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Bioinformatics Advance Access originally published online on December 16, 2004
Bioinformatics 2005 21(8):1617-1625; doi:10.1093/bioinformatics/bti225
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Investigating the dynamic behavior of biochemical networks using model families

Marc Daniel Haunschild 1, Bernd Freisleben 2, Ralf Takors 3 and Wolfgang Wiechert 1,*

1Department of Simulation, University of Siegen Paul-Bonatz-Strasse 9-11, D-57068 Siegen, Germany
2Department of Mathematics and Computer Science, University of Marburg Hans-Meerwein-Strasse, D-35032 Marburg, Germany
3Institute of Biotechnology, Research Center Juelich D-52425 Juelich, Germany

*To whom correspondence should be addressed.

Motivation: Supporting the evolutionary modeling process of dynamic biochemical networks based on sampled in vivo data requires more than just simulation. In the course of the modeling process, the modeler is typically concerned not only with a single model but also with sequences, alternatives and structural variants of models. Powerful automatic methods are then required to assist the modeler in the organization and the evaluation of alternative models. Moreover, the structure and peculiarities of the data require dedicated tool support.

Summary: To support all stages of an evolutionary modeling process, a new general formalism for the combinatorial specification of large model families is introduced. It allows for automatic navigation in the space of models and excludes biologically meaningless models on the basis of elementary flux mode analysis. An incremental usage of the measured data is supported by using splined data instead of state variables. With MMT2, a versatile tool has been developed as a computational engine intended to be built into a tool chain. Using automatic code generation, automatic differentiation for sensitivity analysis and grid computing technology, a high performance computing environment is achieved. MMT2 supplies XML model specification and several software interfaces. The performance of MMT2 is illustrated by several examples from ongoing research projects.

Availability: http://www.simtec.mb.uni-siegen.de/

Contact: wiechert{at}simtec.mb.uni-siegen.de


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