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20th Workshop on Principles of Advanced and Distributed Simulation (PADS'06) (2006)
May 24, 2006 to May 26, 2006
ISSN: 1087-4097
ISBN: 0-7695-2587-3
pp: 92-102
Jan Himmelspach , University of Rostock, Germany
Paola Lecca , University of Trento, Italy
Davide Prandi , University of Trento, Italy
Corado Priami , University of Trento, Italy
Paola Quaglia , University of Trento, Italy
Adelinde Uhrmacher , University of Rostock, Germany
BETA-BINDERS form a recently developed extension of stochastic \pi CALCULUS to describe micro-biological systems. It introduces special binders to wrap processes just as membranes enclose some living matter and hence to mimic biological interfaces. One means to define the operational semantics of a modeling formalism is by an abstract simulator description. In developing an abstract simulator for BETA-BINDERS concepts are adopted that have been developed in the context of JAMES II. Processors of the simulator are structured into a hierarchy and each of them is splitted into different methods. This design reflects the structure of BETA-BINDERS models and facilitates experimenting with different operational semantics. Two discrete event simulation schemes, the First-Gillespie method and Gibson-Bruck method, are combined to calculate the reactions that occur within and between the modeled bioprocesses, respectively. The functioning of the simulator is illustrated by processing step-wise the reaction of an immune cell to the occurrence of a virus. %

C. Priami, P. Quaglia, P. Lecca, D. Prandi, A. Uhrmacher and J. Himmelspach, "Developing An Hierarchical Simulator for Beta-binders," 20th Workshop on Principles of Advanced and Distributed Simulation (PADS'06)(PADS), Singapore, 2006, pp. 92-102.
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