Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions
Adriana Compagnoni (Stevens Institute of Technology), Mariangiola, Dezani-Ciancaglini (Universita' di Torino), Paola Giannini (Universita' del, Piemonte Orientale), Karin Sauer (Binghamton University), Vishakha Sharma, (Stevens Institute of Technology)
TL;DR
Parallel BioScape introduces a fully parallel semantics extension to the BioScape language, enabling scalable modeling of large biological systems on multi-core and GPU architectures.
Contribution
The paper presents Parallel BioScape, a novel extension providing fully parallel semantics to BioScape for improved scalability on modern hardware.
Findings
Enables modeling of larger biological systems
Achieves better performance on multi-core and GPU architectures
Extends BioScape with parallel semantics
Abstract
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in treating and preventing biofilm infections. As its predecessor, SPiM, BioScape has a sequential semantics based on Gillespie's algorithm, and its implementation does not scale beyond 1000 agents. However, in order to model larger and more realistic systems, a semantics that may take advantage of the new multi-core and GPU architectures is needed. This motivates the introduction of parallel semantics, which is the contribution of this paper: Parallel BioScape, an extension with fully parallel semantics.
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