Graphics processing units in bioinformatics, computational biology and systems biology

Marco Nobile, Paolo Cazzaniga, Andrea Tangherloni, Daniela Besozzi

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Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures.
Originele taal-2Engels
Pagina's (van-tot)870-885
Aantal pagina's16
TijdschriftBriefings in Bioinformatics
Nummer van het tijdschrift5
StatusGepubliceerd - 1 sep 2017
Extern gepubliceerdJa


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