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
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