{"id":"https://openalex.org/W1931807685","doi":"https://doi.org/10.1002/cpe.1799","title":"An experience report: porting the MG\u2010RAST rapid metagenomics analysis pipeline to the cloud","display_name":"An experience report: porting the MG\u2010RAST rapid metagenomics analysis pipeline to the cloud","publication_year":2011,"publication_date":"2011-07-28","ids":{"openalex":"https://openalex.org/W1931807685","doi":"https://doi.org/10.1002/cpe.1799","mag":"1931807685"},"language":"en","primary_location":{"id":"doi:10.1002/cpe.1799","is_oa":true,"landing_page_url":"https://doi.org/10.1002/cpe.1799","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cpe.1799","source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cpe.1799","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027887614","display_name":"Andreas Wilke","orcid":"https://orcid.org/0000-0002-7699-2267"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Wilke","raw_affiliation_strings":["Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050332036","display_name":"Jared Wilkening","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jared Wilkening","raw_affiliation_strings":["Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111479062","display_name":"Elizabeth M. Glass","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth M. Glass","raw_affiliation_strings":["Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113516752","display_name":"Narayan Desai","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Narayan L. Desai","raw_affiliation_strings":["Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086419862","display_name":"Folker Meyer","orcid":"https://orcid.org/0000-0003-1112-2284"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Folker Meyer","raw_affiliation_strings":["Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","Folker Meyer, Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Avn., Argonne, IL, USA","Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics and Computer Science Division Argonne National Laboratory  Argonne IL USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Folker Meyer, Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Avn., Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086419862"],"corresponding_institution_ids":["https://openalex.org/I1282105669"],"apc_list":{"value":4740,"currency":"USD","value_usd":4740},"apc_paid":null,"fwci":0.7301,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.67414022,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"17","first_page":"2250","last_page":"2257"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9937999844551086,"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":0.9937999844551086,"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":0.9850999712944031,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9811000227928162,"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/porting","display_name":"Porting","score":0.8028311729431152},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.7668918967247009},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7460715770721436},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6629447937011719},{"id":"https://openalex.org/keywords/software-deployment","display_name":"Software deployment","score":0.6615396738052368},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.6017240285873413},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5849384069442749},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.533312976360321},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.510202169418335},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.45498576760292053},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44938886165618896},{"id":"https://openalex.org/keywords/virtual-machine","display_name":"Virtual machine","score":0.42145299911499023},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4185701906681061},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.41282233595848083},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.39492517709732056},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.24800503253936768},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.1957438886165619},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13537275791168213},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09067484736442566}],"concepts":[{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.8028311729431152},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7668918967247009},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7460715770721436},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6629447937011719},{"id":"https://openalex.org/C105339364","wikidata":"https://www.wikidata.org/wiki/Q2297740","display_name":"Software deployment","level":2,"score":0.6615396738052368},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6017240285873413},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5849384069442749},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.533312976360321},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.510202169418335},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.45498576760292053},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44938886165618896},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.42145299911499023},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4185701906681061},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.41282233595848083},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.39492517709732056},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.24800503253936768},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.1957438886165619},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13537275791168213},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09067484736442566},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1002/cpe.1799","is_oa":true,"landing_page_url":"https://doi.org/10.1002/cpe.1799","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cpe.1799","source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","raw_type":"journal-article"},{"id":"pmh:oai:www.research.unipd.it:11577/2379713","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/2379713","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1002/cpe.1799","is_oa":true,"landing_page_url":"https://doi.org/10.1002/cpe.1799","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cpe.1799","source":{"id":"https://openalex.org/S11065456","display_name":"Concurrency and Computation Practice and Experience","issn_l":"1532-0626","issn":["1532-0626","1532-0634"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Concurrency and Computation: Practice and Experience","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.41999998688697815,"display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1931807685.pdf"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1991056282","https://openalex.org/W2040704692","https://openalex.org/W2097341408","https://openalex.org/W2113601822","https://openalex.org/W2124637227","https://openalex.org/W2124985265","https://openalex.org/W2136145671"],"related_works":["https://openalex.org/W2356602486","https://openalex.org/W2351992668","https://openalex.org/W2324828474","https://openalex.org/W2374315191","https://openalex.org/W2391207559","https://openalex.org/W2384715785","https://openalex.org/W2349624418","https://openalex.org/W2064459023","https://openalex.org/W2359852344","https://openalex.org/W2378061014"],"abstract_inverted_index":{"SUMMARY":[0],"Existing":[1],"applications":[2],"in":[3,77],"computational":[4,13,80],"biology":[5],"typically":[6],"favor":[7],"a":[8,17,40,89,93],"local":[9,33],"cluster":[10,34],"based":[11],"integrated":[12],"platform.":[14],"We":[15],"present":[16],"lessons":[18],"learned":[19],"type":[20,59],"report":[21],"for":[22,63,86],"scaling":[23,69],"up":[24],"an":[25],"existing":[26],"metagenomics":[27],"application":[28],"that":[29],"outgrew":[30],"the":[31,56,64,72,79,98,103],"available":[32,62],"hardware.":[35],"In":[36],"our":[37],"example,":[38],"removing":[39],"number":[41,57],"of":[42,60,71,105],"assumptions":[43,75],"linked":[44],"to":[45,49,110],"tight":[46],"integration":[47],"allowed":[48],"expand":[50],"beyond":[51],"one":[52],"administrative":[53],"domain,":[54],"increase":[55],"and":[58,66,101],"machines":[61],"application,":[65],"also":[67],"improved":[68],"properties":[70],"application.":[73],"The":[74],"made":[76],"designing":[78],"client":[81],"make":[82],"it":[83],"well":[84],"suitable":[85],"deployment":[87],"as":[88],"virtual":[90],"machine":[91],"inside":[92],"cloud.":[94],"This":[95],"paper":[96],"discusses":[97],"decision":[99],"process":[100],"describes":[102],"suitability":[104],"deploying":[106],"various":[107],"bioinformatics":[108],"computations":[109],"distributed":[111],"heterogeneous":[112],"machines.":[113],"Copyright":[114],"\u00a9":[115],"2011":[116],"John":[117],"Wiley":[118],"&amp;":[119],"Sons,":[120],"Ltd.":[121]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2016-06-24T00:00:00"}
