{"id":"https://openalex.org/W2036318837","doi":"https://doi.org/10.1371/journal.pcbi.1003285","title":"Ten Simple Rules for Reproducible Computational Research","display_name":"Ten Simple Rules for Reproducible Computational Research","publication_year":2013,"publication_date":"2013-10-24","ids":{"openalex":"https://openalex.org/W2036318837","doi":"https://doi.org/10.1371/journal.pcbi.1003285","mag":"2036318837","pmid":"https://pubmed.ncbi.nlm.nih.gov/24204232"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003285","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003285","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003285&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":"article","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.1003285&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054500587","display_name":"Geir Kjetil Sandve","orcid":"https://orcid.org/0000-0002-4959-1409"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Geir Kjetil Sandve","raw_affiliation_strings":["Department of Informatics, University of Oslo, Blindern, Oslo, Norway ; Centre for Cancer Biomedicine, University of Oslo, Blindern, Oslo, Norway","Centre for Cancer Biomedicine, University of Oslo, Blindern, Oslo, Norway","Department of Informatics, University of Oslo, Blindern, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Oslo, Blindern, Oslo, Norway ; Centre for Cancer Biomedicine, University of Oslo, Blindern, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Centre for Cancer Biomedicine, University of Oslo, Blindern, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Informatics, University of Oslo, Blindern, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065292926","display_name":"Anton Nekrutenko","orcid":"https://orcid.org/0000-0002-5987-8032"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anton Nekrutenko","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology and The Huck Institutes for the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology and The Huck Institutes for the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025611053","display_name":"James Taylor","orcid":"https://orcid.org/0000-0001-5079-840X"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Taylor","raw_affiliation_strings":["Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, United States of America","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083493986","display_name":"Eivind Hovig","orcid":"https://orcid.org/0000-0002-9103-1077"},"institutions":[{"id":"https://openalex.org/I1281400175","display_name":"Oslo University Hospital","ror":"https://ror.org/00j9c2840","country_code":"NO","type":"healthcare","lineage":["https://openalex.org/I1281400175"]},{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]},{"id":"https://openalex.org/I2801049993","display_name":"Norwegian Cancer Society","ror":"https://ror.org/01925vb10","country_code":"NO","type":"nonprofit","lineage":["https://openalex.org/I2801049993"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Eivind Hovig","raw_affiliation_strings":["Department of Informatics, University of Oslo, Blindern, Oslo, Norway","Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway","Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Oslo, Blindern, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway","institution_ids":["https://openalex.org/I1281400175","https://openalex.org/I2801049993"]},{"raw_affiliation_string":"Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway","institution_ids":["https://openalex.org/I1281400175"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5054500587"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":109.3285,"has_fulltext":true,"cited_by_count":840,"citation_normalized_percentile":{"value":0.99966007,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"9","issue":"10","first_page":"e1003285","last_page":"e1003285"},"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":0.9666000008583069,"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/simple","display_name":"Simple (philosophy)","score":0.715582013130188},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5595791339874268},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3669698238372803},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19173598289489746}],"concepts":[{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.715582013130188},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5595791339874268},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3669698238372803},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19173598289489746},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1003285","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003285","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003285&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:24204232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24204232","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:pcbi00:1003285","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285","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:5aee2d1cb8a4445e934e74bc17698609","is_oa":true,"landing_page_url":"https://doaj.org/article/5aee2d1cb8a4445e934e74bc17698609","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"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 9, Iss 10, p e1003285 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2808931","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3812051","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3812051","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3812051","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"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.1003285","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003285","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003285&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":[{"id":"https://openalex.org/G1567103826","display_name":null,"funder_award_id":"HG004909","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2220218202","display_name":null,"funder_award_id":"R01 HG004909","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G505996347","display_name":null,"funder_award_id":"HG005133","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5101641226","display_name":null,"funder_award_id":"R21 HG005133","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7470937020","display_name":null,"funder_award_id":"HG004909","funder_id":"https://openalex.org/F4320308109","funder_display_name":"Pennsylvania Department of Health"},{"id":"https://openalex.org/G7624479807","display_name":null,"funder_award_id":"U41 HG006620","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7714384854","display_name":null,"funder_award_id":"HG005133","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7895748443","display_name":null,"funder_award_id":"HG006620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7943371043","display_name":"Cyberinfrastructure for Accessible and Reproducible Research in Life Sciences","funder_award_id":"0850103","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G83632010","display_name":null,"funder_award_id":"HG006620","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8939430086","display_name":null,"funder_award_id":"HG004909","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308109","display_name":"Pennsylvania Department of Health","ror":"https://ror.org/00ra1fg11"},{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320310419","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333182","display_name":"Huck Institutes of the Life Sciences","ror":null},{"id":"https://openalex.org/F4320334254","display_name":"Institute for Computational and Data Sciences, Pennsylvania State University","ror":null},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2036318837.pdf","grobid_xml":"https://content.openalex.org/works/W2036318837.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1520411860","https://openalex.org/W1544923801","https://openalex.org/W1968659469","https://openalex.org/W1977859620","https://openalex.org/W1987777080","https://openalex.org/W2002955157","https://openalex.org/W2008985174","https://openalex.org/W2019866696","https://openalex.org/W2020541351","https://openalex.org/W2022406334","https://openalex.org/W2046766973","https://openalex.org/W2067833766","https://openalex.org/W2069529061","https://openalex.org/W2089088376","https://openalex.org/W2090469606","https://openalex.org/W2096435507","https://openalex.org/W2100471807","https://openalex.org/W2121907019","https://openalex.org/W2129666400","https://openalex.org/W2136482257","https://openalex.org/W2140157849","https://openalex.org/W2142188478","https://openalex.org/W2161027533","https://openalex