Introducing variable ports and multi-couplings for cell biological modeling in DEVS

Authors:
Adelinde M. Uhrmacher;Jan Himmelspach;Mathias Röhl;Roland Ewald
Affiliations:
University of Rostock, Rostock, Germany;University of Rostock, Rostock, Germany;University of Rostock, Rostock, Germany;University of Rostock, Rostock, Germany
Venue:
Proceedings of the 38th conference on Winter simulation
Year:
2006

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Abstract

Motivated by the requirements of molecular biological applications, we are suggesting an extension of the DEVS formalism. Starting with DYNDEVS a reflective variant of DEVS which supports dynamic behavior, composition, and interaction pattern, we develop ρ-DEVS. Dynamic ports and multi-couplings are introduced whose combination allows models to reflect significant state changes to the outside world and enabling or disabling certain interactions at the same time. An abstract simulator describes the operational semantics of the developed formalism, and the Tryptophan operon model illustrates the developed ideas and concepts.