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Bioinformatics Vol. 19 no. 9 2003
Pages 1169-1176
© 2003 Oxford University Press

Modular modeling of cellular systems with ProMoT/Diva

M. Ginkel , A. Kremling *, T. Nutsch , R. Rehner and E. D. Gilles

Max-Planck-Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany

Received on April 9, 2002 ; revised on August 22, 2002 and November 18, 2002 ; accepted on November 29, 2002

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{at}mpi-magdeburg.mpg.de

Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/promot

* To whom correspondence should be addressed.


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