{"id":"https://openalex.org/W4281683366","doi":"https://doi.org/10.1371/journal.pcbi.1010193","title":"Advancing code sharing in the computational biology community","display_name":"Advancing code sharing in the computational biology community","publication_year":2022,"publication_date":"2022-06-02","ids":{"openalex":"https://openalex.org/W4281683366","doi":"https://doi.org/10.1371/journal.pcbi.1010193","pmid":"https://pubmed.ncbi.nlm.nih.gov/35653366"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010193","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010193","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010193&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.1010193&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019050078","display_name":"Lauren Cadwallader","orcid":"https://orcid.org/0000-0002-7571-3502"},"institutions":[{"id":"https://openalex.org/I108652713","display_name":"Public Library of Science","ror":"https://ror.org/008zgvp64","country_code":"US","type":"archive","lineage":["https://openalex.org/I108652713"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lauren Cadwallader","raw_affiliation_strings":["PLOS, San Francisco, California, United States of America"],"affiliations":[{"raw_affiliation_string":"PLOS, San Francisco, California, United States of America","institution_ids":["https://openalex.org/I108652713"]}]},{"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 and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","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":false,"raw_author_name":"Jason 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":"last","author":{"id":"https://openalex.org/A5090120637","display_name":"Virginia E. Pitzer","orcid":"https://orcid.org/0000-0003-1015-2289"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Virginia E. Pitzer","raw_affiliation_strings":["Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology of Microbial Diseases and Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019050078"],"corresponding_institution_ids":["https://openalex.org/I108652713"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":8.828,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.97113756,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"18","issue":"6","first_page":"e1010193","last_page":"e1010193"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.991100013256073,"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/T11937","display_name":"Research Data Management Practices","score":0.9879000186920166,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5073918700218201},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4925113618373871},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4787023365497589},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3428877592086792},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3317226469516754},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24257132411003113}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5073918700218201},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4925113618373871},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4787023365497589},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3428877592086792},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3317226469516754},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24257132411003113},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1010193","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010193","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010193&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:35653366","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35653366","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:doaj.org/article:a5af73bc78884d649d57d825f37bb81b","is_oa":true,"landing_page_url":"https://doaj.org/article/a5af73bc78884d649d57d825f37bb81b","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 6, p e1010193 (2022)","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:c24de16487134b6f8b447ecd2ad9a8d3","is_oa":true,"landing_page_url":"https://doaj.org/article/c24de16487134b6f8b447ecd2ad9a8d3","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 6 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9162310","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9162310","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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.1010193","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010193","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010193&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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281683366.pdf","grobid_xml":"https://content.openalex.org/works/W4281683366.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2036318837","https://openalex.org/W2072876893","https://openalex.org/W2903593834","https://openalex.org/W2949379258","https://openalex.org/W2964148489","https://openalex.org/W3027376788","https://openalex.org/W3081423956","https://openalex.org/W3128076107","https://openalex.org/W3128384707","https://openalex.org/W3148723922","https://openalex.org/W4292589909"],"related_works":["https://openalex.org/W2373724792","https://openalex.org/W2281360585","https://openalex.org/W2160620982","https://openalex.org/W2060012464","https://openalex.org/W2084957735","https://openalex.org/W4255567883","https://openalex.org/W2374073571","https://openalex.org/W2381194467","https://openalex.org/W1812531695","https://openalex.org/W2557652470"],"abstract_inverted_index":{"a":[0,17,42,84,198],"new":[1,81],"code":[2,15,46,61,95,156,202],"sharing":[3,47,157,203],"policy":[4,12,33,82,91,126,191],"was":[5,34,83],"introduced":[6,35],"at":[7],"PLOS":[8,73],"Computational":[9],"Biology":[10],"This":[11,62,184],"requires":[13],"any":[14,169],"supporting":[16],"publication":[18],"to":[19,38,48,115,121,131,151,217],"be":[20],"shared":[21],"unless":[22],"there":[23],"are":[24],"ethical":[25],"or":[26,119,176],"legal":[27],"restrictions":[28],"that":[29,52,165],"prevent":[30],"sharing.":[31],"The":[32,90,125],"in":[36,105,133,155,204],"response":[37],"community":[39,57],"desire":[40],"for":[41,65,87,137],"stronger":[43],"position":[44],"on":[45,93,172,187],"reflect":[49],"the":[50,53,56,72,77,80,88,140,143,147,173,177,188,193,205],"fact":[51],"majority":[54],"of":[55,79,142,146,161,190,201],"already":[58],"voluntarily":[59],"share":[60,122,166],"community-driven":[63],"support":[64,108],"open":[66],"science":[67],"practices":[68],"aligns":[69],"well":[70],"with":[71],"mission,":[74],"and,":[75],"therefore,":[76],"implementation":[78],"logical":[85],"progression":[86],"journal.":[89],"focuses":[92],"increasing":[94],"sAU":[96],":":[97],"Pleasenotet":[98],"haring":[99],"as":[100],"its":[101],"primary":[102],"aim,":[103],"which,":[104],"turn,":[106],"will":[107],"reproducibility,":[109,221],"and":[110,180,209,222],"so":[111],"is":[112],"not":[113],"prescriptive":[114],"authors":[116,130],"about":[117],"how":[118,211],"where":[120],"their":[123],"code.":[124],"(https://journals.plos.org/":[127],"ploscompbiol/s/code-availability)":[128],"allows":[129],"comply":[132],"ways":[134],"which":[135],"work":[136],"them.":[138],"By":[139],"end":[141],"first":[144,194],"year":[145],"policy,":[148],"we":[149],"expected":[150],"see":[152],"an":[153],"increase":[154],"rates":[158],"(the":[159],"percentage":[160],"published":[162],"research":[163],"articles":[164],"code)":[167],"without":[168],"negative":[170],"impact":[171,189],"publishing":[174],"demographics":[175],"author,":[178],"editor,":[179],"journal":[181,206],"staff":[182],"experiences.":[183],"Editorial":[185],"reports":[186],"over":[192],"12":[195],"months,":[196],"provides":[197],"longitudinal":[199],"view":[200],"since":[207],"2019,":[208],"articulates":[210],"this":[212],"effort":[213],"can":[214],"move":[215],"forward":[216],"enhance":[218],"further":[219],"sharing,":[220],"openness.":[223]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
