{"id":"https://openalex.org/W2145904912","doi":"https://doi.org/10.1093/bib/bbl026","title":"Open source tools and toolkits for bioinformatics: significance, and where are we?","display_name":"Open source tools and toolkits for bioinformatics: significance, and where are we?","publication_year":2006,"publication_date":"2006-05-23","ids":{"openalex":"https://openalex.org/W2145904912","doi":"https://doi.org/10.1093/bib/bbl026","mag":"2145904912","pmid":"https://pubmed.ncbi.nlm.nih.gov/16899494"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbl026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl026","pdf_url":"https://academic.oup.com/bib/article-pdf/7/3/287/935144/bbl026.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/7/3/287/935144/bbl026.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052869398","display_name":"Jason Stajich","orcid":"https://orcid.org/0000-0002-7591-0020"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. E. Stajich","raw_affiliation_strings":["Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA. jason.stajich@duke.edu"],"affiliations":[{"raw_affiliation_string":"Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA. jason.stajich@duke.edu","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5052869398"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.1793,"has_fulltext":false,"cited_by_count":54,"citation_normalized_percentile":{"value":0.86949092,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"7","issue":"3","first_page":"287","last_page":"296"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9965000152587891,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9911999702453613,"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":0.6644184589385986},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.61958909034729},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36808598041534424},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3560190796852112},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3368653655052185},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32583218812942505},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2626940608024597},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15839806199073792},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.07901665568351746}],"concepts":[{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.6644184589385986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.61958909034729},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36808598041534424},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3560190796852112},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3368653655052185},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32583218812942505},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2626940608024597},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15839806199073792},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.07901665568351746}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbl026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl026","pdf_url":"https://academic.oup.com/bib/article-pdf/7/3/287/935144/bbl026.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16899494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16899494","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbl026","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbl026","pdf_url":"https://academic.oup.com/bib/article-pdf/7/3/287/935144/bbl026.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2145904912.pdf","grobid_xml":"https://content.openalex.org/works/W2145904912.grobid-xml"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W66419302","https://openalex.org/W1510316655","https://openalex.org/W1527927437","https://openalex.org/W1543796220","https://openalex.org/W1767772592","https://openalex.org/W1909512798","https://openalex.org/W1950410402","https://openalex.org/W1957709438","https://openalex.org/W1988431525","https://openalex.org/W1992102171","https://openalex.org/W1996423252","https://openalex.org/W1996902131","https://openalex.org/W2015292449","https://openalex.org/W2042881722","https://openalex.org/W2045408108","https://openalex.org/W2053673723","https://openalex.org/W2064345118","https://openalex.org/W2069516109","https://openalex.org/W2079165446","https://openalex.org/W2081730254","https://openalex.org/W2087815309","https://openalex.org/W2090415636","https://openalex.org/W2096143996","https://openalex.org/W2103162938","https://openalex.org/W2103248995","https://openalex.org/W2107751776","https://openalex.org/W2109745159","https://openalex.org/W2114124787","https://openalex.org/W2114592519","https://openalex.org/W2118487996","https://openalex.org/W2120321361","https://openalex.org/W2120789186","https://openalex.org/W2123171788","https://openalex.org/W2123246614","https://openalex.org/W2123859786","https://openalex.org/W2124786890","https://openalex.org/W2128374023","https://openalex.org/W2130063668","https://openalex.org/W2134980868","https://openalex.org/W2135663335","https://openalex.org/W2137464714","https://openalex.org/W2138107070","https://openalex.org/W2140302584","https://openalex.org/W2141497252","https://openalex.org/W2141729174","https://openalex.org/W2142946358","https://openalex.org/W2145477956","https://openalex.org/W2146453000","https://openalex.org/W2146931904","https://openalex.org/W2148047088","https://openalex.org/W2148300596","https://openalex.org/W2150770935","https://openalex.org/W2150934173","https://openalex.org/W2151409320","https://openalex.org/W2152015607","https://openalex.org/W2153657280","https://openalex.org/W2155931743","https://openalex.org/W2158304452","https://openalex.org/W2158714788","https://openalex.org/W2160697532","https://openalex.org/W2164085656","https://openalex.org/W2165482734","https://openalex.org/W2168103533","https://openalex.org/W2168172687","https://openalex.org/W2169718128","https://openalex.org/W2611511275"],"related_works":["https://openalex.org/W2748952813","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"],"abstract_inverted_index":{"This":[0],"review":[1],"summarizes":[2],"important":[3,97],"work":[4],"in":[5],"open-source":[6,88],"bioinformatics":[7],"software":[8,89],"that":[9],"has":[10,31],"occurred":[11],"over":[12,59],"the":[13,60,93],"past":[14],"couple":[15],"of":[16,45,55],"years.":[17],"The":[18],"survey":[19],"is":[20],"intended":[21],"to":[22,81],"illustrate":[23],"how":[24,83],"programs":[25],"and":[26,78,86,101],"toolkits":[27],"whose":[28],"source":[29],"code":[30],"been":[32],"developed":[33,58],"or":[34],"released":[35],"under":[36],"an":[37],"Open":[38],"Source":[39],"license":[40],"have":[41],"changed":[42],"informatics-heavy":[43],"areas":[44],"life":[46],"science":[47],"research.":[48],"Rather":[49],"than":[50],"creating":[51],"a":[52,66],"comprehensive":[53],"list":[54],"all":[56],"tools":[57],"last":[61],"2-3":[62],"years,":[63],"we":[64],"use":[65],"few":[67],"selected":[68],"projects":[69],"encompassing":[70],"toolkit":[71],"libraries,":[72],"analysis":[73,76,99],"tools,":[74],"data":[75],"environments":[77],"interoperability":[79],"standards":[80],"show":[82],"freely":[84],"available":[85],"modifiable":[87],"can":[90],"serve":[91],"as":[92],"foundation":[94],"for":[95],"building":[96],"applications,":[98],"workflows":[100],"resources.":[102]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
