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Bioinformatics Advance Access published online on December 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti225
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received July 22, 2004
Revised November 30, 2004
Accepted December 13, 2004

Article

Investigating the dynamic behavior of biochemical networks using model families

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

1 Department of Simulation, University of Siegen, Paul-Bonatz-Str. 9-11, D-57068 Siegen, Germany
2 Dept. of Math. and Comp. Science, University of Marburg, Hans-Meerwein-Str., D-35032 Marburg, Germany
3 Institute of Biotechnology, Research Center Juelich, D-52425 Juelich, Germany

* To whom correspondence should be addressed.
Wolfgang Wiechert, E-mail: wiechert{at}simtec.mb.uni-siegen.de


  Abstract

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 not only concerned with a single model but with sequences, alternatives and structural variants of models. Powerful automatic methods are then required to assist the modeler in the organization and 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 to automatically navigate in the space of models and to exclude 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. By the use of 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/.


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