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Bioinformatics Advance Access originally published online on June 16, 2006
Bioinformatics 2006 22(16):2051-2052; doi:10.1093/bioinformatics/btl322
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

JCell—a Java-based framework for inferring regulatory networks from time series data

C. Spieth *, J. Supper , F. Streichert , N. Speer and A. Zell

Centre for Bioinformatics Tübingen (ZBIT), University of Tübingen Sand 1, 72076 Tübingen, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: JCell is a Java-based application for reconstructing gene regulatory networks from experimental data. The framework provides several algorithms to identify genetic and metabolic dependencies based on experimental data conjoint with mathematical models to describe and simulate regulatory systems. Owing to the modular structure, researchers can easily implement new methods. JCell is a pure Java application with additional scripting capabilities and thus widely usable, e.g. on parallel or cluster computers.

Availability: The software is freely available for download at http://www-ra.informatik.uni-tuebingen.de/software/JCell

Contact: christian.spieth{at}uni-tuebingen.de

Associate Editor: Chris Stoeckert

Received on April 11, 2006; revised on June 5, 2006; accepted on June 7, 2006

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