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Bioinformatics Advance Access originally published online on November 29, 2005
Bioinformatics 2006 22(3):346-353; doi:10.1093/bioinformatics/bti800
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Conservation analysis of large biochemical networks

Ravishankar Rao Vallabhajosyula *, Vijay Chickarmane and Herbert M. Sauro

Keck Graduate Institute 535 Watson Drive, Claremont, CA 91711, USA

*To whom correspondence should be addressed.

Motivation: Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available software tools, often resulting in inaccurate computation of the number and form of conserved cycles. Such errors have profound effects on subsequent calculations, particularly in the evaluation of the Jacobian which is a critical quantity in many other calculations. The goal of this paper is to outline a new algorithm that is computationally efficient and robust at extracting the correct conservation laws for very large biochemical networks.

Results: We show that our algorithm can perform the conservation analysis of large biochemical networks, and can evaluate the correct conserved cycles when compared with other similar software tools. Biochemical simulators such as Jarnac and COPASI are successful at extracting only a subset of the conservation laws that our algorithm can. This is illustrated with examples for some large networks which show the advantages of our method.

Availability: The software is available as part of the latest release of Systems Biology Workbench (SBW version 2.5.0) and can be downloaded from http://www.sys-bio.org. The software is licensed under the BSD open source license and is freely available at sourceforge.

Contact: rrao{at}kgi.edu

Received on September 23, 2005; revised on November 22, 2005; accepted on November 23, 2005

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