{"id":"https://openalex.org/W2090469606","doi":"https://doi.org/10.1371/journal.pcbi.1002802","title":"Ten Simple Rules for the Open Development of Scientific Software","display_name":"Ten Simple Rules for the Open Development of Scientific Software","publication_year":2012,"publication_date":"2012-12-06","ids":{"openalex":"https://openalex.org/W2090469606","doi":"https://doi.org/10.1371/journal.pcbi.1002802","mag":"2090469606","pmid":"https://pubmed.ncbi.nlm.nih.gov/23236269"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1002802","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002802","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002802&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.1002802&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077634829","display_name":"Andreas Prli\u0107","orcid":"https://orcid.org/0000-0001-6346-6391"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andreas Prli\u0107","raw_affiliation_strings":["San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America","San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America"],"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023826543","display_name":"James B Procter","orcid":"https://orcid.org/0000-0002-7865-7382"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James B. Procter","raw_affiliation_strings":["School of Life Sciences Research, College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences Research, College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom","institution_ids":["https://openalex.org/I177639307"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077634829"],"corresponding_institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":25.16566593,"has_fulltext":true,"cited_by_count":145,"citation_normalized_percentile":{"value":0.99462366,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"8","issue":"12","first_page":"e1002802","last_page":"e1002802"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9873999953269958,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9638000130653381,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.6977336406707764},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6409502029418945},{"id":"https://openalex.org/keywords/open-science","display_name":"Open science","score":0.6174556016921997},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.607251763343811},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5518803596496582},{"id":"https://openalex.org/keywords/open-data","display_name":"Open data","score":0.5314406752586365},{"id":"https://openalex.org/keywords/intellectual-property","display_name":"Intellectual property","score":0.5206417441368103},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5143114328384399},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.4521328806877136},{"id":"https://openalex.org/keywords/publishing","display_name":"Publishing","score":0.4394795298576355},{"id":"https://openalex.org/keywords/open-source-software-development","display_name":"Open-source software development","score":0.42135974764823914},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3659229874610901},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3472052812576294},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.14388936758041382}],"concepts":[{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.6977336406707764},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6409502029418945},{"id":"https://openalex.org/C2778149293","wikidata":"https://www.wikidata.org/wiki/Q309823","display_name":"Open science","level":2,"score":0.6174556016921997},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.607251763343811},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5518803596496582},{"id":"https://openalex.org/C2780535194","wikidata":"https://www.wikidata.org/wiki/Q309901","display_name":"Open data","level":2,"score":0.5314406752586365},{"id":"https://openalex.org/C34974158","wikidata":"https://www.wikidata.org/wiki/Q131257","display_name":"Intellectual property","level":2,"score":0.5206417441368103},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5143114328384399},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.4521328806877136},{"id":"https://openalex.org/C151719136","wikidata":"https://www.wikidata.org/wiki/Q3972943","display_name":"Publishing","level":2,"score":0.4394795298576355},{"id":"https://openalex.org/C2778642129","wikidata":"https://www.wikidata.org/wiki/Q7096425","display_name":"Open-source software development","level":4,"score":0.42135974764823914},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3659229874610901},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3472052812576294},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.14388936758041382},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1002802","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002802","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002802&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:23236269","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23236269","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:pcbi00:1002802","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002802","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:761d4be3cb0d44c59a30a8de82aedf78","is_oa":true,"landing_page_url":"https://doaj.org/article/761d4be3cb0d44c59a30a8de82aedf78","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 8, Iss 12, p e1002802 (2012)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2519958","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3516539","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1002802","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1002802","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002802&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":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G2588893951","display_name":null,"funder_award_id":"BB/G022682/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2090469606.pdf","grobid_xml":"https://content.openalex.org/works/W2090469606.