WellInverter

WellInverter is a web application implementing 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.

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

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 JSON-encoded data and Ajax (Asynchronous JavaScript) calls.

WellInverter uses a plug-in system for defining high-level routines for parsing data files produced by microplate readers from different manufacturers. Parsers for Tecan and Perkin-Elmer microplate readers are currently available.

Access to WellInverter

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

https://wellinverter.inrialpes.fr

The demo version does not allow the user to upload his/her own data sets. However, sample data is supplied: two primary data sets of E. coli fluorescent reporter gene experiments, as well as a completely treated version of one of these data sets.

WellInverter IFB. WellInverter is also accessible through the cloud of the French Institute for Bioinformatics (IFB). The user needs an IFB account that can be created at the following adress:

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

The IFB account allows the user to save and manage data sets from different experiments.

WellInverter Inria. WellInverter is also deployed on an Inria server:

http://ibis-public.inrialpes.fr:8000/

Contrary to the IFB version, no user registration is needed. The absence of a user account, however, does not allow treated data files to be stored on the server and the user needs to download and locally save the analysis results before the end of the session.

WellInverter stand-alone. In order to obtain a stand-alone version of the software, please contact Hidde de Jong.

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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