{"id":"https://openalex.org/W2503380660","doi":"https://doi.org/10.1145/2908961.2931687","title":"Benchmarking Genetically Improved BarraCUDA on Epigenetic Methylation NGS datasets and nVidia GPUs","display_name":"Benchmarking Genetically Improved BarraCUDA on Epigenetic Methylation NGS datasets and nVidia GPUs","publication_year":2016,"publication_date":"2016-07-20","ids":{"openalex":"https://openalex.org/W2503380660","doi":"https://doi.org/10.1145/2908961.2931687","mag":"2503380660"},"language":"en","primary_location":{"id":"doi:10.1145/2908961.2931687","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2908961.2931687","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://discovery.ucl.ac.uk/1521866/1/Langdon_2016_GI.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112258107","display_name":"William B. Langdon","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"William B. Langdon","raw_affiliation_strings":["University College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"University College London, London, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086993200","display_name":"Albert J. Vilella","orcid":"https://orcid.org/0000-0002-2005-2516"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Albert Vilella","raw_affiliation_strings":["Cambridge Epigenetix, Cambridge, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Cambridge Epigenetix, Cambridge, United Kingdom","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023028829","display_name":"Brian Lam","orcid":"https://orcid.org/0000-0002-3638-9025"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Brian Yee Hong Lam","raw_affiliation_strings":["University of Cambridge, Cambridge, United Kingdom"],"affiliations":[{"raw_affiliation_string":"University of Cambridge, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065281209","display_name":"Justyna Petke","orcid":"https://orcid.org/0000-0002-7833-6044"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Justyna Petke","raw_affiliation_strings":["University College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"University College London, London, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000019783","display_name":"Mark Harman","orcid":"https://orcid.org/0000-0002-5864-4488"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Harman","raw_affiliation_strings":["University College London, London, WI, United Kingdom"],"affiliations":[{"raw_affiliation_string":"University College London, London, WI, United Kingdom","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5112258107"],"corresponding_institution_ids":["https://openalex.org/I45129253"],"apc_list":null,"apc_paid":null,"fwci":2.1676,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.87895623,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1131","last_page":"1132"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9901999831199646,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.9786999821662903,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7412619590759277},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.6853300929069519},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6487839221954346},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5889964699745178},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.437014102935791},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3504430949687958},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34272125363349915},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23537400364875793},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22612112760543823},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08725845813751221}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7412619590759277},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.6853300929069519},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6487839221954346},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5889964699745178},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.437014102935791},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3504430949687958},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34272125363349915},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23537400364875793},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22612112760543823},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08725845813751221},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2908961.2931687","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2908961.2931687","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion","raw_type":"proceedings-article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1521866","is_oa":true,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1521866/","pdf_url":"https://discovery.ucl.ac.uk/1521866/1/Langdon_2016_GI.pdf","source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"     In: Friedrich, T and Neumann, F and Sutton, AM, (eds.) GECCO '16 Companion: Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion.  (pp. pp. 1131-1132).  Association for Computing Machinery (ACM): New York, NY, USA. (2016)     ","raw_type":"Proceedings paper"}],"best_oa_location":{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1521866","is_oa":true,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1521866/","pdf_url":"https://discovery.ucl.ac.uk/1521866/1/Langdon_2016_GI.pdf","source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"     In: Friedrich, T and Neumann, F and Sutton, AM, (eds.) GECCO '16 Companion: Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion.  (pp. pp. 1131-1132).  Association for Computing Machinery (ACM): New York, NY, USA. (2016)     ","raw_type":"Proceedings paper"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6794522244","display_name":null,"funder_award_id":"EP/J017515/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8774360244","display_name":null,"funder_award_id":"EP/M025853/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2503380660.pdf","grobid_xml":"https://content.openalex.org/works/W2503380660.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2019313821","https://openalex.org/W2037748100","https://openalex.org/W2305591663"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2011676020","https://openalex.org/W2000169967"],"abstract_inverted_index":{"BarraCUDA":[0],"uses":[1],"CUDA":[2],"graphics":[3],"cards":[4],"to":[5,9],"map":[6],"DNA":[7],"reads":[8],"the":[10,40],"human":[11],"genome.":[12],"Previously":[13],"its":[14],"software":[15],"source":[16],"code":[17,43],"was":[18],"genetically":[19],"improved":[20],"for":[21],"short":[22],"paired":[23],"end":[24],"next":[25],"generation":[26],"sequences.":[27],"On":[28],"longer":[29],"noisy":[30],"epigenetics":[31],"strings":[32],"using":[33],"nVidia":[34],"Titan":[35],"and":[36],"twin":[37],"Tesla":[38],"K40":[39],"same":[41],"GI-ed":[42],"is":[44],"more":[45],"than":[46,50],"3":[47],"times":[48],"faster":[49],"bwa-meth":[51],"on":[52],"an":[53],"8":[54],"core":[55],"CPU.":[56]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
