{"id":"https://openalex.org/W3128076107","doi":"https://doi.org/10.1371/journal.pcbi.1008725","title":"On the open-source landscape of PLOS Computational Biology","display_name":"On the open-source landscape of PLOS Computational Biology","publication_year":2021,"publication_date":"2021-02-11","ids":{"openalex":"https://openalex.org/W3128076107","doi":"https://doi.org/10.1371/journal.pcbi.1008725","mag":"3128076107","pmid":"https://pubmed.ncbi.nlm.nih.gov/33571204"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008725","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008725","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008725&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.1008725&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002864670","display_name":"Mathieu Boudreau","orcid":"https://orcid.org/0000-0002-7726-4456"},"institutions":[{"id":"https://openalex.org/I2800290161","display_name":"Montreal Heart Institute","ror":"https://ror.org/03vs03g62","country_code":"CA","type":"funder","lineage":["https://openalex.org/I2800290161"]},{"id":"https://openalex.org/I45683168","display_name":"Polytechnique Montr\u00e9al","ror":"https://ror.org/05f8d4e86","country_code":"CA","type":"education","lineage":["https://openalex.org/I45683168"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mathieu Boudreau","raw_affiliation_strings":["Montreal Heart Institute, Montr\u00e9al, Qu\u00e9bec, Canada","NeuroPoly Lab, Polytechnique Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0002-7726-4456","affiliations":[{"raw_affiliation_string":"Montreal Heart Institute, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I2800290161"]},{"raw_affiliation_string":"NeuroPoly Lab, Polytechnique Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I45683168"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069918313","display_name":"Jean\u2010Baptiste Poline","orcid":"https://orcid.org/0000-0002-9794-749X"},"institutions":[{"id":"https://openalex.org/I1292859797","display_name":"Montreal Neurological Institute and Hospital","ror":"https://ror.org/05ghs6f64","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1292859797"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jean-Baptiste Poline","raw_affiliation_strings":["Montreal Neurological Institute, McGill University, Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0002-9794-749X","affiliations":[{"raw_affiliation_string":"Montreal Neurological Institute, McGill University, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I1292859797","https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009114084","display_name":"Pierre Bellec","orcid":"https://orcid.org/0000-0002-9111-0699"},"institutions":[{"id":"https://openalex.org/I4210126907","display_name":"Institut Universitaire de G\u00e9riatrie de Montr\u00e9al","ror":"https://ror.org/031z68d90","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210126907"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pierre Bellec","raw_affiliation_strings":["Centre de recherche de l'Institut universitaire de g\u00e9riatrie de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre de recherche de l'Institut universitaire de g\u00e9riatrie de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I4210126907"]},{"raw_affiliation_string":"Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I70931966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033295830","display_name":"Nikola Stikov","orcid":"https://orcid.org/0000-0002-8480-5230"},"institutions":[{"id":"https://openalex.org/I2800290161","display_name":"Montreal Heart Institute","ror":"https://ror.org/03vs03g62","country_code":"CA","type":"funder","lineage":["https://openalex.org/I2800290161"]},{"id":"https://openalex.org/I45683168","display_name":"Polytechnique Montr\u00e9al","ror":"https://ror.org/05f8d4e86","country_code":"CA","type":"education","lineage":["https://openalex.org/I45683168"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nikola Stikov","raw_affiliation_strings":["Montreal Heart Institute, Montr\u00e9al, Qu\u00e9bec, Canada","NeuroPoly Lab, Polytechnique Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0002-8480-5230","affiliations":[{"raw_affiliation_string":"Montreal Heart Institute, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I2800290161"]},{"raw_affiliation_string":"NeuroPoly Lab, Polytechnique Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I45683168"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002864670"],"corresponding_institution_ids":["https://openalex.org/I2800290161","https://openalex.org/I45683168"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.2214,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.7819867,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"2","first_page":"e1008725","last_page":"e1008725"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9904000163078308,"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"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9904000163078308,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9890999794006348,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9775999784469604,"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/open-source","display_name":"Open