Modular modeling of cellular systems with ProMoT/Diva

Motivation: Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells Results: A computer framework is described which allows the building of modularly structured models using an abstract,...

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Bibliographic Details
Published in:Bioinformatics 2003-06, Vol.19 (9), p.1169-1176
Main Authors: Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., Gilles, E. D.
Format: Article
Language:English
Subjects:
Algorithms
Cell Physiological Phenomena
Computer Simulation
Databases, Factual
Metabolism - physiology
Models, Biological
Software
Software Design
User-Computer Interface
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Summary:Motivation: Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells Results: A computer framework is described which allows the building of modularly structured models using an abstract, modular and general modeling methodology. With this methodology, reusable modeling entities are introduced which lead to the development of a modeling library within the modeling tool ProMot. The simulation environment Diva is used for numerical analysis and parameter identification of the models. The simulation environment provides a number of tools and algorithms to simulate and analyze complex biochemical networks. The described tools are the first steps towards an integrated computer-based modeling, simulation and visualization environment Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries Contact: ginkel@mpi-magdeburg.mpg.de Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/promot * To whom correspondence should be addressed.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btg128