{"id":"https://openalex.org/W2172031170","doi":"https://doi.org/10.1093/bioinformatics/btt013","title":"ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems","display_name":"ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems","publication_year":2013,"publication_date":"2013-01-29","ids":{"openalex":"https://openalex.org/W2172031170","doi":"https://doi.org/10.1093/bioinformatics/btt013","mag":"2172031170","pmid":"https://pubmed.ncbi.nlm.nih.gov/23361326"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt013","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/bioinformatics/btt013","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013287908","display_name":"Christopher Oehmen","orcid":"https://orcid.org/0009-0004-5246-930X"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher S. Oehmen","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99352, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99352, USA","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021728091","display_name":"Douglas Baxter","orcid":null},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas J. Baxter","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, WA 99352, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, WA 99352, USA","institution_ids":["https://openalex.org/I142606810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013287908"],"corresponding_institution_ids":["https://openalex.org/I142606810"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":2.5007,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.89886371,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"29","issue":"6","first_page":"797","last_page":"798"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962999820709229,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9961000084877014,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.77579665184021},{"id":"https://openalex.org/keywords/multiprocessing","display_name":"Multiprocessing","score":0.766157865524292},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.6543684005737305},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6488478183746338},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.6439345479011536},{"id":"https://openalex.org/keywords/fault-tolerance","display_name":"Fault tolerance","score":0.5996410250663757},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.585529625415802},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4669901728630066},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.448872834444046},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.32719576358795166},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23925542831420898},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.13873004913330078},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11575138568878174}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.77579665184021},{"id":"https://openalex.org/C4822641","wikidata":"https://www.wikidata.org/wiki/Q846651","display_name":"Multiprocessing","level":2,"score":0.766157865524292},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.6543684005737305},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6488478183746338},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.6439345479011536},{"id":"https://openalex.org/C63540848","wikidata":"https://www.wikidata.org/wiki/Q3140932","display_name":"Fault tolerance","level":2,"score":0.5996410250663757},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.585529625415802},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4669901728630066},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.448872834444046},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.32719576358795166},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23925542831420898},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.13873004913330078},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11575138568878174}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt013","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23361326","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23361326","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2596309","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3597145","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:10.1093/bioinformatics/btt013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt013","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W2055043387","https://openalex.org/W2155957132","https://openalex.org/W6606052223"],"related_works":["https://openalex.org/W300950598","https://openalex.org/W1517776641","https://openalex.org/W99192079","https://openalex.org/W2366027386","https://openalex.org/W1988348725","https://openalex.org/W2378666660","https://openalex.org/W2593142409","https://openalex.org/W1705919733","https://openalex.org/W121003525","https://openalex.org/W3016212467"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"BLAST":[2,66],"remains":[3],"one":[4],"of":[5,30,33],"the":[6,28,37],"most":[7],"widely":[8],"used":[9],"tools":[10],"in":[11],"computational":[12],"biology.":[13],"The":[14],"rate":[15],"at":[16],"which":[17],"new":[18,31],"sequence":[19],"data":[20],"is":[21],"available":[22],"continues":[23],"to":[24,52,61,82,87],"grow":[25],"exponentially,":[26],"driving":[27],"emergence":[29],"fields":[32],"biological":[34],"research.":[35],"At":[36],"same":[38],"time,":[39],"multicore":[40],"systems":[41,57],"and":[42],"conventional":[43,55],"clusters":[44],"are":[45],"more":[46],"accessible.":[47],"ScalaBLAST":[48,91],"has":[49],"been":[50],"designed":[51],"run":[53],"on":[54],"multiprocessor":[56],"with":[58,73,85],"an":[59],"eye":[60],"extreme":[62],"parallelism,":[63],"enabling":[64],"parallel":[65],"calculations":[67],"using":[68],">16":[69],"000":[70],"processing":[71],"cores":[72],"a":[74],"portable,":[75],"robust,":[76],"fault-resilient":[77],"design":[78],"that":[79],"introduces":[80],"little":[81],"no":[83],"overhead":[84],"respect":[86],"serial":[88],"BLAST.":[89],"Availability:":[90],"2.0":[92],"source":[93],"code":[94],"can":[95],"be":[96],"freely":[97],"downloaded":[98],"from":[99],"http://omics.pnl.gov/software/ScalaBLAST.php.":[100],"Contact:":[101],"christopher.oehmen@pnl.gov":[102]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":5}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}