source","score":0.49136295914649963},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46365153789520264},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3937840461730957},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3904186487197876},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.34642165899276733},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.337049663066864},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.32043927907943726},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.1715160608291626}],"concepts":[{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.49136295914649963},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46365153789520264},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3937840461730957},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3904186487197876},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.34642165899276733},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.337049663066864},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.32043927907943726},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.1715160608291626},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1008725","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008725","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008725&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:33571204","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33571204","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:publications.polymtl.ca:9358","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401013","display_name":"PolyPublie (\u00c9cole Polytechnique de Montr\u00e9al)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45683168","host_organization_name":"Polytechnique Montr\u00e9al","host_organization_lineage":["https://openalex.org/I45683168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:doaj.org/article:48158e2b256e4f6199fa0db9b1ec8fd3","is_oa":true,"landing_page_url":"https://doaj.org/article/48158e2b256e4f6199fa0db9b1ec8fd3","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 17, Iss 2, p e1008725 (2021)","raw_type":"article"},{"id":"pmh:oai:publications.polymtl.ca:47342","is_oa":false,"landing_page_url":"https://publications.polymtl.ca/47342/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401013","display_name":"PolyPublie (\u00c9cole Polytechnique de Montr\u00e9al)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45683168","host_organization_name":"Polytechnique Montr\u00e9al","host_organization_lineage":["https://openalex.org/I45683168"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article de revue"},{"id":"pmh:oai:pubmedcentral.nih.gov:7877734","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7877734","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.1008725","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008725","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008725&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":[{"display_name":"Climate action","score":0.5,"id":"https://metadata.un.org/sdg/13"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3128076107.pdf","grobid_xml":"https://content.openalex.org/works/W3128076107.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2800783103","https://openalex.org/W2934566196","https://openalex.org/W2950904558","https://openalex.org/W2968320779"],"related_works":["https://openalex.org/W2124842464","https://openalex.org/W2382657549","https://openalex.org/W4376877853","https://openalex.org/W75565505","https://openalex.org/W3200575725","https://openalex.org/W4242732953","https://openalex.org/W4214847518","https://openalex.org/W1535063848","https://openalex.org/W2186225517","https://openalex.org/W1153144596"],"abstract_inverted_index":{"Over":[0],"the":[1,9,21,28,78,93,97,119,123,145,157,176],"past":[2],"year,":[3],"I":[4,26],"(M.B.)":[5],"have":[6],"been":[7,46],"investigating":[8],"landscape":[10,95,125,159],"of":[11,23,38,80,92,118,122,144,160,175],"code-sharing":[12],"in":[13,48,61,101,178],"academic":[14],"journals":[15],"across":[16],"different":[17,169],"research":[18,82,109,179],"fields.":[19],"At":[20],"end":[22],"my":[24,39],"PhD,":[25],"made":[27],"choice":[29],"to":[30],"share":[31],"code":[32,148],"that":[33,127,149,188],"reproduces":[34],"figures":[35],"from":[36,170],"one":[37],"papers":[40],"[1],":[41],"and":[42,53,55,64,77,137],"since":[43],"then,":[44],"I've":[45],"involved":[47],"several":[49],"open-source":[50,94,124,158],"projects":[51],"(qMRLab":[52],"AxonDeepSeg)":[54],"initiatives":[56],"dealing":[57],"with":[58],"open":[59],"science":[60],"publishing":[62],"(NeuroLibre":[63],"Canadian":[65],"Open":[66],"Neuroscience":[67],"Platform).":[68],"Recently,":[69],"following":[70],"an":[71,90,185],"editorial":[72],"by":[73],"N.S.":[74],"on":[75,107,191],"reproducibility":[76],"future":[79],"MRI":[81,108],"[2],":[83],"we":[84,155],"wrote":[85],"a":[86,116],"blog":[87],"post":[88],"presenting":[89],"analysis":[91],"for":[96,110,126],"journal":[98,128,187],"Magnetic":[99],"Resonance":[100],"Medicine":[102],"(MRM),":[103],"which":[104],"broadly":[105],"focuses":[106,189],"medical":[111],"applications.":[112],"These":[113],"findings":[114],"provided":[115],"snapshot":[117],"current":[120],"state":[121],"(e.g.,":[129],"most":[130],"used":[131],"coding":[132],"language":[133],"is":[134,167],"still":[135],"MATLAB)":[136],"some":[138],"insights":[139],"into":[140],"new":[141],"trends":[142],"(12%":[143],"articles":[146],"shared":[147],"reproduced":[150],"figures).":[151],"In":[152],"this":[153],"editorial,":[154],"examine":[156],"PLOS":[161,164],"Computational":[162,165],"Biology.":[163],"Biology":[166],"inherently":[168],"MRM":[171],"not":[172],"only":[173],"because":[174,183],"difference":[177],"topics,":[180],"but":[181],"also":[182],"it's":[184],"openaccess":[186],"primarily":[190],"computational":[192],"studies.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
