{"id":"https://openalex.org/W2779904828","doi":"https://doi.org/10.1186/s12859-017-1902-7","title":"Scaling bioinformatics applications on HPC","display_name":"Scaling bioinformatics applications on HPC","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2779904828","doi":"https://doi.org/10.1186/s12859-017-1902-7","mag":"2779904828","pmid":"https://pubmed.ncbi.nlm.nih.gov/29297287"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1902-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1902-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-017-1902-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015914340","display_name":"Mike Mikailov","orcid":"https://orcid.org/0000-0002-1700-4230"},"institutions":[{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I39565521","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08","country_code":"US","type":"government","lineage":["https://openalex.org/I1330989302","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I1335686170","display_name":"Center for Devices and Radiological Health","ror":"https://ror.org/007x9se63","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1335686170"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mike Mikailov","raw_affiliation_strings":["Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA","institution_ids":["https://openalex.org/I1335686170","https://openalex.org/I1320320070","https://openalex.org/I39565521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008926613","display_name":"Fu-Jyh Luo","orcid":null},"institutions":[{"id":"https://openalex.org/I1335686170","display_name":"Center for Devices and Radiological Health","ror":"https://ror.org/007x9se63","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1335686170"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I39565521","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08","country_code":"US","type":"government","lineage":["https://openalex.org/I1330989302","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fu-Jyh Luo","raw_affiliation_strings":["Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA","institution_ids":["https://openalex.org/I1335686170","https://openalex.org/I1320320070","https://openalex.org/I39565521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082624850","display_name":"Stuart J. Barkley","orcid":"https://orcid.org/0000-0003-2046-7751"},"institutions":[{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1335686170","display_name":"Center for Devices and Radiological Health","ror":"https://ror.org/007x9se63","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1335686170"]},{"id":"https://openalex.org/I39565521","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08","country_code":"US","type":"government","lineage":["https://openalex.org/I1330989302","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stuart Barkley","raw_affiliation_strings":["Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA","institution_ids":["https://openalex.org/I1335686170","https://openalex.org/I1320320070","https://openalex.org/I39565521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086054621","display_name":"Lohit Valleru","orcid":null},"institutions":[{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1335686170","display_name":"Center for Devices and Radiological Health","ror":"https://ror.org/007x9se63","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1335686170"]},{"id":"https://openalex.org/I39565521","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08","country_code":"US","type":"government","lineage":["https://openalex.org/I1330989302","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lohit Valleru","raw_affiliation_strings":["Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA","institution_ids":["https://openalex.org/I1335686170","https://openalex.org/I1320320070","https://openalex.org/I39565521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072059074","display_name":"Stephen Whitney","orcid":null},"institutions":[{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1335686170","display_name":"Center for Devices and Radiological Health","ror":"https://ror.org/007x9se63","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1335686170"]},{"id":"https://openalex.org/I39565521","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08","country_code":"US","type":"government","lineage":["https://openalex.org/I1330989302","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen Whitney","raw_affiliation_strings":["Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA","institution_ids":["https://openalex.org/I1335686170","https://openalex.org/I1320320070","https://openalex.org/I39565521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100459801","display_name":"Zhichao Liu","orcid":"https://orcid.org/0000-0002-3379-6258"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhichao Liu","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070704034","display_name":"Shraddha Thakkar","orcid":"https://orcid.org/0000-0002-2920-7713"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shraddha Thakkar","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068886380","display_name":"Weida