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Bioinformatics Advance Access published online on June 16, 2006
Bioinformatics, 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
Received April 11, 2006
Revised June 5, 2006
Accepted June 7, 2006

Applications note

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

C. Spieth 1 *, J. Supper 1, F. Streichert 1, N. Speer 1, and A. Zell 1

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

* To whom correspondence should be addressed.
C. Spieth, E-mail: christian.spieth{at}uni-tuebingen.de


  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. Due 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.

Associate Editor: Chris Stoeckert
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