MIDER

Description

MIDER (Mutual Information Distance and Entropy Reduction) is a general purpose software tool for inferring network structures. It has been developed with biological networks in mind, but can be applied in other areas.

MIDER calculates distances among variables using an entropic measure based on mutual information, which takes into account time delays. For this purpose the user can choose between several definitions and normalizations of mutual information.

Implementation and Requirements

MIDER runs under Matlab or Octave. The only requisite for its use is that some versión of Matlab or Octave is installed in the user's system. It is self-contained: it has no dependencies with external software.

MIDER runs on Windows, Linux and OSX.

Documentation

A manual is available here.

Contact

MIDER is maintained by Alejandro F. Villaverde (BioProcess Engineering Group, IIM-CSIC). Email: afvillaverde [at] iim.csic.es Web: https://sites.google.com/site/alexfvillaverde/

Publications

Please cite this paper if you use MIDER in a publication:

[1] Villaverde, A., Ross, J., Morán, F., and Banga, J.R. (2014). MIDER: network inference with mutual information distance and entropy reduction. PloS ONE 9(5):e96732 (article)

MIDER's data preprocessing capabilities are described in:

[2] Folch-Fortuny, A., Villaverde, A.F., Ferrer, A., and Banga, J.R. "Enabling network inference methods to handle missing data and outliers". BMC Bioinformatics 16(1), 283 (article).