Tong","orcid":"https://orcid.org/0000-0003-3488-6148"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weida Tong","raw_affiliation_strings":["Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006593300","display_name":"Nicholas Petrick","orcid":"https://orcid.org/0000-0001-5167-8899"},"institutions":[{"id":"https://openalex.org/I39565521","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08","country_code":"US","type":"government","lineage":["https://openalex.org/I1330989302","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I1335686170","display_name":"Center for Devices and Radiological Health","ror":"https://ror.org/007x9se63","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1335686170"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Petrick","raw_affiliation_strings":["Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA. Nicholas.Petrick@fda.hhs.gov","Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA. Nicholas.Petrick@fda.hhs.gov","institution_ids":[]},{"raw_affiliation_string":"Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, MD, 20993, USA","institution_ids":["https://openalex.org/I1335686170","https://openalex.org/I1320320070","https://openalex.org/I39565521"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5015914340"],"corresponding_institution_ids":["https://openalex.org/I1320320070","https://openalex.org/I1335686170","https://openalex.org/I39565521"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6729,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.70124415,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"S14","first_page":"501","last_page":"501"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.2953999936580658,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.2953999936580658,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.27900001406669617,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.04360000044107437,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7332196235656738},{"id":"https://openalex.org/keywords/message-passing-interface","display_name":"Message Passing Interface","score":0.5413863658905029},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.49819231033325195},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4827798902988434},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.43070030212402344},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.41523459553718567},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.41210103034973145},{"id":"https://openalex.org/keywords/message-passing","display_name":"Message passing","score":0.23624441027641296},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22468411922454834},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20875602960586548},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10038590431213379}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7332196235656738},{"id":"https://openalex.org/C166782233","wikidata":"https://www.wikidata.org/wiki/Q127879","display_name":"Message Passing Interface","level":3,"score":0.5413863658905029},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.49819231033325195},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4827798902988434},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.43070030212402344},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.41523459553718567},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.41210103034973145},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.23624441027641296},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22468411922454834},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20875602960586548},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10038590431213379},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1902-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1902-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29297287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29297287","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5f2e64c1170b4c9991707aa86ed3d110","is_oa":true,"landing_page_url":"https://doaj.org/article/5f2e64c1170b4c9991707aa86ed3d110","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 18, Iss S14, Pp 163-169 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4668075","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5751788","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1902-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1902-7","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2124351063","https://openalex.org/W2136145671","https://openalex.org/W2162260260","https://openalex.org/W2162993740","https://openalex.org/W2513506562","https://openalex.org/W2527784658","https://openalex.org/W2906926620"],"related_works":["https://openalex.org/W141820298","https://openalex.org/W4378770497","https://openalex.org/W2049584446","https://openalex.org/W2079781215","https://openalex.org/W2064404759","https://openalex.org/W4308245303","https://openalex.org/W2533634483","https://openalex.org/W2159817808","https://openalex.org/W2050539045","https://openalex.org/W3197250739"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recent":[1