WellInverter

WellInverter is a web application developed in the Ibis group. It implements linear inversion methods for the reconstruction of gene expression profiles from fluorescent or luminescent reporter gene data.

As input, WellInverter reads the primary data file produced by a multi-well microplate reader, containing time-series measurements of the absorbance (optical density) as well as the fluorescence and luminescence levels in each well (if available). Various modules exist to analyze the data, in particular for detecting outliers, subtracting background, estimating growth rates, promoter activities and protein concentrations, visualizing expression profiles, computing statistics on replicate profiles, etc.

Hidde de Jong

Screenshot of WellInverter

WellInverter architecture

The server part of WellInverter is based on the Python library WellFARE, the computational core of the application. It also provides methods for managing experimental and user data as well as storing analysis results in JavaScript Object Notation (JSON) format.

The client part of WellInverter is the graphical user interface of the application, working in a web browser. It allows the user to upload, analyze, and visualize the results of a reporter gene experiment as well as downloading the results for further treatment. The client part is written in Javascript, and communicates with the server using Ajax (Asynchronous JavaScript and XML) calls.

WellInverter uses a plug-in system for defining high-level routines for parsing different types of primary data files. Parsers for Tecan and Perkin-Elmer microplate readers are currently available.

Access to WellInverter

A demo version of WellInverter can be accessed at the following address :

https://wellinverter.inrialpes.fr

WellInverter is accessible through the cloud of the French Institute for Bioinformatics (IFB). An account for the IFB cloud can be created at the following adress:

https://cloud.france-bioinformatique.fr/accounts/register/

Please contact Hidde de Jong for obtaining a stand-alone version of the software.

More information on how to use WellInverter can be found in the tutorial.

The Python library WellFARE, implementing the linear inversion methods on which WellInverter is based, is separately available under an LGPL license at the following address :

https://github.com/ibis-inria/wellfare

Developers of WellInverter

WellInverter has been developed by Yannick Martin, Michel Page, Valentin Zulkower, and Hidde de Jong, with help from Johannes Geiselmann and Delphine Ropers. The development of the application has been supported by the French Institute for Bioinformatics (IFB).

Reference

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