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Bioinformatics Advance Access originally published online on July 24, 2009
Bioinformatics 2009 25(21):2816-2823; doi:10.1093/bioinformatics/btp451
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Irina Surovtsova 1,*, Natalia Simus 1, Thomas Lorenz 2, Artjom König 1, Sven Sahle 1 and Ursula Kummer 1

1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany

* To whom correspondence should be addressed.


  Abstract

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{at}bioquant.uni-heidelberg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Trey Ideker

Received on December 11, 2008; revised on May 22, 2009; accepted on June 29, 2009

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