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J Himmelspach, P Lecca, D Prandi, C Priami, P Quaglia, and A Uhrmacher (2006)

Developing An Hierarchical Simulator for Beta-binders

In: 20th Workshop on Principles of Advanced and Distributed Simulation (PADS'06), pp. 92–102, Los Alamitos, CA, USA, IEEE Computer Society.

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.

issn 1087-4097
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