Developing An Hierarchical Simulator for Beta-binders

  • Authors:

  • Jan Himmelspach;Paola Lecca;Davide Prandi;Corado Priami;Paola Quaglia;Adelinde Uhrmacher

  • Affiliations:

  • University of Rostock, Germany;University of Trento, Italy;University of Trento, Italy;University of Trento, Italy;University of Trento, Italy;University of Rostock, Germany

  • Venue:
  • Proceedings of the 20th Workshop on Principles of Advanced and Distributed Simulation
  • Year:
  • 2006

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Abstract

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.%