The Many Roads to the Simulation of Reaction Systems

• Autorzy: Ferretti Claudio , Leporati Alberto , Manzoni Luca , Porreca Antonio E.

Identyfikatory

DOI

10.3233/FI-2020-1878

• Języki publikacji: EN

Abstrakty

EN

Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool for biochemical systems, but in order to be able to employ them effectively in the field the presence of efficient and widely available simulators is essential. Here we explore three different algorithms and implementations of the simulation, comparing them to the current state of the art. We also show that we can obtain performances comparable to GPU-based simulations on real-world systems by using a carefully tuned CPU-based simulator.

Słowa kluczowe

EN

reaction systems; simulation of biochemical systems

• Wydawca: IOS Press
• Czasopismo: Fundamenta Informaticae
• Rocznik: 2020
• Tom: Vol. 171, nr 1-4
• Strony: 175--188
• Opis fizyczny: Bibliogr. 26 poz., rys., tab.

Twórcy

autor

Ferretti Claudio

• Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20126 Milan, Italy

autor

Leporati Alberto

• Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20126 Milan, Italy

autor

Manzoni Luca

• Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20126 Milan, Italy

autor

Porreca Antonio E.

• Aix Marseille Université, Université de Toulon, CNRS, LIS, Marseille, France

Bibliografia

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Uwagi

Opracowanie rekordu ze środków MNiSW, umowa Nr 461252 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2020).