{"id":"https://openalex.org/W2594401995","doi":"https://doi.org/10.1109/escience.2016.7870889","title":"Conducting reproducible research with Umbrella: Tracking, creating, and preserving execution environments","display_name":"Conducting reproducible research with Umbrella: Tracking, creating, and preserving execution environments","publication_year":2016,"publication_date":"2016-10-01","ids":{"openalex":"https://openalex.org/W2594401995","doi":"https://doi.org/10.1109/escience.2016.7870889","mag":"2594401995"},"language":"en","primary_location":{"id":"doi:10.1109/escience.2016.7870889","is_oa":false,"landing_page_url":"https://doi.org/10.1109/escience.2016.7870889","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE 12th International Conference on e-Science (e-Science)","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/A5104306486","display_name":"Haiyan Meng","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":"Haiyan Meng","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Notre Dame, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Notre Dame, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"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":["Department of Computer Science and Engineering, University of Notre Dame, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Notre Dame, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020714658","display_name":"Alexander Vyushkov","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":false,"raw_author_name":"Alexander Vyushkov","raw_affiliation_strings":["Center for Research Computing University of Notre Dame, USA"],"affiliations":[{"raw_affiliation_string":"Center for Research Computing University of Notre Dame, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106332815","display_name":"Matthias Wolf","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":false,"raw_author_name":"Matthias Wolf","raw_affiliation_strings":["Department of Physics University of Notre Dame, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics University of Notre Dame, USA","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101715118","display_name":"Anna Woodard","orcid":"https://orcid.org/0000-0002-8640-5417"},"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":"Anna Woodard","raw_affiliation_strings":["Department of Physics University of Notre Dame, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics University of Notre Dame, USA","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5104306486"],"corresponding_institution_ids":["https://openalex.org/I107639228"],"apc_list":null,"apc_paid":null,"fwci":2.829,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.93783881,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"1","issue":null,"first_page":"91","last_page":"100"},"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/T11937","display_name":"Research Data Management Practices","score":0.9883999824523926,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9775999784469604,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.8432224988937378},{"id":"https://openalex.org/keywords/sandbox","display_name":"Sandbox (software development)","score":0.7991807460784912},{"id":"https://openalex.org/keywords/virtual-machine","display_name":"Virtual machine","score":0.6106106042861938},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.5246185064315796},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.430111825466156},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4276217222213745},{"id":"https://openalex.org/keywords/execution-model","display_name":"Execution model","score":0.4238736927509308}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8432224988937378},{"id":"https://openalex.org/C167981075","wikidata":"https://www.wikidata.org/wiki/Q2667186","display_name":"Sandbox (software development)","level":2,"score":0.7991807460784912},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.6106106042861938},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.5246185064315796},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.430111825466156},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4276217222213745},{"id":"https://openalex.org/C2776834041","wikidata":"https://www.wikidata.org/wiki/Q25346349","display_name":"Execution model","level":2,"score":0.4238736927509308}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/escience.2016.7870889","is_oa":false,"landing_page_url":"https://doi.org/10.1109/escience.2016.7870889","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE 12th International Conference on e-Science (e-Science)","raw_type":"proceedings-article"},{"id":"mag:2746375966","is_oa":false,"landing_page_url":"http://jglobal.jst.go.jp/en/public/201702239975463464","pdf_url":null,"source":{"id":"https://openalex.org/S4306512817","display_name":"IEEE