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1484115408","https://openalex.org/W1816998076","https://openalex.org/W1986142097","https://openalex.org/W2055043387","https://openalex.org/W2055623935","https://openalex.org/W2057414058","https://openalex.org/W2085885912","https://openalex.org/W2095192690","https://openalex.org/W2100790938","https://openalex.org/W2100827887","https://openalex.org/W2104483961","https://openalex.org/W2105803236","https://openalex.org/W2106882534","https://openalex.org/W2114850508","https://openalex.org/W2128189891","https://openalex.org/W2128567635","https://openalex.org/W2131966673","https://openalex.org/W2150934173","https://openalex.org/W2158714788","https://openalex.org/W2170351296"],"related_works":["https://openalex.org/W2400751427","https://openalex.org/W2482697570","https://openalex.org/W2738396072","https://openalex.org/W2345835657","https://openalex.org/W4285196440","https://openalex.org/W4229077818","https://openalex.org/W4390554521","https://openalex.org/W3017109063","https://openalex.org/W2188588845","https://openalex.org/W4311627903"],"abstract_inverted_index":{"Open-source":[0],"software":[1,18,51,129,203,232,271,281,295,387,395],"development":[2,254,356,383],"has":[3,357],"had":[4],"significant":[5],"impact,":[6],"not":[7,42,86,159,199,215],"only":[8,87],"on":[9,13,287,365,376],"society,":[10],"but":[11,93],"also":[12,94],"scientific":[14,39,386],"research.":[15,123],"Papers":[16],"describing":[17],"published":[19],"as":[20,132,134,406],"open":[21,50,71,211,253,323,353,385],"source":[22,82,126,208],"are":[23,68,99,402],"amongst":[24],"the":[25,74,81,125,128,184,207,237,256,260,280,283,294,329,342,349,366,382,391,398],"most":[26],"widely":[27],"cited":[28],"publications":[29],"(e.g.,":[30],"BLAST":[31],"[1],":[32],"[2]":[33],"and":[34,115,137,146,175,197,246,274,282,322,331,338,371,390],"Clustal-W":[35],"[3]),":[36],"suggesting":[37],"many":[38],"studies":[40],"may":[41,78,309],"have":[43,348],"been":[44],"possible":[45],"without":[46,275],"some":[47],"kind":[48],"of":[49,80,111,231,279,344,368,384,393],"to":[52,100,103,141,152,165,179,188,222,298,327,334,341,355,363,374,404],"collect":[53],"observations,":[54],"analyze":[55],"data,":[56],"or":[57,150,171,300,317],"present":[58],"results.":[59,106,155],"It":[60,360],"is":[61,95,108,177,214,235,248,265,272],"surprising,":[62],"therefore,":[63],"that":[64,76,186,250],"so":[65],"few":[66],"papers":[67],"accompanied":[69],"by":[70,241,314],"software,":[72],"given":[73],"benefits":[75],"this":[77],"bring.\r\n\r\nPublication":[79],"code":[83,221],"you":[84,130,182,218,326,347,362],"write":[85],"can":[88,193,258],"increase":[89],"your":[90,105,144,170,172,220,315,345,377],"impact":[91],"[4],":[92],"essential":[96],"if":[97,217],"others":[98,140,373],"be":[101,161,194],"able":[102],"reproduce":[104],"Reproducibility":[107],"a":[109,289,292,407],"tenet":[110],"computational":[112,411],"science":[113],"[5],":[114],"critical":[116],"for":[117,127,303,409],"pipelines":[118],"employed":[119],"in":[120,252],"data-driven":[121],"biological":[122],"Publishing":[124],"created":[131],"well":[133],"input":[135],"data":[136],"results":[138],"allows":[139,325,361],"better":[142],"understand":[143],"methodology,":[145],"why":[147],"it":[148,176,247,285],"produces,":[149],"fails":[151],"produce,":[153],"expected":[154],"Public":[156],"release":[157,204],"might":[158],"always":[160,200],"possible,":[162],"perhaps":[163],"due":[164],"intellectual":[166],"property":[167],"policies":[168,312],"at":[169],"collaborators'":[173],"institutes;":[174],"important":[178],"make":[180,259,381],"sure":[181],"know":[183],"regulations":[185],"apply":[187],"you.":[189],"Open":[190],"licensing":[191],"models":[192],"incredibly":[195],"flexible":[196],"do":[198],"prevent":[201],"commercial":[202],"[5].\r\n\r\nSimply":[205],"releasing":[206],"under":[209],"an":[210,352],"license,":[212],"however,":[213],"sufficient":[216],"wish":[219],"remain":[223],"useful":[224],"beyond":[225],"its":[226],"publication":[227,234],"[6].":[228],"The":[229],"sustainability":[230,343],"after":[233,269],"probably":[236],"biggest":[238,261],"problem":[239],"faced":[240],"researchers":[242],"who":[243],"develop":[244],"it,":[245],"here":[249],"participating":[251],"from":[255],"outset":[257],"impact.":[262],"Grant-based":[263],"funding":[264,318],"often":[266],"exhausted":[267],"shortly":[268],"new":[270],"released,":[273],"support,":[276],"in-house":[277],"maintenance":[278,332],"systems":[284],"depends":[286],"becomes":[288],"struggle.":[290],"As":[291],"consequence,":[293],"will":[296],"cease":[297],"work":[299,367],"become":[301],"unavailable":[302],"download":[304],"fairly":[305],"quickly":[306],"[7],":[307],"which":[308],"contravene":[310],"archival":[311],"stipulated":[313],"journal":[316],"body.":[319],"A":[320],"collaborative":[321],"project":[324],"spread":[328],"resource":[330],"load":[333],"minimize":[335],"these":[336],"risks,":[337],"significantly":[339],"contributes":[340],"software.\r\n\r\nIf":[346],"choice,":[350],"embracing":[351],"approach":[354],"tremendous":[358],"benefits.":[359],"build":[364,375],"other":[369],"scientists,":[370],"enables":[372],"own":[378],"efforts.":[379],"To":[380],"more":[388,396],"rewarding":[389],"experience":[392],"using":[394],"positive,":[397],"following":[399],"ten":[400],"rules":[401],"intended":[403],"serve":[405],"guide":[408],"any":[410],"scientist.":[412]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":13},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