.org/W2161645441","https://openalex.org/W2168103533","https://openalex.org/W2171301910","https://openalex.org/W4253759977"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W1585007175","https://openalex.org/W2382521049","https://openalex.org/W2390279801","https://openalex.org/W2144385241","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4253593777"],"abstract_inverted_index":{"Replication":[0],"is":[1,52,216,253,303,340,417,422,466,673,684,721],"the":[2,21,24,72,86,190,225,296,308,315,327,367,402,414,425,445,452,457,461,481,497,502,517,537,544,574,580,593],"cornerstone":[3],"of":[4,16,23,46,74,100,108,151,198,232,251,273,285,326,335,344,349,413,427,454,480,499,539,546,555,584,592,614,622,639,642,668,697,730,745,757],"a":[5,60,90,148,196,219,230,237,248,293,332,355,434,449,477,563,599,607,619,632,654,688,698,702,727],"cumulative":[6],"science":[7,84],"[1].":[8],"However,":[9,492],"new":[10,267,278],"tools":[11],"and":[12,20,88,98,110,146,169,177,203,275,323,337,347,440,456,649,708,714,743],"technologies,":[13],"massive":[14],"amounts":[15],"data,":[17,268],"interdisciplinary":[18],"approaches,":[19],"complexity":[22],"questions":[25],"being":[26,483],"asked":[27],"are":[28,33,353,381],"complicating":[29],"replication":[30,45,109],"efforts,":[31],"as":[32,65,241,305,314,391,508,560],"increased":[34,738],"pressures":[35],"on":[36,48,103,162,266,419],"scientists":[37],"to":[38,94,160,181,194,204,212,224,257,262,270,291,358,374,429,447,459,505,515,529,572,595,626,656,685,701,722,737,771],"advance":[39],"their":[40],"research":[41,64,313,462,594,774],"[2].":[42],"As":[43,245],"full":[44,407],"studies":[47,117,131],"independently":[49],"collected":[50],"data":[51,105],"often":[53,617],"not":[54,217],"feasible,":[55],"there":[56,672],"has":[57,112,158,186],"recently":[58,113],"been":[59,114,187],"call":[61],"for":[62,70,128,200,207,239,277,411,543,631,755,767,778,781],"reproducible":[63,312],"an":[66,140,242,246,387,552,636],"attainable":[67],"minimum":[68],"standard":[69],"assessing":[71],"value":[73],"scientific":[75,120,191,226],"claims":[76,209],"[3].":[77],"This":[78,157,469,577],"requires":[79],"that":[80,119,174,189,214,229,301,310,317,476,536,557,653,676,724],"papers":[81,121,144],"in":[82,142,255,295,342,624,670,695],"experimental":[83,125,137],"describe":[85],"results":[87,138,276,575,694],"provide":[89,406],"sufficiently":[91],"clear":[92],"protocol":[93],"allow":[95,258,271],"successful":[96],"repetition":[97],"extension":[99,683,720],"analyses":[101,385,482,556],"based":[102],"original":[104],"[4].\r\n\r\nThe":[106],"importance":[107],"reproducibility":[111,215,233,252,286,302,455,540,615,669,756],"exemplified":[115],"through":[116,147,386],"showing":[118,132],"commonly":[122],"leave":[123],"out":[124,290,463,485,559],"details":[126],"essential":[127],"reproduction":[129,662],"[5],":[130],"difficulties":[133],"with":[134,222,437,496,598],"replicating":[135],"published":[136,208],"[6],":[139,748],"increase":[141,175,715],"retracted":[143],"[7],":[145],"high":[149],"number":[150,638],"failing":[152],"clinical":[153],"trials":[154],"[8],":[155],"[9].":[156],"led":[159],"discussions":[161],"how":[163,428],"individual":[164,243],"researchers,":[165],"institutions,":[166],"funding":[167],"bodies,":[168],"journals":[170],"can":[171,234,318,677,692,706,735,762],"establish":[172],"routines":[173],"transparency":[176],"reproducibility.":[178],"In":[179,280],"order":[180,256,625],"foster":[182],"such":[183],"aspects,":[184],"it":[185,206,465,509,531,603,777],"suggested":[188],"community":[192],"needs":[193],"develop":[195],"\u201cculture":[197],"reproducibility\u201d":[199],"computational":[201,758],"science,":[202],"require":[205,618],"[3].\r\n\r\nWe":[210],"want":[211,770],"emphasize":[213],"only":[218],"moral":[220],"responsibility":[221],"respect":[223],"field,":[227],"but":[228],"lack":[231],"also":[235],"be":[236,263,292,512,570,596,627,635,678,763],"burden":[238],"you":[240,352,370,380,566,691,705,769],"researcher.":[244],"example,":[247],"good":[249,283],"practice":[250],"necessary":[254,518],"previously":[259],"developed":[260],"methodology":[261],"effectively":[264],"applied":[265],"or":[269,399,408,780],"reuse":[272,710],"code":[274],"projects.":[279],"other":[281],"words,":[282],"habits":[284,309],"may":[287,404,443,510,604,659],"actually":[288],"turn":[289],"time-saver":[294],"longer":[297],"run.