Conference Proceedings","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":"IEEE Conference Proceedings","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310260","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W59965179","https://openalex.org/W138849684","https://openalex.org/W1229457308","https://openalex.org/W1598312013","https://openalex.org/W1659560869","https://openalex.org/W1893864409","https://openalex.org/W1981745715","https://openalex.org/W1994326726","https://openalex.org/W2025088419","https://openalex.org/W2027585589","https://openalex.org/W2032549894","https://openalex.org/W2049776754","https://openalex.org/W2056735075","https://openalex.org/W2058775476","https://openalex.org/W2072327049","https://openalex.org/W2083600658","https://openalex.org/W2103732378","https://openalex.org/W2104279568","https://openalex.org/W2121542813","https://openalex.org/W2141782735","https://openalex.org/W2150454120","https://openalex.org/W2159721641","https://openalex.org/W2245228454","https://openalex.org/W2277037180","https://openalex.org/W2296335794","https://openalex.org/W2521825536","https://openalex.org/W2540151287","https://openalex.org/W2592868829","https://openalex.org/W2758409057","https://openalex.org/W3081767002","https://openalex.org/W3100379359","https://openalex.org/W4230625563","https://openalex.org/W4285719527","https://openalex.org/W6605738145","https://openalex.org/W6628053425","https://openalex.org/W6635643217","https://openalex.org/W6637181491","https://openalex.org/W6675404675","https://openalex.org/W6675762642","https://openalex.org/W6694906831","https://openalex.org/W6697144307","https://openalex.org/W6727374762","https://openalex.org/W6744542489","https://openalex.org/W6782809326"],"related_works":["https://openalex.org/W3124171372","https://openalex.org/W2235294519","https://openalex.org/W4248174414","https://openalex.org/W2943837643","https://openalex.org/W2075174112","https://openalex.org/W2622620488","https://openalex.org/W2976854232","https://openalex.org/W2931307517","https://openalex.org/W2779209348","https://openalex.org/W2947326503"],"abstract_inverted_index":{"Publishing":[0],"scientific":[1,154],"results":[2,11,194],"without":[3],"the":[4,10,21,25,28,31,52,62,84,166,176,179,211],"detailed":[5],"execution":[6,32,64,76,80,86,94,109,126],"environments":[7,33,65],"describing":[8],"how":[9],"were":[12],"collected":[13],"makes":[14],"it":[15,150],"difficult":[16],"or":[17],"even":[18,209],"impossible":[19],"for":[20,141,186],"reader":[22],"to":[23,37,123,136,151,190],"reproduce":[24,152],"work.":[26],"However,":[27],"configurations":[29],"of":[30,54,171,178],"are":[34],"too":[35],"complex":[36],"be":[38,137,200],"described":[39],"easily":[40],"by":[41,57,139,148],"authors.":[42],"To":[43],"solve":[44],"this":[45],"problem,":[46],"we":[47],"propose":[48],"a":[49,71],"framework":[50,69,147],"facilitating":[51],"conduct":[53],"reproducible":[55],"research":[56],"tracking,":[58],"creating,":[59],"and":[60,74,88,103,120,128,160,168,175,183,207,213],"preserving":[61],"comprehensive":[63],"with":[66],"Umbrella.":[67],"The":[68,108],"includes":[70],"lightweight,":[72],"persistent":[73,97],"deployable":[75],"environment":[77,95],"specification,":[78],"an":[79,89,93,125],"engine":[81,110],"which":[82,91],"creates":[83],"specified":[85],"environments,":[87],"archiver":[90],"archives":[92],"into":[96],"storage":[98],"services":[99],"like":[100,114,132],"Amazon":[101],"S3":[102],"Open":[104],"Science":[105],"Framework":[106],"(OSF).":[107],"utilizes":[111],"sandbox":[112,204],"techniques":[113,205],"virtual":[115],"machines":[116],"(VMs),":[117],"Linux":[118],"containers":[119],"user-space":[121],"tracers,":[122],"create":[124],"environment,":[127],"allows":[129],"common":[130],"dependencies":[131],"base":[133],"OS":[134],"images":[135],"shared":[138],"sandboxes":[140],"different":[142,188,203],"applications.":[143],"We":[144,164],"evaluate":[145,165],"our":[146],"utilizing":[149],"three":[153],"applications":[155,189,198],"from":[156],"epidemiology,":[157],"scene":[158],"rendering,":[159],"high":[161],"energy":[162],"physics.":[163],"time":[167],"space":[169],"overhead":[170,212],"reproducing":[172],"these":[173,197],"applications,":[174],"effectiveness":[177],"chosen":[180],"archive":[181],"unit":[182],"mounting":[184],"mechanism":[185],"allowing":[187],"share":[191],"dependencies.":[192],"Our":[193],"show":[195],"that":[196],"can":[199],"reproduced":[201],"using":[202],"successfully":[206],"efficiently,":[208],"through":[210],"performance":[214],"slightly":[215],"vary.":[216]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
