments where file type and API allow. The bulk of the work here involved adding support for sequence data stored in fasta files (particularly some flybase releases). This should act as a nascient API for future work with such data.
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| 19 June, 2008 | Get it | Get it | Get it |
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