{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:04:10Z","timestamp":1762506250137},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Quantification of the contribution of genetic variation to phenotypic variation for complex traits becomes increasingly computationally demanding with increasing numbers of single-nucleotide polymorphisms and individuals. To meet the challenges in making feasible large-scale studies, we present the REgional heritability advanced complex trait analysis software. Adapted from advanced complex trait analysis (and, in turn, genome-wide complex trait analysis), it is tailored to exploit the parallelism present in modern traditional and graphics processing unit (GPU)-accelerated machines, from workstations to supercomputers.<\/jats:p>\n               <jats:p>Results: We adapt the genetic relationship matrix estimation algorithm to remove limitations on memory, allowing the analysis of large datasets. We build on this to develop a version of the code able to efficiently exploit GPU-accelerated systems for both the genetic relationship matrix and REstricted maximum likelihood (REML) parts of the analysis, offering substantial speedup over the traditional central processing unit version. We develop the ability to analyze multiple small regions of the genome across multiple compute nodes in parallel, following the \u2018regional heritability\u2019 approach. We demonstrate the new software using 1024 GPUs in parallel on one of the world\u2019s fastest supercomputers.<\/jats:p>\n               <jats:p>Availability: The code is freely available at http:\/\/www.epcc.ed.ac.uk\/software-products<\/jats:p>\n               <jats:p>Contact: \u00a0a.gray@ed.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt754","type":"journal-article","created":{"date-parts":[[2014,1,9]],"date-time":"2014-01-09T01:18:36Z","timestamp":1389230316000},"page":"1177-1179","source":"Crossref","is-referenced-by-count":21,"title":["Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures"],"prefix":"10.1093","volume":"30","author":[{"given":"L.","family":"Cebamanos","sequence":"first","affiliation":[{"name":"1 EPCC and 2The Roslin Institute, The University of Edinburgh, Edinburgh, UK"}]},{"given":"A.","family":"Gray","sequence":"additional","affiliation":[{"name":"1 EPCC and 2The Roslin Institute, The University of Edinburgh, Edinburgh, UK"}]},{"given":"I.","family":"Stewart","sequence":"additional","affiliation":[{"name":"1 EPCC and 2The Roslin Institute, The University of Edinburgh, Edinburgh, UK"}]},{"given":"A.","family":"Tenesa","sequence":"additional","affiliation":[{"name":"1 EPCC and 2The Roslin Institute, The University of Edinburgh, Edinburgh, UK"}]}],"member":"286","published-online":{"date-parts":[[2014,1,7]]},"reference":[{"key":"2023012710490785700_btt754-B4","first-page":"1","article-title":"Numerical linear algebra on emerging architectures: the PLASMA and MAGMA projects","volume":"180","author":"Agullo","year":"2009","journal-title":"J. Phys."},{"key":"2023012710490785700_btt754-B2","doi-asserted-by":"crossref","first-page":"3134","DOI":"10.1093\/bioinformatics\/bts571","article-title":"Advanced complex trait analysis","volume":"28","author":"Gray","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012710490785700_btt754-B5","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1093\/bioinformatics\/btt177","article-title":"A powerful and efficient set test for genetic markers that handles confounders","volume":"29","author":"Listgarten","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012710490785700_btt754-B1","doi-asserted-by":"crossref","first-page":"e46501","DOI":"10.1371\/journal.pone.0046501","article-title":"Localising loci underlying complex trait variation using regional genomic relationship mapping","volume":"7","author":"Nagamine","year":"2012","journal-title":"PLoS One"},{"key":"2023012710490785700_btt754-B3","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","article-title":"GCTA: a tool for genome-wide complex trait analysis","volume":"88","author":"Yang","year":"2011","journal-title":"Am. J. Hum. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/8\/1177\/48922775\/bioinformatics_30_8_1177.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/8\/1177\/48922775\/bioinformatics_30_8_1177.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T10:53:13Z","timestamp":1674816793000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/8\/1177\/255210"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1,7]]},"references-count":5,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2014,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt754","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,4,15]]},"published":{"date-parts":[[2014,1,7]]}}}