TY - JOUR
T1 - Parallel BioScape
T2 - 6th Workshop on Membrane Computing and Biologically Inspired Process Calculi, MeCBIC 2012
AU - Compagnoni, Adriana
AU - Sharma, Vishakha
AU - Dezani-Ciancaglini, Mariangiola
AU - Troina, Angelo
AU - Giannini, Paola
AU - Sauer, Karin
N1 - Funding Information:
∗Extended Abstract. This research is funded by the BioBITs Project (Converging Technologies 2007, area: Biotechnology– ICT), Regione Piemonte.
PY - 2012/11/15
Y1 - 2012/11/15
N2 - BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials [5]. 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 [12], BioScape has a sequential semantics based on Gillespie's algorithm [7], 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.
AB - BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials [5]. 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 [12], BioScape has a sequential semantics based on Gillespie's algorithm [7], 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.
UR - http://www.scopus.com/inward/record.url?scp=84940796633&partnerID=8YFLogxK
U2 - 10.4204/EPTCS.100.7
DO - 10.4204/EPTCS.100.7
M3 - Conference article
AN - SCOPUS:84940796633
SN - 2075-2180
VL - 100
SP - 101
EP - 106
JO - Electronic Proceedings in Theoretical Computer Science, EPTCS
JF - Electronic Proceedings in Theoretical Computer Science, EPTCS
Y2 - 8 September 2012
ER -