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)
Angelo Troina
(Universita' di Torino)

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.

In Gabriel Ciobanu: Proceedings 6th Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2012), Newcastle, UK, 8th September 2012, Electronic Proceedings in Theoretical Computer Science 100, pp. 101–106.
Published: 15th November 2012.

ArXived at: http://dx.doi.org/10.4204/EPTCS.100.7 bibtex PDF
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