Parallel BioScape: A stochastic & parallel language for mobile & spatial interactions

Adriana Compagnoni; Vishakha Sharma; Mariangiola Dezani-Ciancaglini; Angelo Troina; Paola Giannini; Karin Sauer

doi:10.4204/EPTCS.100.7

Parallel BioScape: A stochastic & parallel language for mobile & spatial interactions

Adriana Compagnoni
, Vishakha Sharma
, Mariangiola Dezani-Ciancaglini
, Angelo Troina
, Paola Giannini
, Karin Sauer

Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica

Risultato della ricerca: Contributo su rivista › Articolo da conferenza › peer review

Abstract

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.

Lingua originale	Inglese
pagine (da-a)	101-106
Numero di pagine	6
Rivista	Electronic Proceedings in Theoretical Computer Science, EPTCS
Volume	100
DOI	https://doi.org/10.4204/EPTCS.100.7
Stato di pubblicazione	Pubblicato - 15 nov 2012
Evento	6th Workshop on Membrane Computing and Biologically Inspired Process Calculi, MeCBIC 2012 - Newcastle upon Tyne, United Kingdom Durata: 8 set 2012 → …

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10.4204/EPTCS.100.7

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title = "Parallel BioScape: A stochastic \& parallel language for mobile \& spatial interactions",

abstract = "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.",

author = "Adriana Compagnoni and Vishakha Sharma and Mariangiola Dezani-Ciancaglini and Angelo Troina and Paola Giannini and Karin Sauer",

note = "Funding Information: ∗Extended Abstract. This research is funded by the BioBITs Project (Converging Technologies 2007, area: Biotechnology– ICT), Regione Piemonte.; 6th Workshop on Membrane Computing and Biologically Inspired Process Calculi, MeCBIC 2012 ; Conference date: 08-09-2012",

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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 - https://www.scopus.com/pages/publications/84940796633

U2 - 10.4204/EPTCS.100.7

DO - 10.4204/EPTCS.100.7

M3 - Conference article

AN - SCOPUS:84940796633

SN - 2075-2180

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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 -

Parallel BioScape: A stochastic & parallel language for mobile & spatial interactions

Abstract

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