{"id":"https://openalex.org/W2084525266","doi":"https://doi.org/10.1145/1851476.1851547","title":"Biocompute","display_name":"Biocompute","publication_year":2010,"publication_date":"2010-06-21","ids":{"openalex":"https://openalex.org/W2084525266","doi":"https://doi.org/10.1145/1851476.1851547","mag":"2084525266"},"language":"en","primary_location":{"id":"doi:10.1145/1851476.1851547","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1851476.1851547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing","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/A5020456148","display_name":"Rory Carmichael","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rory Carmichael","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072321928","display_name":"Patrick Braga\u2010Henebry","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Patrick Braga-Henebry","raw_affiliation_strings":["IMC Financial Markets, Chicago, IL"],"affiliations":[{"raw_affiliation_string":"IMC Financial Markets, Chicago, IL","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007301255","display_name":"Douglas Thain","orcid":"https://orcid.org/0000-0001-5218-1956"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas Thain","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019857186","display_name":"Scott Emrich","orcid":"https://orcid.org/0000-0002-5741-4517"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Emrich","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020456148"],"corresponding_institution_ids":["https://openalex.org/I107639228"],"apc_list":null,"apc_paid":null,"fwci":3.3343,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.93190537,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"489","last_page":"498"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9997000098228455,"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"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9907000064849854,"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":0.8297726511955261},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7355549931526184},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5833739638328552},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5471502542495728},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4476833641529083},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.4258959889411926},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.42105287313461304},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3338584005832672},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14692264795303345}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8297726511955261},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7355549931526184},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5833739638328552},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5471502542495728},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4476833641529083},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.4258959889411926},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.42105287313461304},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3338584005832672},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14692264795303345},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1851476.1851547","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1851476.1851547","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G7745122914","display_name":null,"funder_award_id":"CNS0643229","funder_id":"https://openalex.org/F4320337388","funder_display_name":"Division of Computer and Network Systems"}],"funders":[{"id":"https://openalex.org/F4320337388","display_name":"Division of Computer and Network Systems","ror":"https://ror.org/02rdzmk74"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W145805655","https://openalex.org/W1882963036","https://openalex.org/W1971744183","https://openalex.org/W1988545508","https://openalex.org/W1996345933","https://openalex.org/W2027172230","https://openalex.org/W2055043387","https://openalex.org/W2087064593","https://openalex.org/W2130651654","https://openalex.org/W2140332639","https://openalex.org/W2142619120","https://openalex.org/W2146341019","https://openalex.org/W2147499400","https://openalex.org/W2153527981","https://openalex.org/W2203887455","https://openalex.org/W4240861547"],"related_works":["https://openalex.org/W2375304607","https://openalex.org/W2391168633","https://openalex.org/W2035995658","https://openalex.org/W2353477037","https://openalex.org/W1574425962","https://openalex.org/W2385499106","https://openalex.org/W2354357087","https://openalex.org/W2352774566","https://openalex.org/W4243836028","https://openalex.org/W2376671203"],"abstract_inverted_index":{"The":[0,62,86,99],"explosion":[1],"of":[2,11,83,95,112,121,129],"data":[3,36,50,74],"in":[4,47,106,174],"the":[5,9,78,81,90,110,119,159,164,171],"biological":[6,146],"community":[7],"demands":[8],"development":[10],"more":[12],"scalable":[13],"and":[14,32,52,68,93,141,147,161,168,170],"flexible":[15],"portals":[16],"for":[17,29,35,80],"bioinformatic":[18,148],"computation.":[19],"To":[20],"address":[21],"this":[22,155],"need,":[23],"we":[24,157],"put":[25],"forth":[26],"characteristics":[27,44],"needed":[28],"rigorous,":[30],"reproducible,":[31],"collaborative":[33],"resources":[34],"intensive":[37],"science.":[38],"Implementing":[39],"a":[40],"system":[41,69],"with":[42],"these":[43,60],"exposed":[45],"challenges":[46],"user":[48,66],"interface,":[49],"distribution,":[51],"workflow":[53,88],"description/execution.":[54],"We":[55],"describe":[56,158],"several":[57],"responses":[58],"to":[59,144,163],"challenges.":[61],"Data-Action-Queue":[63],"metaphor":[64],"addresses":[65],"interface":[67,162],"organization":[70],"concepts.":[71],"A":[72],"dynamic":[73],"distribution":[75],"mechanism":[76],"lays":[77],"foundation":[79],"management":[82],"persistent":[84],"datasets.":[85],"Makeflow":[87],"facilitates":[89],"simple":[91],"description":[92],"execution":[94],"complex":[96],"multipart":[97],"jobs.":[98],"resulting":[100],"web":[101],"portal,":[102],"Biocompute,":[103],"has":[104,124],"been":[105],"production":[107],"use":[108],"at":[109],"University":[111],"Notre":[113],"Dame's":[114],"Bioinformatics":[115],"Core":[116],"Facility":[117],"since":[118],"summer":[120],"2009.":[122],"It":[123],"provided":[125],"over":[126],"seven":[127],"years":[128],"CPU":[130],"time":[131],"through":[132],"its":[133,166,175],"three":[134,152],"sequence":[135],"search":[136],"modules":[137],"---":[138,143],"BLAST,":[139],"SSAHA,":[140],"SHRIMP":[142],"ten":[145],"research":[149],"groups":[150],"spanning":[151],"universities.":[153],"In":[154],"paper":[156],"goals":[160],"system,":[165],"architecture":[167],"performance,":[169],"insights":[172],"gained":[173],"development.":[176]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
