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20th Workshop on Principles of Advanced and Distributed Simulation (PADS'06)
Developing An Hierarchical Simulator for Beta-binders
Singapore
May 24-May 26
ISBN: 0-7695-2587-3
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. %
Citation:
Jan Himmelspach, Paola Lecca, Davide Prandi, Corado Priami, Paola Quaglia, Adelinde Uhrmacher, "Developing An Hierarchical Simulator for Beta-binders," pads, pp.92-102, 20th Workshop on Principles of Advanced and Distributed Simulation (PADS'06), 2006
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