Journal Article

Accessible methods for the dynamic time-scale decomposition of biochemical systems

Irina Surovtsova, Natalia Simus, Thomas Lorenz, Artjom König, Sven Sahle and Ursula Kummer

in Bioinformatics

Volume 25, issue 21, pages 2816-2823
Published in print November 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp451
Accessible methods for the dynamic time-scale decomposition of biochemical systems

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Motivation: The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the system without any heuristics employed. Important for the success of such an approach is its accessibility and the clarity of the presentation of the results.

Results: In order to achieve this goal, we developed a method which is a modification of the classical approach of time-scale separation. This modified method as well as the more classical approach have been implemented for time-dependent application within the widely used software COPASI. The implementation includes different possibilities for the representation of the results including 3D-visualization.

Availability: The methods are included in COPASI which is free for academic use and available at www.copasi.org.

Contact: irina.surovtsova@bioquant.uni-heidelberg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5701 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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