],"breakthroughs":[2],"in":[3,38,50,69,190,223,276,328,341,366,378,430],"molecular":[4],"biology":[5],"and":[6,73,133,201,264,293,309,333,356],"next":[7],"generation":[8],"sequencing":[9],"technologies":[10],"have":[11],"led":[12],"to":[13,71,93,123,154,162,173,177,179,199,235,252,270,391,422],"the":[14,18,79,95,98,104,124,164,167,175,180,182,191,203,220,277,290,329,352,443],"expenential":[15],"growh":[16],"of":[17,41,81,87,100,106,119,184,188,206,279,296,302,312,319,354],"sequence":[19],"databases.":[20],"Researchrs":[21],"use":[22,353],"BLAST":[23,42,125,168,227,402],"for":[24,46,57,215,325,380,449],"processing":[25,47],"these":[26,48,381,386],"sequences.":[27],"However":[28],"traditional":[29],"software":[30],"parallelization":[31,60],"techniques":[32,387],"(threads,":[33],"message":[34],"passing":[35],"interface)":[36],"applied":[37],"newer":[39],"versios":[40],"are":[43,388],"not":[44],"adequate":[45],"sequences":[49],"timely":[51],"manner.":[52],"METHODS:":[53],"A":[54],"new":[55,165],"method":[56],"array":[58,82],"job":[59,83,96,285,313,419],"has":[61],"been":[62],"developed":[63,197],"which":[64,218],"offers":[65],"O(T)":[66],"theoretical":[67],"speed-up":[68],"comparison":[70],"multi-threading":[72],"MPI":[74],"techniques.":[75],"Here":[76],"T":[77,101],"is":[78,115,151,442],"number":[80,86,105,183,187,205,278],"tasks.":[84],"(The":[85],"CPUs":[88,107,251,263,371],"that":[89,209,229,241,420],"will":[90],"be":[91,428,454],"used":[92,108,421],"complete":[94,340],"equals":[97],"product":[99],"multiplied":[102],"by":[103,109],"a":[110,156,253,317,413,418,437],"single":[111,254,410],"task.)":[112],"The":[113,194,273,346,360],"approach":[114],"based":[116],"on":[117,249,436],"segmentation":[118,213,288,383],"both":[120],"input":[121],"datasets":[122],"process,":[126],"combining":[127],"partial":[128,207],"solutions":[129],"published":[130],"earlier":[131],"(Dhanker":[132],"Gupta,":[134],"Int":[135],"J":[136],"Comput":[137],"Sci":[138],"Inf":[139],"Technol_5:4818-4820,":[140],"2014),":[141],"(Grant":[142],"et":[143],"al.,":[144],"Bioinformatics_18:765-766,":[145],"2002),":[146],"(Mathog,":[147],"Bioinformatics_19:1865-1866,":[148],"2003).":[149],"It":[150],"accordingly":[152],"referred":[153],"as":[155,401],"\"dual":[157],"segmentation\"":[158],"method.":[159],"In":[160],"order":[161],"implement":[163],"method,":[166],"source":[169],"code":[170],"was":[171,364],"modified":[172],"allow":[174],"researcher":[176],"pass":[178],"program":[181],"records":[185],"(effective":[186],"sequences)":[189],"original":[192],"database.":[193],"team":[195],"also":[196,350],"methods":[198],"manage":[200],"consolidate":[202],"large":[204],"results":[208],"get":[210],"produced.":[211],"Dual":[212],"allows":[214,351],"massive":[216,274],"parallelization,":[217],"lifts":[219],"scaling":[221],"ceiling":[222],"exciting":[224],"ways.":[225],"RESULTS:":[226],"jobs":[228,334],"hitherto":[230],"failed":[231],"or":[232,435],"slogged":[233],"inefficiently":[234],"completion":[236],"now":[237,427],"finish":[238],"with":[239,286,372],"speeds":[240],"characteristically":[242],"reduce":[243],"wallclock":[244],"time":[245,295,327,344],"from":[246],"27":[247],"days":[248,425],"40":[250],"day":[255],"using":[256],"4104":[257],"tasks,":[258],"each":[259,297],"task":[260,348],"utilizing":[261],"eight":[262],"taking":[265],"less":[266,357,431],"than":[267,432],"7":[268],"minutes":[269],"complete.":[271],"CONCLUSIONS:":[272],"increase":[275],"tasks":[280,322],"when":[281],"running":[282],"an":[283,433],"analysis":[284],"dual":[287,382],"reduces":[289],"size,":[291],"scope":[292],"execution":[294],"task.":[298],"Besides":[299],"significant":[300],"speed":[301],"completion,":[303],"additional":[304],"benefits":[305],"include":[306],"fine-grained":[307],"checkpointing":[308],"increased":[310],"flexibility":[311],"submission.":[314],"\"Trickling":[315],"in\"":[316],"swarm":[318],"individual":[320],"small":[321],"tempers":[323],"competition":[324],"CPU":[326],"shared":[330],"HPC":[331],"environment,":[332],"submitted":[335],"during":[336],"quiet":[337],"periods":[338],"can":[339,426,453],"extraordinarily":[342],"short":[343],"frames.":[345],"smaller":[347],"size":[349],"older":[355],"powerful":[358],"hardware.":[359],"CDRH":[361],"workhorse":[362],"cluster":[363],"commissioned":[365],"2010,":[367],"yet":[368],"its":[369],"eight-core":[370],"only":[373],"24GB":[374],"RAM":[375],"work":[376],"well":[377],"2017":[379],"jobs.":[384],"Finally,":[385],"excitingly":[389],"friendly":[390],"budget":[392],"conscious":[393],"scientific":[394],"research":[395],"organizations":[396],"where":[397],"probabilistic":[398],"algorithms":[399],"such":[400],"might":[403],"discourage":[404],"attempts":[405],"at":[406,445],"greater":[407],"certainty":[408],"because":[409],"runs":[411,448],"represent":[412],"major":[414],"resource":[415],"drain.":[416],"If":[417],"take":[423],"24":[424],"completed":[429],"hour":[434],"space":[438],"available":[439],"basis":[440],"(which":[441],"case":[444],"CDRH),":[446],"repeated":[447],"more":[450],"exhaustive":[451],"analyses":[452],"usefully":[455],"contemplated.":[456]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
