[Savannah-hackers] Re: submission of ABE, A bioassay analysis program written in Python - savannah.gnu.org

[Mathieu Roy]

Hi,

I'm evaluating the project you submitted for approval in Savannah.

address@hidden said:

> A package was submitted to savannah.gnu.org
> This mail was sent to address@hidden, address@hidden
> 
> Gordon Webster <address@hidden> described the package as follows:
> License: gpl
> Other License: 
> Package: ABE, A bioassay analysis program written in Python
> System name: abe
> Type: GNU
> 
> Description:
> ABE Version 1.0 (stable), released today on sourceforge.net, is the first 
> public release of ABE, a bioassay analysis program for cell biologists and 
> molecular biologists working in biotechnology companies or academic 
> laboratories. 
> 
> The ABE source code and docs are available at:
> http://sourceforge.net/projects/abe-module

In order to release your project under the GPL you
should write copyright notices and copying permission
statements at the beginning of every source-code file, and
include a copy of the plain text version of the GPL
(http://www.gnu.org/licenses/gpl.txt). Copy it for instance
into a file named COPYING.

Please follow the advice of http://www.gnu.org/licenses/gpl-howto.html

The GPL FAQ can also help you understand the reason behind
thoses recommendations. For example, there is an entry explaining
why the GPL requires including a copy of the GPL with
every copy of the program:
 http://www.gnu.org/licenses/gpl-faq.html#WhyMustIInclude


> 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 Hettinger\'s 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. 
> 
> Using the \'py2exe\' extension of the Python \'distutils\' library, 
> convenient, pre-compiled and standalone ABE executables can be generated, 
> that can be run without a Python installation.
> 
> Other Software Required:
> To work with the source code, a user of ABE would require the following 
> Python distributions/packages (all freely available):
> 
> Python 2.2 or higher
> The Numeric Python package (http://www.pfdubois.com/numpy/)
> The Scientific Python package (http://www.scipy.org)
> Raymond Hettinger\'s \'Matfunc\' Python module (address@hidden)

Please register your project once more with the changes mentioned
above. The way we handle pending projects makes it difficult to keep
track of projects that have been answered but have not been approved
yet, so we erase them and we ask you to register the project again every
time some change has to be done to the registration, and users might
have to register their projects several times. Thank you for your
understanding.

Some users find it useful to use the big re-registration URL provided in
the acknowledgment e-mail you received after registration.

Regards,


-- 
Mathieu Roy
 
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