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.
|Titolo:||Developing An Hierarchical Simulator for Beta-binders|
|Autori:||J., Himmelspach; Lecca, Paola; Prandi, Davide; Priami, Corrado; Quaglia, Paola; A., Uhrmacher|
|Titolo del volume contenente il saggio:||Proc. 20th IEEE/ACM/SCS Workshop on Principles of Advanced and Distributed Simulation, PADS 2006, Singapore, May 24-26, 2006|
|Luogo di edizione:||Los Alamitos|
|Casa editrice:||IEEE Computer Society|
|Anno di pubblicazione:||2006|
|Appare nelle tipologie:||04.1 Saggio in atti di convegno (Paper in proceedings)|