{"id":"https://openalex.org/W2114591546","doi":"https://doi.org/10.1093/bioinformatics/bts573","title":"Creating reusable tools from scripts: the Galaxy Tool Factory","display_name":"Creating reusable tools from scripts: the Galaxy Tool Factory","publication_year":2012,"publication_date":"2012-09-28","ids":{"openalex":"https://openalex.org/W2114591546","doi":"https://doi.org/10.1093/bioinformatics/bts573","mag":"2114591546","pmid":"https://pubmed.ncbi.nlm.nih.gov/23024011"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3139/50694920/bioinformatics_28_23_3139.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3139/50694920/bioinformatics_28_23_3139.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006440422","display_name":"Ross Lazarus","orcid":"https://orcid.org/0000-0003-3939-1961"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Ross Lazarus","raw_affiliation_strings":["Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia. ross.lazarus@channing.harvard.edu","Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia"],"affiliations":[{"raw_affiliation_string":"Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia. ross.lazarus@channing.harvard.edu","institution_ids":["https://openalex.org/I142471025"]},{"raw_affiliation_string":"Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia","institution_ids":["https://openalex.org/I142471025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059094848","display_name":"Antony Kaspi","orcid":"https://orcid.org/0000-0001-6576-5862"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Antony Kaspi","raw_affiliation_strings":["Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia"],"affiliations":[{"raw_affiliation_string":"Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia","institution_ids":["https://openalex.org/I142471025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017271798","display_name":"Mark Ziemann","orcid":"https://orcid.org/0000-0002-7688-6974"},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Mark Ziemann","raw_affiliation_strings":["Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia"],"affiliations":[{"raw_affiliation_string":"Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia","institution_ids":["https://openalex.org/I142471025"]}]},{"author_position":"last","author":{"id":null,"display_name":"The Galaxy Team","orcid":null},"institutions":[{"id":"https://openalex.org/I142471025","display_name":"Baker Heart and Diabetes Institute","ror":"https://ror.org/03rke0285","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I142471025"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"The Galaxy Team","raw_affiliation_strings":["Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia"],"affiliations":[{"raw_affiliation_string":"Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia","institution_ids":["https://openalex.org/I142471025"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5006440422"],"corresponding_institution_ids":["https://openalex.org/I142471025"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6934,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.94089682,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"28","issue":"23","first_page":"3139","last_page":"3140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994000196456909,"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":0.9994000196456909,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9958000183105469,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.8215329051017761},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.68443763256073},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6121989488601685},{"id":"https://openalex.org/keywords/galaxy","display_name":"Galaxy","score":0.5663902759552002},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5561583042144775},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.4981997013092041},{"id":"https://openalex.org/keywords/software-deployment","display_name":"Software deployment","score":0.45688942074775696},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4484380781650543},{"id":"https://openalex.org/keywords/factory","display_name":"Factory (object-oriented programming)","score":0.42903149127960205},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.41340452432632446},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4057347774505615},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.37213099002838135},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35939180850982666},{"id":"https://openalex.org/keywords/astrophysics","display_name":"Astrophysics","score":0.1886037290096283},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16595306992530823},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11741182208061218}],"concepts":[{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.8215329051017761},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.68443763256073},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6121989488601685},{"id":"https://openalex.org/C98444146","wikidata":"https://www.wikidata.org/wiki/Q318","display_name":"Galaxy","level":2,"score":0.5663902759552002},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5561583042144775},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.4981997013092041},{"id":"https://openalex.org/C105339364","wikidata":"https://www.wikidata.org/wiki/Q2297740","display_name":"Software deployment","level":2,"score":0.45688942074775696},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4484380781650543},{"id":"https://openalex.org/C40149104","wikidata":"https://www.wikidata.org/wiki/Q5620977","display_name":"Factory (object-oriented programming)","level":2,"score":0.42903149127960205},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.41340452432632446},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4057347774505615},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.37213099002838135},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35939180850982666},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.1886037290096283},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16595306992530823},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11741182208061218},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001330","descriptor_name":"Electronic Data Processing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3139/50694920/bioinformatics_28_23_3139.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23024011","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23024011","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:dro.deakin.edu.au:DU:30112750","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401102","display_name":"Own your potential (DEAKIN)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149704539","host_organization_name":"Deakin University","host_organization_lineage":["https://openalex.org/I149704539"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2826959","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3509488","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/23/3139/50694920/bioinformatics_28_23_3139.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6100000143051147,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1567103826","display_name":null,"funder_award_id":"HG004909","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7470937020","display_name":null,"funder_award_id":"HG004909","funder_id":"https://openalex.org/F4320308109","funder_display_name":"Pennsylvania Department of Health"},{"id":"https://openalex.org/G7672504477","display_name":"Tailoring Genomic Data to the Needs of Experimental Biologists and Educators","funder_award_id":"0543285","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7714384854","display_name":null,"funder_award_id":"HG005133","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7895748443","display_name":null,"funder_award_id":"HG006620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8927429335","display_name":null,"funder_award_id":"HG005542","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308109","display_name":"Pennsylvania Department of Health","ror":"https://ror.org/00ra1fg11"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114591546.pdf","grobid_xml":"https://content.openalex.org/works/W2114591546.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1583240815","https://openalex.org/W1968659469","https://openalex.org/W2136482257"],"related_works":["https://openalex.org/W2344367508","https://openalex.org/W2571988079","https://openalex.org/W2367815957","https://openalex.org/W2098629748","https://openalex.org/W4244608052","https://openalex.org/W2144528247","https://openalex.org/W2147884840","https://openalex.org/W4312050194","https://openalex.org/W3188088379","https://openalex.org/W2997255751"],"abstract_inverted_index":{"ross.lazarus@channing.harvard.edu.":[0]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
