Accelerated analysis of biological parameters space using GPUs

Marco S. Nobile, Giancarlo Mauri

Onderzoeksoutput: Hoofdstuk in Boek/Rapport/CongresprocedureConferentiebijdrageAcademicpeer review

3 Citaten (Scopus)

Samenvatting

Mathematical modeling and computer simulation represent a valuable mean to integrate experimental research for the study of biological systems. However, many computational methods—e.g., sensitivity analysis—require the execution of a massive number of simulations to investigate the model behavior in physiological or perturbed conditions, which can be a computationally challenging task. This huge amount of simulations is necessary to collect data in the vast space of kinetic parameters. This paper provides the state-of-the-art of biochemical simulators relying on Graphics Processing Units (GPUs) in the context of Systems Biology. Moreover, we discuss two examples of integration of such simulators into computational methods for parameter sweep and sensitivity analysis, both implemented using the Python language.

Originele taal-2Engels
TitelParallel Computing Technologies - 14th International Conference, PaCT 2017, Proceedings
RedacteurenVictor Malyshkin
Plaats van productieCham
UitgeverijSpringer
Pagina's70-81
Aantal pagina's12
ISBN van elektronische versie978-3-319-62932-2
ISBN van geprinte versie978-3-319-62931-5
DOI's
StatusGepubliceerd - 1 jan 2017
Extern gepubliceerdJa
Evenement14th International Conference on Parallel Computing Technologies, PaCT 2017 - Nizhny Novgorod, Rusland
Duur: 4 sep 20178 sep 2017

Publicatie series

NaamLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10421 LNCS
ISSN van geprinte versie0302-9743
ISSN van elektronische versie1611-3349

Congres

Congres14th International Conference on Parallel Computing Technologies, PaCT 2017
LandRusland
StadNizhny Novgorod
Periode4/09/178/09/17

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