\r\n\r\nWe":[298],"further":[299],"note":[300],"just":[304],"much":[306,525,674],"about":[307],"ensure":[311,506,723],"technologies":[316],"make":[319,448,660,772],"these":[320,431],"processes":[321],"efficient":[322],"realistic.":[324],"Each":[325],"following":[328],"ten":[329,752],"rules":[330,754,761],"captures":[331],"specific":[333],"aspect":[334],"reproducibility,":[336,507],"discusses":[338],"what":[339],"needed":[341,418],"terms":[343],"information":[345],"handling":[346],"tracking":[348],"procedures.":[350],"If":[351,379],"taking":[354],"bare-bones":[356],"approach":[357],"bioinformatics":[359],"analysis,":[360],"i.e.,":[361],"running":[362],"various":[363],"custom":[364],"scripts":[365],"from":[366,520,687],"command":[368],"line,":[369],"will":[371,541,616,630],"probably":[372],"need":[373,446,458],"handle":[375],"each":[376],"rule":[377],"explicitly.":[378],"instead":[382],"performing":[383],"your":[384,420,711,716,732,746,765,773,782],"integrated":[388],"framework":[389],"(such":[390],"GenePattern":[392],"[10],":[393],"Galaxy":[394],"[11],":[395],"LONI":[396],"pipeline":[397],"[12],":[398],"Taverna":[400],"[13]),":[401],"system":[403],"already":[405,511],"partial":[409],"support":[410],"most":[412,581],"rules.":[415],"What":[416],"part":[421,479],"then":[423],"merely":[424],"knowledge":[426],"exploit":[430],"existing":[432],"possibilities.\r\n\r\nIn":[433],"pragmatic":[435],"setting,":[436],"publication":[438],"pressure":[439],"deadlines,":[441],"one":[442,494],"face":[444],"trade-off":[450,470],"between":[451],"ideals":[453],"get":[460],"while":[464,532],"still":[467],"relevant.":[468],"becomes":[471],"more":[472,526,675,775],"important":[473],"when":[474],"considering":[475],"large":[478],"tried":[484],"never":[486],"end":[487],"up":[488],"yielding":[489],"any":[490,588],"results.":[491],"frequently":[493],"will,":[495],"wisdom":[498],"hindsight,":[500],"contemplate":[501],"missed":[503],"opportunity":[504],"too":[513],"late":[514],"take":[516,657],"notes":[519,658],"memory":[521],"(or":[522],"at":[523,568,764],"least":[524,569],"difficult":[527],"than":[528],"do":[530],"underway).":[533],"We":[534],"believe":[535],"rewards":[538],"compensate":[542],"risk":[545],"having":[547],"spent":[548],"valuable":[549],"time":[550],"developing":[551],"annotated":[553],"catalog":[554],"turned":[558],"blind":[561],"alleys.\r\n\r\nAs":[562],"minimal":[564],"requirement,":[565,610],"should":[567],"able":[571],"reproduce":[573,693],"yourself.":[576],"would":[578],"satisfy":[579],"basic":[582,666],"requirements":[583],"sound":[585,605],"research,":[586],"allowing":[587],"substantial":[589],"future":[590,783],"questioning":[591],"met":[597],"precise":[600],"explanation.":[601],"Although":[602],"like":[606],"very":[608],"weak":[609],"even":[611],"this":[612,665],"level":[613,621,667,689,703],"certain":[620],"care":[623],"met.":[628],"There":[629],"given":[633],"analysis":[634],"exponential":[637],"possible":[640],"combinations":[641],"software":[643],"versions,":[644],"parameter":[645],"values,":[646],"pre-processing":[647],"steps,":[648],"so":[650],"on,":[651],"meaning":[652],"failure":[655],"exact":[661],"essentially":[663],"impossible.\r\n\r\nWith":[664],"place,":[671],"wished":[679],"for.":[680],"An":[681],"obvious":[682],"go":[686],"where":[690,704],"case":[696],"critical":[699],"situation":[700],"practically":[707],"routinely":[709],"previous":[712],"work":[713,747],"productivity.":[717],"A":[718],"second":[719],"peers":[725,779],"have":[726],"practical":[728],"possibility":[729],"reproducing":[731],"results,":[733],"which":[734],"lead":[736],"trust":[739],"in,":[740],"interest":[741],"for,":[742],"citations":[744],"[14].\r\n\r\nWe":[749],"here":[750],"present":[751],"simple":[753],"research.":[759],"These":[760],"disposal":[766],"whenever":[768],"accessible\u2014be":[776],"self.":[784]},"counts_by_year":[{"year":2026,"cited_by_count":79},{"year":2025,"cited_by_count":60},{"year":2024,"cited_by_count":54},{"year":2023,"cited_by_count":52},{"year":2022,"cited_by_count":69},{"year":2021,"cited_by_count":70},{"year":2020,"cited_by_count":70},{"year":2019,"cited_by_count":99},{"year":2018,"cited_by_count":82},{"year":2017,"cited_by_count":70},{"year":2016,"cited_by_count":62},{"year":2015,"cited_by_count":44},{"year":2014,"cited_by_count":25},{"year":2013,"cited_by_count":3}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
