Mostrar o rexistro simple do ítem
Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS
dc.contributor.author | González-Domínguez, Jorge | |
dc.contributor.author | Schmidt, Bertil | |
dc.contributor.author | Kässens, Jan Christian | |
dc.contributor.author | Wienbrandt, Lars | |
dc.date.accessioned | 2018-08-28T09:32:23Z | |
dc.date.available | 2018-08-28T09:32:23Z | |
dc.date.issued | 2014-08 | |
dc.identifier.citation | González-Domínguez J., Schmidt B., Kässens J.C., Wienbrandt L. (2014) Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. In: Silva F., Dutra I., Santos Costa V. (eds) Euro-Par 2014 Parallel Processing. Euro-Par 2014. Lecture Notes in Computer Science, vol 8632. Springer, Cham | es_ES |
dc.identifier.isbn | 978-3-319-09872-2 | |
dc.identifier.isbn | 978-3-319-09873-9 | |
dc.identifier.issn | 0302-9743 | |
dc.identifier.issn | 1611-3349 | |
dc.identifier.uri | http://hdl.handle.net/2183/20977 | |
dc.description | This is a post-peer-review, pre-copyedit version of an article published in Lecture Notes in Computer Science. The final authenticated version is available online at: https://doi.org/10.1007/978-3-319-09873-9_57 | es_ES |
dc.description.abstract | [Abstract] High-throughput genotyping technologies allow the collection of up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as 2-SNP interactions, in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. In this work we present EpistSearch, a parallelized tool that, following the log-linear model approach, uses a novel filter to determine the interactions between all SNP-pairs. Our tool is parallelized using a hybrid combination of Pthreads and CUDA in order to take advantage of CPU/GPU architectures. Experimental results with simulated and real datasets show that EpistSearch outperforms previous approaches, either using GPUs or only CPU cores. For instance, an exhaustive analysis of a real-world dataset with 500,000 SNPs and 5,000 individuals requires less than 42 minutes on a machine with 6 CPU cores and a GTX Titan GPU. | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Springer | es_ES |
dc.relation.uri | https://doi.org/10.1007/978-3-319-09873-9_57 | es_ES |
dc.subject | Bioinformatics | es_ES |
dc.subject | GWAS | es_ES |
dc.subject | Epistasis | es_ES |
dc.subject | Pthreads | es_ES |
dc.subject | CUDA | es_ES |
dc.title | Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS | es_ES |
dc.type | info:eu-repo/semantics/conferenceObject | es_ES |
dc.rights.access | info:eu-repo/semantics/openAccess | es_ES |
UDC.journalTitle | Lecture Notes in Computer Science | es_ES |
UDC.volume | 8632 | es_ES |
UDC.startPage | 680 | es_ES |
UDC.endPage | 691 | es_ES |
dc.identifier.doi | 10.1007/978-3-319-09873-9_57 | |
UDC.conferenceTitle | European Conference on Parallel Processing | es_ES |