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Adelinde M Uhrmacher, Jan Himmelspach, Mathias Röhl, and Roland Ewald (2006)

Introducing Variable Ports and Multi-Couplings for Cell Biological Modeling in DEVS

In: Proceedings of the 2006 Winter Simulation Conference, ed. by L. F. Perrone and F. P. Wieland and J. Liu and B. G. Lawson and D. M. Nicol and R. M. Fujimoto, pp. 832-840, Institute of Electrical and Electronics Engineers, Inc., Institute of Electrical and Electronics Engineers, Inc.

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 rho-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 trp operon model illustrates the developed ideas and concepts.