ABE, A bioassay analysis program written in Python - Summary

This group is not part of the GNU Project.

ABE visualizes and analyzes the data from biossay experiments such as cell proliferation assays, and allows the user to model the experimental data using either polynomials, or a more specific sigmoidal dose-response model.

ABE reads the experimental data in XML format, constructs mathematical models of the data and allows the user to graphically compare the observed and modeled data. A complete record of the analysis is kept in a comprehensive activity log and any generated graphs can be saved in PostScript (TM) format, allowing the user to include detailed and accurate records of the analysis as part of his/her laboratory notes.

Since many excellent data-graphing packages already exist, the graph options in ABE were deliberately kept to a minimum to keep the code simple and to focus on the mathematical part of the analysis.ABE does however allow the user to export a data table containing a summary of the analysis into programs such as Microsoft Excel (TM) for further analysis, visualization and archiving.

ABE is written in Python 2.2 and uses the Tkinter graphic library to generate a friendly graphical user interface (GUI) for manipulating and visualizing the data. As a result, the program should be capable of being run on any platform with a standard Python 2.2 (or higher distribution.

For the data modeling, ABE uses the nonlinear regression routines from the Scientific Python (SciPy) and Numeric libraries as well as the polyfit function from Raymond Hettingers Matfunc module (Public Domain), for computing the fitted polynomial coefficients from the supplied data. Functions for computing the derivatives of the fitted polynomials, solving polynomial roots and estimating the initial parameters for the nonlinear regression were added by the author and are included in the body of the main Abe module. In addition to the libraries of the standard Python distribution therefore, only the SciPy, Numeric and Matfunc modules need to be included in the Python path for ABE to be run.

Registration Date: Fri 10 Jan 2003 02:46:13 PM UTC
License: GNU General Public License v2 or later
Development Status: 3 - Alpha