Section: New Software and Platforms

WellReader, WellFARE, and WellInverter

Participants : Johannes Geiselmann, Hidde de Jong [Correspondent] , Michel Page, Delphine Ropers, Valentin Zulkower.

Keywords. Gene expression, reporter gene data

WellReader is a program for the analysis of gene expression data obtained by means of fluorescent and luminescent reporter genes. Wellreader reads data files in an XML format or in a format produced by microplate readers, and allows the user to detect outliers, perform background corrections and spline fits, compute promoter activities and protein concentrations, and compare expression profiles across different conditions. WellReader has been written in MATLAB and is available under an LGPL licence, both as source code (M files) and compiled code (platform-specific binary files). For more information, see: http://ibis.inrialpes.fr/article957.html .

In the past year, we developed novel approaches towards the analysis of reporter gene data, based on regularized linear inversion (Section  6.3 ). The linear inversion methods were implemented in the Python package WellFARE , relying on the scientific Python libraries NumPy and SciPy. In addition, the package provides utilities for parsing data files and removing possible outliers from the absorbance and fluorescence signals. The WellFARE package is available under an LGPL license, but has also been integrated into a web application called WellInverter , which provides a graphical user interface allowing access to the linear inversion methods through a web browser (Figure 5). The user can upload data files by means of WellInverter , remove outliers and subtract background, and launch the procedures for computing growth rates, promoter activities, and protein concentrations. For more information, see: http://ibis.inrialpes.fr/article1080.html?menu=menu4 .