{"id":"https://openalex.org/W2083612007","doi":"https://doi.org/10.1186/1471-2105-9-82","title":"A comparison of common programming languages used in bioinformatics","display_name":"A comparison of common programming languages used in bioinformatics","publication_year":2008,"publication_date":"2008-02-05","ids":{"openalex":"https://openalex.org/W2083612007","doi":"https://doi.org/10.1186/1471-2105-9-82","mag":"2083612007","pmid":"https://pubmed.ncbi.nlm.nih.gov/18251993"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-82","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-82","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-82","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/10.1186/1471-2105-9-82","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070262421","display_name":"Mathieu Fourment","orcid":"https://orcid.org/0000-0001-8153-9822"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Mathieu Fourment","raw_affiliation_strings":["Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia. m.fourment@gmail.com","Department of Biological Sciences Macquarie University  Sydney Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia. m.fourment@gmail.com","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"Department of Biological Sciences Macquarie University  Sydney Australia","institution_ids":["https://openalex.org/I99043593"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055770757","display_name":"Michael R. Gillings","orcid":"https://orcid.org/0000-0002-4043-4351"},"institutions":[{"id":"https://openalex.org/I99043593","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89","country_code":"AU","type":"education","lineage":["https://openalex.org/I99043593"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Michael R Gillings","raw_affiliation_strings":["Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia","Department of Biological Sciences Macquarie University  Sydney Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia","institution_ids":["https://openalex.org/I99043593"]},{"raw_affiliation_string":"Department of Biological Sciences Macquarie University  Sydney Australia","institution_ids":["https://openalex.org/I99043593"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5070262421"],"corresponding_institution_ids":["https://openalex.org/I99043593"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.9657,"has_fulltext":true,"cited_by_count":151,"citation_normalized_percentile":{"value":0.85800079,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"9","issue":"1","first_page":"82","last_page":"82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.5569999814033508,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.5569999814033508,"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":0.21639999747276306,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.06340000033378601,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.8784537315368652},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8672161102294922},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8012577295303345},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.7389673590660095},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6450947523117065},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.454863965511322},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.4340810179710388}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.8784537315368652},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8672161102294922},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8012577295303345},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.7389673590660095},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6450947523117065},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.454863965511322},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.4340810179710388}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-9-82","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-82","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-82","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:18251993","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18251993","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:doaj.org/article:d50bdfa512f149b98b4af9bce0b5fe91","is_oa":false,"landing_page_url":"https://doaj.org/article/d50bdfa512f149b98b4af9bce0b5fe91","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss 1, p 82 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2267699","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2267699","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-82","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-82","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-82","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":[{"id":"https://openalex.org/F4320320591","display_name":"Macquarie University","ror":"https://ror.org/01sf06y89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2083612007.pdf","grobid_xml":"https://content.openalex.org/works/W2083612007.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1567621547","https://openalex.org/W1648311451","https://openalex.org/W1807494956","https://openalex.org/W1867732144","https://openalex.org/W1977618577","https://openalex.org/W2022366078","https://openalex.org/W2055043387","https://openalex.org/W2059935965","https://openalex.org/W2064632458","https://openalex.org/W2097706568","https://openalex.org/W2100243754","https://openalex.org/W2103546861","https://openalex.org/W2109582694","https://openalex.org/W2130301347","https://openalex.org/W2141408320","https://openalex.org/W2164154943","https://openalex.org/W2168775768"],"related_works":["https://openalex.org/W2412623563","https://openalex.org/W190299232","https://openalex.org/W1521481095","https://openalex.org/W594361471","https://openalex.org/W2604964690","https://openalex.org/W2417897055","https://openalex.org/W2613359208","https://openalex.org/W2291334382","https://openalex.org/W66419302","https://openalex.org/W2992663142"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,119,170],"performance":[2,114,121,187],"of":[3,28,40,94,107,115,122,137,159],"different":[4,42,167],"programming":[5,43,163],"languages":[6,89,125,164],"has":[7],"previously":[8],"been":[9],"benchmarked":[10],"using":[11,17,38],"abstract":[12],"mathematical":[13],"algorithms,":[14],"but":[15],"not":[16,127],"standard":[18,32],"bioinformatics":[19,33],"algorithms.":[20],"We":[21],"compared":[22],"the":[23,47,50,83,105,112,123,186,190],"memory":[24],"usage":[25],"and":[26,55,71,77,81,97,109,111,117,133,146,189],"speed":[27],"execution":[29],"for":[30,46,58,193],"three":[31],"methods,":[34],"implemented":[35,64],"in":[36,65,75,87],"programs":[37],"one":[39],"six":[41,160],"languages.":[44],"Programs":[45,86],"Sellers":[48],"algorithm,":[49],"Neighbor-Joining":[51],"tree":[52],"construction":[53],"algorithm":[54,57],"an":[56,179],"parsing":[59],"BLAST":[60],"file":[61],"outputs":[62],"were":[63,79],"C,":[66],"C++,":[67],"C#,":[68],"Java,":[69],"Perl":[70,108],"Python.":[72],"RESULTS:":[73],"Implementations":[74],"C":[76,116],"C++":[78],"fastest":[80],"used":[82,162],"least":[84],"memory.":[85],"these":[88],"generally":[90],"contained":[91],"more":[92],"lines":[93],"code.":[95],"Java":[96],"C#":[98],"appeared":[99],"to":[100,131],"be":[101],"a":[102,138,157,175],"compromise":[103],"between":[104],"flexibility":[106],"Python":[110],"fast":[113],"C++.":[118],"relative":[120],"tested":[124],"did":[126],"change":[128],"from":[129,151],"Windows":[130],"Linux":[132],"no":[134],"clear":[135],"evidence":[136],"faster":[139],"operating":[140,168],"system":[141],"was":[142],"found.":[143],"Source":[144],"code":[145],"additional":[147],"information":[148],"are":[149],"available":[150],"http://www.bioinformatics.org/benchmark/.":[152],"CONCLUSION:":[153],"This":[154],"benchmark":[155],"provides":[156],"comparison":[158,172],"commonly":[161],"under":[165],"two":[166],"systems.":[169],"overall":[171],"shows":[173],"that":[174],"developer":[176],"should":[177],"choose":[178],"appropriate":[180],"language":[181],"carefully,":[182],"taking":[183],"into":[184],"account":[185],"expected":[188],"library":[191],"availability":[192],"each":[194],"language.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-27T08:28:00.272161","created_date":"2025-10-10T00:00:00"}
