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Bioinformatics Advance Access originally published online on May 26, 2006
Bioinformatics 2006 22(15):1930-1931; doi:10.1093/bioinformatics/btl267
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Metatool 5.0: fast and flexible elementary modes analysis

Axel von Kamp * and Stefan Schuster

Department of Bioinformatics, Friedrich-Schiller-University Jena 07743 Jena, Germany

*To whom correspondence should be addressed.

Summary: Elementary modes analysis is a powerful tool in the constraint-based modeling of metabolic networks. In recent years, new approaches to calculating elementary modes in biochemical reaction networks have been developed. As a consequence, the program Metatool, which is one of the first programs dedicated to this purpose, has been reimplemented in order to make use of these new approaches. The performance of Metatool has been significantly increased and the new version 5.0 can now be run inside the GNU octave or Matlab environments to allow more flexible usage and integration with other tools.

Availability: The script files and compiled shared libraries can be downloaded from the Metatool website at http://pinguin.biologie.uni-jena.de/bioinformatik/networks/index.html. Metatool consists of script files (m-files) for GNU octave as well as Matlab and shared libraries. The scripts are licensed under the GNU Public License and the use of the shared libraries is free for academic users and testing purposes. Commercial use of Metatool requires a special contract.

Contact: kamp{at}minet.uni-jena.de

Received on January 15, 2006; revised on May 16, 2006; accepted on May 18, 2006

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