{"id":"https://openalex.org/W3027376788","doi":"https://doi.org/10.1371/journal.pcbi.1007881","title":"Improving reproducibility in computational biology research","display_name":"Improving reproducibility in computational biology research","publication_year":2020,"publication_date":"2020-05-19","ids":{"openalex":"https://openalex.org/W3027376788","doi":"https://doi.org/10.1371/journal.pcbi.1007881","mag":"3027376788","pmid":"https://pubmed.ncbi.nlm.nih.gov/32427998"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007881","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007881","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007881&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"editorial","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007881&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045576072","display_name":"Feilim Mac Gabhann","orcid":"https://orcid.org/0000-0003-3481-7740"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Feilim Mac Gabhann","raw_affiliation_strings":["Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086460310","display_name":"David Nickerson","orcid":"https://orcid.org/0000-0003-4667-9779"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"David Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077187288","display_name":"Anand Rampadarath","orcid":"https://orcid.org/0000-0001-8830-6212"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Anand Rampadarath","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000119406","https://openalex.org/A5086460310"],"corresponding_institution_ids":["https://openalex.org/I154130895","https://openalex.org/I51556381"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":11.87379295,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.98210145,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"16","issue":"5","first_page":"e1007881","last_page":"e1007881"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9908000230789185,"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":0.9850999712944031,"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/reproducibility","display_name":"Reproducibility","score":0.7192386388778687},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4530971348285675},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4106501340866089},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3622971475124359},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22009187936782837},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09238079190254211}],"concepts":[{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.7192386388778687},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4530971348285675},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4106501340866089},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3622971475124359},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22009187936782837},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09238079190254211}],"mesh":[{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012106","descriptor_name":"Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1007881","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007881","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007881&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32427998","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32427998","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1007881","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007881","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:47ea7c0a7727481183e525a19e4a8e52","is_oa":true,"landing_page_url":"https://doaj.org/article/47ea7c0a7727481183e525a19e4a8e52","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 5, p e1007881 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7236972","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7236972","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007881","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007881","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007881&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3027376788.pdf","grobid_xml":"https://content.openalex.org/works/W3027376788.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2036318837","https://openalex.org/W2144981148","https://openalex.org/W2302501749","https://openalex.org/W2320969362","https://openalex.org/W2331384579","https://openalex.org/W2406493898","https://openalex.org/W2773787581","https://openalex.org/W2790858109","https://openalex.org/W2964148489"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2413717610","https://openalex.org/W1973270181","https://openalex.org/W2417696084","https://openalex.org/W2368782778","https://openalex.org/W2119695867","https://openalex.org/W2087830269","https://openalex.org/W2130076355"],"abstract_inverted_index":{"There":[0],"has":[1,17,49],"been":[2,18,50],"much":[3],"discussion":[4],"in":[5,14,57,63,70,91,186,217,245,287],"the":[6,21,37,58,64,107,127,195,218,237,240,246,248,255,268,273,277,283,288,296,307,310,325],"scientific":[7,43],"literature":[8],"on":[9,36,117],"a":[10,46,53,76,80,134,204,220,293,313],"crisis":[11],"of":[12,23,55,89,106,239,276,309],"reproducibility":[13,90,211,238,308],"science":[15],"[1,2].It":[16],"reported":[19],"that":[20,25,82,140,145,162,295],"percentage":[22],"studies":[24],"are":[26,137,312],"reproducible":[27,155],"is":[28,74],"as":[29,31,167],"low":[30],"10%":[32],"or":[33,103,122,176],"less,":[34],"depending":[35],"discipline":[38],"[3].This":[39],"inability":[40],"to":[41,52,98,119,125,132,149,202,209,215,228,234,266,281,318],"reproduce":[42],"findings":[44],"from":[45],"given":[47,135],"paper":[48],"attributed":[51,97],"lack":[54,88],"clarity":[56],"methods":[59],"and":[60,182,302,305],"inherent":[61],"variability":[62],"biological":[65],"system":[66],"being":[67],"studied":[68],"[4].Reproducibility":[69],"computational":[71,92,151,241],"biology":[72,93,152],"research":[73,94,153],"certainly":[75],"problem,":[77],"yet":[78],"perhaps":[79],"challenge":[81],"our":[83,229,258],"field":[84],"can":[85,95,147,251,264,327],"uniquely":[86],"tackle.A":[87],"be":[96,224],"many":[99],"factors,":[100],"but":[101],"incomplete":[102,115],"erroneous":[104],"descriptions":[105],"simulations":[108],"(e.g.,":[109,156],"which":[110],"software":[111],"version":[112],"was":[113],"used),":[114],"documentation":[116],"how":[118],"run":[120,133],"simulations,":[121],"simply":[123],"failing":[124],"post":[126],"relevant":[128],"computer":[129],"code":[130],"needed":[131],"simulation":[136],"common":[138],"issues":[139],"occur.Many":[141],"tools":[142],"have":[143,267,282],"emerged":[144],"we":[146,316],"leverage":[148],"make":[150],"more":[154],"http://co.mbine.org/and":[157],"https://normsys.h-its.org/)and":[158],"there":[159],"exist":[160],"articles":[161],"propose":[163],"best":[164],"practices,":[165],"such":[166],"Ten":[168,177],"Simple":[169,178],"Rules":[170,179],"for":[171,180,197,254],"Reproducible":[172,198],"Computational":[173,184,190],"Research":[174],"[5]":[175],"Writing":[181],"Sharing":[183],"Analyses":[185],"Jupyter":[187],"Notebooks":[188],"[6].PLOS":[189],"Biology":[191],"recently":[192],"partnered":[193],"with":[194,260,292,320],"Center":[196],"Biomedical":[199],"Modeling":[200],"(https://reproduciblebiomodels.org/)":[201],"launch":[203],"pilot":[205,326],"peer":[206,221,231,249,269],"review":[207,232,284,298],"workflow":[208],"assess":[210,304],"(https://blogs.plos.org/biologue/2020/05/05/improving-reproducibilityof-computational-models/).After":[212],"authors":[213,263,303],"opt-in":[214],"participation":[216],"pilot,":[219,322],"reviewer":[222],"will":[223,299],"solicited":[225],"(in":[226],"addition":[227],"normal":[230],"assessment)":[233],"specifically":[235],"evaluate":[236],"modeling":[242],"aspects":[243],"described":[244],"submission.All":[247],"reviewers":[250],"receive":[252],"credit":[253],"reviews":[256,270],"through":[257],"partnership":[259],"ORCID":[261],"(https://blogs.plos.org/plos/2019/06/youve-completed-your-review-now-get-credit-withorcid/)and":[262],"elect":[265],"published":[271],"alongside":[272],"final":[274],"publication":[275],"work":[278],"(https://blogs.plos.org/plos/2019/05/plos-journals-now-open-for-published-peerreview/).We":[279],"aim":[280],"process":[285],"completed":[286],"usual":[289],"time":[290],"frame":[291],"hope":[294],"additional":[297],"help":[300],"editors":[301],"improve":[306],"work.There":[311],"few":[314],"questions":[315,324],"intend":[317],"investigate":[319],"this":[321],"including":[323],"answer":[328],"directly":[329]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":3}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
