{"id":"https://openalex.org/W2088393741","doi":"https://doi.org/10.1145/2792745.2792749","title":"NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture","display_name":"NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture","publication_year":2015,"publication_date":"2015-01-01","ids":{"openalex":"https://openalex.org/W2088393741","doi":"https://doi.org/10.1145/2792745.2792749","mag":"2088393741"},"language":"en","primary_location":{"id":"doi:10.1145/2792745.2792749","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2792745.2792749","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011173783","display_name":"Arun S. Seetharam","orcid":"https://orcid.org/0000-0002-6789-9298"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arun Seetharam","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109890245","display_name":"A. Gomez","orcid":null},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Antonio Gomez","raw_affiliation_strings":["Texas Advanced Computing Center, Austin, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, Austin, TX","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103793193","display_name":"Catherine M. Purcell","orcid":"https://orcid.org/0000-0002-7524-4427"},"institutions":[{"id":"https://openalex.org/I106745318","display_name":"NOAA National Marine Fisheries Service","ror":"https://ror.org/033mqx355","country_code":"US","type":"government","lineage":["https://openalex.org/I106745318","https://openalex.org/I1308126019","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I4210109599","display_name":"NOAA National Marine Fisheries Service Southwest Fisheries Science Center","ror":"https://ror.org/022d75229","country_code":"US","type":"government","lineage":["https://openalex.org/I106745318","https://openalex.org/I1308126019","https://openalex.org/I1343035065","https://openalex.org/I4210109599"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catherine M. Purcell","raw_affiliation_strings":["NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California","institution_ids":["https://openalex.org/I4210109599","https://openalex.org/I106745318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113842039","display_name":"John R. Hyde","orcid":"https://orcid.org/0000-0002-2658-3254"},"institutions":[{"id":"https://openalex.org/I106745318","display_name":"NOAA National Marine Fisheries Service","ror":"https://ror.org/033mqx355","country_code":"US","type":"government","lineage":["https://openalex.org/I106745318","https://openalex.org/I1308126019","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I4210109599","display_name":"NOAA National Marine Fisheries Service Southwest Fisheries Science Center","ror":"https://ror.org/022d75229","country_code":"US","type":"government","lineage":["https://openalex.org/I106745318","https://openalex.org/I1308126019","https://openalex.org/I1343035065","https://openalex.org/I4210109599"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John R. Hyde","raw_affiliation_strings":["NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California","institution_ids":["https://openalex.org/I4210109599","https://openalex.org/I106745318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037662959","display_name":"Philip D. Blood","orcid":"https://orcid.org/0000-0002-9129-1223"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip D. Blood","raw_affiliation_strings":["Carnegie Mellon University, St. Pittsburgh, PA","Carnegie Mellon University, St. Pittsburgh, PA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carnegie Mellon University, St. Pittsburgh, PA","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Carnegie Mellon University, St. Pittsburgh, PA#TAB#","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070520368","display_name":"Andrew Severin","orcid":"https://orcid.org/0000-0002-8015-9665"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew J. Severin","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3012,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.62068051,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9811999797821045,"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/T12388","display_name":"Identification and Quantification in Food","score":0.9498000144958496,"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/bottleneck","display_name":"Bottleneck","score":0.8609786033630371},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8012186884880066},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5550800561904907},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.47831466794013977},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.4488976001739502},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4171158969402313},{"id":"https://openalex.org/keywords/aquaculture","display_name":"Aquaculture","score":0.41449862718582153},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.36462002992630005},{"id":"https://openalex.org/keywords/fish-actinopterygii","display_name":"Fish <Actinopterygii>","score":0.3352826237678528},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3207889199256897},{"id":"https://openalex.org/keywords/fishery","display_name":"Fishery","score":0.24335840344429016},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14135023951530457},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11788550019264221},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.08849811553955078},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08686885237693787}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.8609786033630371},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8012186884880066},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5550800561904907},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.47831466794013977},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.4488976001739502},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4171158969402313},{"id":"https://openalex.org/C86909935","wikidata":"https://www.wikidata.org/wiki/Q188989","display_name":"Aquaculture","level":3,"score":0.41449862718582153},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36462002992630005},{"id":"https://openalex.org/C2909208804","wikidata":"https://www.wikidata.org/wiki/Q127282","display_name":"Fish <Actinopterygii>","level":2,"score":0.3352826237678528},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3207889199256897},{"id":"https://openalex.org/C505870484","wikidata":"https://www.wikidata.org/wiki/Q180538","display_name":"Fishery","level":1,"score":0.24335840344429016},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14135023951530457},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11788550019264221},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.08849811553955078},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08686885237693787},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2792745.2792749","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2792745.2792749","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2015 XSEDE Conference on Scientific Advancements Enabled by Enhanced Cyberinfrastructure - XSEDE '15","raw_type":"proceedings-article"},{"id":"pmh:oai:lib.dr.iastate.edu:genomeinformatics_conf-1001","is_oa":false,"landing_page_url":"https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1001&amp;amp;context=genomeinformatics_conf","pdf_url":null,"source":{"id":"https://openalex.org/S4377196104","display_name":"Iowa State University Digital Repository (Iowa State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173911158","host_organization_name":"Iowa State University","host_organization_lineage":["https://openalex.org/I173911158"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genome Informatics Facility Conference Proceedings","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/12"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2049923077","https://openalex.org/W2055043387","https://openalex.org/W2055666215","https://openalex.org/W2096041635","https://openalex.org/W2115036455","https://openalex.org/W2126419817"],"related_works":["https://openalex.org/W2595172197","https://openalex.org/W2084856301","https://openalex.org/W2127970246","https://openalex.org/W2885125400","https://openalex.org/W1989889224","https://openalex.org/W4382618745","https://openalex.org/W1973775000","https://openalex.org/W2748922771","https://openalex.org/W1987128138","https://openalex.org/W2743976221"],"abstract_inverted_index":{"The":[0,20],"development":[1],"of":[2,5,15,81,91,103,164,171,187],"genomic":[3,56,70],"resources":[4,37,71],"non-model":[6],"organisms":[7],"is":[8,34],"now":[9],"becoming":[10],"commonplace":[11],"as":[12],"the":[13,27,52,101,123,127,150,158,168,185],"cost":[14],"sequencing":[16,189],"continues":[17],"to":[18,54,68,78,99,106,149,184],"decrease.":[19],"Genome":[21],"Informatics":[22],"Facility":[23],"in":[24,41,51,178],"collaboration":[25],"with":[26,132],"Southwest":[28],"Fisheries":[29],"Science":[30],"Center":[31],"(SWFSC),":[32],"NOAA":[33],"creating":[35],"these":[36],"for":[38,72,122,191],"sustainable":[39],"aquaculture":[40],"Seriola":[42,73],"lalandi.":[43],"Gene":[44],"prediction":[45],"and":[46,62,161],"annotation":[47,186],"are":[48,59,147],"common":[49],"steps":[50,67],"pipeline":[53],"generate":[55],"resources,":[57],"which":[58,130],"computationally":[60],"intense":[61],"time":[63,104],"consuming.":[64],"In":[65,114],"our":[66,82,92,108,145],"create":[69],"lalandi,":[74],"we":[75,88,117],"found":[76],"BLAST":[77,124,152,172,179],"be":[79,181],"one":[80],"most":[83],"rate":[84],"limiting":[85],"steps.":[86],"Therefore,":[87],"took":[89],"advantage":[90],"XSEDE":[93],"Extended":[94],"Collaborative":[95],"Support":[96],"Services":[97],"(ECSS)":[98],"reduce":[100],"amount":[102],"required":[105],"process":[107],"transcriptome":[109],"data":[110],"by":[111],"300":[112],"percent.":[113],"this":[115,175],"paper,":[116],"describe":[118],"an":[119],"optimized":[120],"method":[121],"tool":[125],"on":[126],"Stampede":[128],"cluster,":[129],"works":[131],"any":[133,139,192],"existing":[134],"datasets":[135,190],"or":[136],"database,":[137],"without":[138],"modification.":[140],"At":[141],"modest":[142],"core":[143],"counts,":[144],"results":[146],"similar":[148],"MPI-enabled":[151],"algorithm":[153],"(mpiBLAST),":[154],"but":[155],"also":[156],"allow":[157],"much":[159],"needed":[160],"improved":[162],"flexibility":[163],"output":[165],"formats":[166],"that":[167],"latest":[169],"versions":[170],"provide.":[173],"Reducing":[174],"time-consuming":[176],"bottleneck":[177],"will":[180],"broadly":[182],"applicable":[183],"large":[188],"organism.":[193]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
