{"id":"https://openalex.org/W4392717596","doi":"https://doi.org/10.1186/s12859-024-05695-9","title":"CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications","display_name":"CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications","publication_year":2024,"publication_date":"2024-03-12","ids":{"openalex":"https://openalex.org/W4392717596","doi":"https://doi.org/10.1186/s12859-024-05695-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/38475691"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05695-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05695-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05695-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05695-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111145148","display_name":"S. Alessandri","orcid":null},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Alessandri","raw_affiliation_strings":["Polytechnic of Turin, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Polytechnic of Turin, Turin, Italy","institution_ids":["https://openalex.org/I177477856"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040417512","display_name":"Maria Luisa Ratto","orcid":"https://orcid.org/0000-0003-2610-242X"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Maria L. Ratto","raw_affiliation_strings":["Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080720267","display_name":"Sergio Rabellino","orcid":"https://orcid.org/0000-0002-1757-2000"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sergio Rabellino","raw_affiliation_strings":["Department of Computer Science, University of Torino, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013260949","display_name":"Gabriele Piacenti","orcid":"https://orcid.org/0000-0001-9775-2863"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriele Piacenti","raw_affiliation_strings":["Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086053123","display_name":"Sandro Gepiro Contaldo","orcid":"https://orcid.org/0009-0007-3889-8644"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sandro Gepiro Contaldo","raw_affiliation_strings":["Department of Computer Science, University of Torino, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082219669","display_name":"Simone Pernice","orcid":"https://orcid.org/0000-0001-7124-4676"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Pernice","raw_affiliation_strings":["Department of Computer Science, University of Torino, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002392135","display_name":"Marco Beccuti","orcid":"https://orcid.org/0000-0001-6125-9460"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Beccuti","raw_affiliation_strings":["Department of Computer Science, University of Torino, Turin, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025014550","display_name":"Raffaele Calogero","orcid":"https://orcid.org/0000-0002-2848-628X"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Raffaele A. Calogero","raw_affiliation_strings":["Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy. raffaele.calogero@unito.it"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy. raffaele.calogero@unito.it","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058272351","display_name":"Luca Alessandr\u00ec","orcid":"https://orcid.org/0000-0003-4678-3349"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Luca Alessandri","raw_affiliation_strings":["Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy","Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025014550"],"corresponding_institution_ids":["https://openalex.org/I55143463"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":4.7514,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.95039251,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"25","issue":"1","first_page":"110","last_page":"110"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.4620000123977661,"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":0.4620000123977661,"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":0.3571000099182129,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.09099999815225601,"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/computer-science","display_name":"Computer science","score":0.7393932342529297},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5462713241577148},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.4966149926185608},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.48911720514297485},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.47305360436439514},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4454699456691742},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34595564007759094},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2527819275856018},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.24431651830673218}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7393932342529297},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5462713241577148},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.4966149926185608},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.48911720514297485},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.47305360436439514},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4454699456691742},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34595564007759094},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2527819275856018},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.24431651830673218}],"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":"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},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05695-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05695-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05695-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38475691","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38475691","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10935966","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10935966","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10935966/pdf/12859_2024_Article_5695.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:75ad9c145c0c4f70b80f3e75ae7b3efa","is_oa":true,"landing_page_url":"https://doaj.org/article/75ad9c145c0c4f70b80f3e75ae7b3efa","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":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-16 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05695-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05695-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05695-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392717596.pdf"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2025004204","https://openalex.org/W2110417468","https://openalex.org/W2160697532","https://openalex.org/W2792069497","https://openalex.org/W3029719380","https://openalex.org/W3048367007","https://openalex.org/W3102028509","https://openalex.org/W3112973112","https://openalex.org/W3197064270","https://openalex.org/W4226049133"],"related_works":["https://openalex.org/W2378767206","https://openalex.org/W1540871478","https://openalex.org/W328308450","https://openalex.org/W282641168","https://openalex.org/W2376963063","https://openalex.org/W2066396794","https://openalex.org/W2366734808","https://openalex.org/W2002476357","https://openalex.org/W2391444248","https://openalex.org/W2390716080"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,118,165],"analysis":[2,30],"of":[3,26,45,107],"large":[4],"and":[5,23,43,48,67,95,113,135,140,148,168,202],"complex":[6],"biological":[7],"datasets":[8],"in":[9,28,38,51,116,121,150,199],"bioinformatics":[10,46,81,101,200],"poses":[11],"a":[12,74,87,123,151,192],"significant":[13],"challenge":[14],"to":[15,21,36,89,154,171,184],"achieving":[16],"reproducible":[17],"research":[18,47,115,201],"outcomes":[19],"due":[20],"inconsistencies":[22],"the":[24,29,41,52,105,128],"lack":[25],"standardization":[27],"process.":[31,54],"These":[32],"issues":[33,92,198],"can":[34],"lead":[35],"discrepancies":[37],"results,":[39],"undermining":[40],"credibility":[42],"impact":[44],"creating":[49,127],"mistrust":[50],"scientific":[53],"To":[55],"address":[56],"these":[57],"challenges,":[58],"open":[59,204],"science":[60,205],"practices":[61],"such":[62,137],"as":[63,86,138],"sharing":[64],"data,":[65],"code,":[66],"methods":[68],"have":[69],"been":[70,84],"encouraged.":[71],"RESULTS:":[72],"CREDO,":[73],"Customizable,":[75],"REproducible,":[76],"DOcker":[77],"file":[78],"generator":[79],"for":[80,181,195],"applications,":[82],"has":[83],"developed":[85],"tool":[88,180,194],"moderate":[90],"reproducibility":[91,112,197],"by":[93],"building":[94],"distributing":[96],"docker":[97],"containers":[98],"with":[99],"embedded":[100],"tools.":[102],"CREDO":[103,142,190],"simplifies":[104],"process":[106],"generating":[108,122],"Docker":[109,124,156,174,187],"images,":[110],"facilitating":[111],"efficient":[114],"bioinformatics.":[117],"crucial":[119],"step":[120],"image":[125,157,161],"is":[126,191],"Dockerfile,":[129],"which":[130],"requires":[131],"incorporating":[132],"heterogeneous":[133],"packages":[134],"environments":[136],"Bioconductor":[139],"Conda.":[141],"stores":[143],"all":[144],"required":[145],"package":[146],"information":[147],"dependencies":[149],"Github-compatible":[152],"format":[153],"enhance":[155],"reproducibility,":[158],"allowing":[159],"easy":[160],"creation":[162],"from":[163],"scratch.":[164],"user-friendly":[166],"GUI":[167],"CREDO's":[169],"ability":[170],"generate":[172],"modular":[173],"images":[175],"make":[176],"it":[177],"an":[178],"ideal":[179],"life":[182],"scientists":[183],"efficiently":[185],"create":[186],"images.":[188],"Overall,":[189],"valuable":[193],"addressing":[196],"promoting":[203],"practices.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
