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Bioinformatics Advance Access published online on May 14, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn228
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Computing Chemical Organizations in Biological Networks

F. Centler *, C. Kaleta , P. Speroni di Fenizio {dagger} and Peter Dittrich {ddagger}

Bio Systems Analysis Group, Jena Centre for Bioinformatics (JCB), and Department of Mathematics and Computer Science, Friedrich-Schiller-University Jena, D-07743 Jena, Germany

{ddagger}To whom correspondence should be addressed. Dr. Peter Dittrich, E-mail: dittrich{at}minet.uni-jena.de


  Abstract

Motivation: Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory of chemical organizations has recently been introduced as such a technique that links the topology of biochemical reaction network models to their dynamical repertoire. The network is decomposed into algebraically closed and self-maintaining subnetworks called organizations. They form a hierarchy representing all feasible system states including all steady states.

Results: We present three algorithms to compute the hierarchy of organizations for network models provided in SBML format. Two of them compute the complete organization hierarchy, while the third one uses heuristics to obtain a subset of all organizations for large models. While the constructive approach computes the hierarchy starting from the smallest organization in a bottom-up fashion, the flux-based approach employs self-maintaining flux distributions to determine organizations. A runtime comparison on 16 different network models of natural systems showed that none of the two exhaustive algorithms is superior in all cases. Studying a "genomescale" network model with 762 species and 1193 reactions, we demonstrate how the organization hierarchy helps to uncover the model structure and allows to evaluate the model's quality, for example by detecting components and subsystems of the model whose maintenance is not explained by the model.

Availability: All data and a Java implementation that plugs into the Systems Biology Workbench is available from http://www.minet.uni-jena.de/csb/prj/ot/tools.

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

Associate Editor: Prof. Thomas Lengauer

*Current address: Department of Environmental Microbiology, UFZ - Centre for Environmental Research Leipzig-Halle, Germany

{dagger}Current address; Research Institute in Networks & Communications Engineering (RINCE), Dublin City University, Dublin 9, Ireland

Received on January 9, 2008; revised on March 6, 2008; accepted on May 7, 2008

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