{"id":"https://openalex.org/W4327568792","doi":"https://doi.org/10.1371/journal.pcbi.1010856","title":"An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases","display_name":"An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases","publication_year":2023,"publication_date":"2023-03-16","ids":{"openalex":"https://openalex.org/W4327568792","doi":"https://doi.org/10.1371/journal.pcbi.1010856","pmid":"https://pubmed.ncbi.nlm.nih.gov/36928042"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010856","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010856","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010856&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.1010856&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042334319","display_name":"Darya Pokutnaya","orcid":"https://orcid.org/0000-0003-4699-8411"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Darya Pokutnaya","raw_affiliation_strings":["University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113485085","display_name":"Bruce R. Childers","orcid":null},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bruce Childers","raw_affiliation_strings":["University of Pittsburgh, Department of Computer Science, Pittsburgh, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, Department of Computer Science, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007566217","display_name":"Alice E. Arcury\u2010Quandt","orcid":"https://orcid.org/0000-0001-7295-5939"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alice E. Arcury-Quandt","raw_affiliation_strings":["University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082929960","display_name":"Harry Hochheiser","orcid":"https://orcid.org/0000-0001-8793-9982"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Harry Hochheiser","raw_affiliation_strings":["University of Pittsburgh, Department of Biomedical Informatics and Intelligent Systems Program, Pittsburgh, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, Department of Biomedical Informatics and Intelligent Systems Program, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063821021","display_name":"Willem G. van Panhuis","orcid":"https://orcid.org/0000-0002-7278-9982"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Willem G. Van Panhuis","raw_affiliation_strings":["University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Pittsburgh, Department of Epidemiology, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5007566217","https://openalex.org/A5042334319","https://openalex.org/A5063821021","https://openalex.org/A5082929960","https://openalex.org/A5113485085"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":10.4667,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.97772561,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"e1010856","last_page":"e1010856"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9962000250816345,"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":0.9962000250816345,"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/T11581","display_name":"Viral Infections and Outbreaks Research","score":0.984499990940094,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.982200026512146,"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/computational-model","display_name":"Computational model","score":0.7211243510246277},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.672812819480896},{"id":"https://openalex.org/keywords/transparency","display_name":"Transparency (behavior)","score":0.6710227131843567},{"id":"https://openalex.org/keywords/infectious-disease","display_name":"Infectious disease (medical specialty)","score":0.49958014488220215},{"id":"https://openalex.org/keywords/reproducibility","display_name":"Reproducibility","score":0.48447275161743164},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.480546772480011},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4528452157974243},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.40235334634780884},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.18187358975410461},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.154514342546463},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14239928126335144},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09337809681892395},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.08742159605026245},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08272421360015869}],"concepts":[{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.7211243510246277},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.672812819480896},{"id":"https://openalex.org/C2780233690","wikidata":"https://www.wikidata.org/wiki/Q535347","display_name":"Transparency (behavior)","level":2,"score":0.6710227131843567},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.49958014488220215},{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.48447275161743164},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.480546772480011},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4528452157974243},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.40235334634780884},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.18187358975410461},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.154514342546463},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14239928126335144},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09337809681892395},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.08742159605026245},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08272421360015869},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011634","descriptor_name":"Public Health","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011634","descriptor_name":"Public Health","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011634","descriptor_name":"Public Health","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1010856","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010856","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010856&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:36928042","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36928042","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:pubmedcentral.nih.gov:10019712","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10019712","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10019712/pdf/pcbi.1010856.pdf","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:2af4c24e8f2b459fa5e4734ed2061e56","is_oa":true,"landing_page_url":"https://doaj.org/article/2af4c24e8f2b459fa5e4734ed2061e56","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 19, Iss 3, p e1010856 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010856","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010856","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010856&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":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7799999713897705}],"awards":[{"id":"https://openalex.org/G1634351103","display_name":null,"funder_award_id":"U24GM132013","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4327568792.pdf","grobid_xml":"https://content.openalex.org/works/W4327568792.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W2008985174","https://openalex.org/W2078962046","https://openalex.org/W2406493898","https://openalex.org/W2560471521","https://openalex.org/W2612574351","https://openalex.org/W2782228766","https://openalex.org/W2787225861","https://openalex.org/W2803218236","https://openalex.org/W2906928945","https://openalex.org/W2917207851","https://openalex.org/W2925076033","https://openalex.org/W2991460415","https://openalex.org/W2994819083","https://openalex.org/W3003573988","https://openalex.org/W3016460100","https://openalex.org/W3020857784","https://openalex.org/W3033000097","https://openalex.org/W3085464968","https://openalex.org/W3088993044","https://openalex.org/W3125656585","https://openalex.org/W3136624297","https://openalex.org/W3155036701","https://openalex.org/W3200572611","https://openalex.org/W3207646715","https://openalex.org/W4210918803","https://openalex.org/W4283213997","https://openalex.org/W4285385769","https://openalex.org/W6776331466","https://openalex.org/W6840389296"],"related_works":["https://openalex.org/W2413717610","https://openalex.org/W1973270181","https://openalex.org/W2417696084","https://openalex.org/W2368782778","https://openalex.org/W2087830269","https://openalex.org/W3106281778","https://openalex.org/W4324138256","https://openalex.org/W3134060498","https://openalex.org/W2003643616","https://openalex.org/W2963071509"],"abstract_inverted_index":{"Computational":[0],"models":[1,23,108],"of":[2,21,53,63],"infectious":[3,64],"diseases":[4],"have":[5],"become":[6],"valuable":[7],"tools":[8,104],"for":[9,60,105],"research":[10],"and":[11,31,37,90],"the":[12,28],"public":[13],"health":[14],"response":[15,39],"against":[16],"epidemic":[17],"threats.":[18],"The":[19,68,93],"reproducibility":[20,47,62],"computational":[22,66,81,107],"has":[24],"been":[25],"limited,":[26],"undermining":[27],"scientific":[29,54,99],"process":[30],"possibly":[32],"trust":[33],"in":[34,109],"modeling":[35],"results":[36],"related":[38],"strategies,":[40],"such":[41],"as":[42],"vaccination.":[43],"We":[44],"translated":[45],"published":[46],"guidelines":[48],"from":[49],"a":[50,110],"wide":[51],"range":[52],"disciplines":[55],"into":[56,78],"an":[57],"implementation":[58],"framework":[59,69,94],"improving":[61],"disease":[65],"models.":[67],"comprises":[70],"22":[71],"elements":[72],"that":[73],"should":[74],"be":[75,96],"described,":[76],"grouped":[77],"6":[79],"categories:":[80],"environment,":[82],"analytical":[83],"software,":[84],"model":[85,87],"description,":[86],"implementation,":[88],"data,":[89],"experimental":[91],"protocol.":[92],"can":[95],"used":[97],"by":[98],"communities":[100],"to":[101],"develop":[102],"actionable":[103],"sharing":[106],"reproducible":[111],"way.":[112]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}
