{"id":"https://openalex.org/W2135292616","doi":"https://doi.org/10.1145/1646468.1646480","title":"Highly scalable genome assembly on campus grids","display_name":"Highly scalable genome assembly on campus grids","publication_year":2009,"publication_date":"2009-11-16","ids":{"openalex":"https://openalex.org/W2135292616","doi":"https://doi.org/10.1145/1646468.1646480","mag":"2135292616"},"language":"en","primary_location":{"id":"doi:10.1145/1646468.1646480","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1646468.1646480","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers","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/A5058976449","display_name":"Christopher Moretti","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":"Christopher Moretti","raw_affiliation_strings":["University of Notre Dame"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062433637","display_name":"Mark A. Olson","orcid":"https://orcid.org/0000-0003-0398-5063"},"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":"Michael Olson","raw_affiliation_strings":["University of Notre Dame"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","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"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"last","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"],"affiliations":[{"raw_affiliation_string":"University of Notre Dame","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058976449"],"corresponding_institution_ids":["https://openalex.org/I107639228"],"apc_list":null,"apc_paid":null,"fwci":0.9436,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.74792373,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"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":0.9983000159263611,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.995199978351593,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/speedup","display_name":"Speedup","score":0.9411891102790833},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.8763710260391235},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8489046692848206},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.7557944059371948},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.6315126419067383},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6002938151359558},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5862418413162231},{"id":"https://openalex.org/keywords/grid-computing","display_name":"Grid computing","score":0.5508053302764893},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4794413149356842},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4667872190475464},{"id":"https://openalex.org/keywords/computer-cluster","display_name":"Computer cluster","score":0.43885400891304016},{"id":"https://openalex.org/keywords/ranging","display_name":"Ranging","score":0.43013662099838257},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.42976170778274536},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.42285650968551636},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22001171112060547}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.9411891102790833},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.8763710260391235},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8489046692848206},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.7557944059371948},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.6315126419067383},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6002938151359558},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5862418413162231},{"id":"https://openalex.org/C70429105","wikidata":"https://www.wikidata.org/wiki/Q249999","display_name":"Grid computing","level":3,"score":0.5508053302764893},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4794413149356842},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4667872190475464},{"id":"https://openalex.org/C29140674","wikidata":"https://www.wikidata.org/wiki/Q206637","display_name":"Computer cluster","level":2,"score":0.43885400891304016},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.43013662099838257},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.42976170778274536},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.42285650968551636},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22001171112060547},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/1646468.1646480","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1646468.1646480","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.154.6773","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.154.6773","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.nd.edu/~ccl/research/pubs/assembly-mtags09.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5099999904632568,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G7199261362","display_name":null,"funder_award_id":"HHSN266200400039C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8711048020","display_name":null,"funder_award_id":"CNS06-43229","funder_id":"https://openalex.org/F4320337388","funder_display_name":"Division of Computer and Network Systems"}],"funders":[{"id":"https://openalex.org/F4320310260","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337388","display_name":"Division of Computer and Network Systems","ror":"https://ror.org/02rdzmk74"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W19354846","https://openalex.org/W1560961201","https://openalex.org/W1635391495","https://openalex.org/W1984021931","https://openalex.org/W1990061958","https://openalex.org/W2002875415","https://openalex.org/W2010454899","https://openalex.org/W2016974511","https://openalex.org/W2022685385","https://openalex.org/W2103803358","https://openalex.org/W2121762798","https://openalex.org/W2123130398","https://openalex.org/W2123134606","https://openalex.org/W2124088880","https://openalex.org/W2134523814","https://openalex.org/W2141217788","https://openalex.org/W2143012946","https://openalex.org/W2144662851","https://openalex.org/W2150511069","https://openalex.org/W2161292693","https://openalex.org/W2164631357","https://openalex.org/W2166265186","https://openalex.org/W2168338507","https://openalex.org/W2171397799","https://openalex.org/W2173213060","https://openalex.org/W2584945553","https://openalex.org/W4210348154"],"related_works":["https://openalex.org/W2525033434","https://openalex.org/W4280533024","https://openalex.org/W4300992253","https://openalex.org/W2380944047","https://openalex.org/W1942762218","https://openalex.org/W1985270856","https://openalex.org/W3101274117","https://openalex.org/W2382947212","https://openalex.org/W1868575668","https://openalex.org/W2101972225"],"abstract_inverted_index":{"Bioinformatics":[0],"researchers":[1],"need":[2],"efficient":[3],"means":[4],"to":[5,136,150],"process":[6],"large":[7,47,104],"collections":[8],"of":[9,14,49,90,124],"sequence":[10],"data.":[11],"One":[12],"application":[13],"interest,":[15],"genome":[16,39],"assembly,":[17],"has":[18],"great":[19],"potential":[20],"for":[21,129],"parallelization,":[22],"however":[23],"most":[24],"previous":[25],"attempts":[26],"at":[27],"parallelization":[28],"require":[29],"uncommon":[30],"high-end":[31],"hardware.":[32],"This":[33],"paper":[34],"introduces":[35],"a":[36,58,81,91,147,153,165],"scalable":[37,79,82,96],"modular":[38],"assembler":[40],"that":[41],"can":[42],"achieve":[43],"significant":[44],"speedup":[45,117,167],"using":[46,141],"numbers":[48],"conventional":[50],"desktop":[51],"machines,":[52],"such":[53],"as":[54],"those":[55],"found":[56],"in":[57],"campus":[59,92,142],"computing":[60,101],"grid.":[61],"The":[62],"system":[63],"is":[64],"based":[65],"on":[66,121],"the":[67,86,95,99],"Celera":[68],"open-source":[69],"assembly":[70],"toolkit,":[71],"and":[72,111],"replaces":[73],"two":[74],"independent":[75],"sequential":[76],"modules":[77,107],"with":[78,118,168],"replacements:":[80],"candidate":[83],"selector":[84],"exploits":[85,98],"distributed":[87,100],"memory":[88],"capacity":[89],"grid,":[93],"while":[94,114],"aligner":[97],"capacity.":[102],"For":[103],"problems,":[105],"these":[106],"provide":[108],"robust":[109],"task":[110],"data":[112],"management":[113],"also":[115],"achieving":[116],"high":[119],"efficiency":[120],"several":[122,130],"scales":[123],"resources.":[125],"We":[126],"show":[127],"results":[128],"datasets":[131],"ranging":[132,145],"from":[133,146],"738":[134],"thousand":[135,154],"over":[137],"121":[138],"million":[139],"alignments":[140],"grid":[143],"resources":[144],"small":[148],"cluster":[149],"more":[151],"than":[152],"nodes":[155],"spanning":[156],"three":[157],"institutions.":[158],"Our":[159],"largest":[160],"run":[161],"so":[162],"far":[163],"achieves":[164],"927x":[166],"71.3":[169],"percent":[170],"efficiency.":[171],"1.":[172]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}