Developing An Hierarchical Simulator for Beta-binders

Himmelspach, Jan and Lecca, Paola and Prandi, Davide and Priami, Corrado and Quaglia, Paola and Uhrmacher, Adelinde M. (2006) Developing An Hierarchical Simulator for Beta-binders. In: 20th IEEE/ACM/SCS Workshop on Principles of Advanced and Distributed Simulation, PADS 2006, Singapore, May 23-26, 2006. Proceedings,, pp. 92-102.

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BETA-BINDERS form a recently developed extension of stochastic π 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.

Item Type: Conference or Workshop Item (Paper)