{"id":"https://openalex.org/W2093625616","doi":"https://doi.org/10.1109/escience.2012.6404442","title":"Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses","display_name":"Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2093625616","doi":"https://doi.org/10.1109/escience.2012.6404442","mag":"2093625616"},"language":"en","primary_location":{"id":"doi:10.1109/escience.2012.6404442","is_oa":false,"landing_page_url":"https://doi.org/10.1109/escience.2012.6404442","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 8th International Conference on E-Science","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031069551","display_name":"Jeremy Goecks","orcid":"https://orcid.org/0000-0002-4583-5226"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Goecks","raw_affiliation_strings":["Emory University, Atlanta, GA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Emory University, Atlanta, GA, US","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105235386","display_name":"The Galaxy Team","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"The Galaxy Team","raw_affiliation_strings":["Pennsylvania State University, University Park, PA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, University Park, PA, US","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065292926","display_name":"Anton Nekrutenko","orcid":"https://orcid.org/0000-0002-5987-8032"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anton Nekrutenko","raw_affiliation_strings":["Emory University, Atlanta, GA, US"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Emory University, Atlanta, GA, US","institution_ids":["https://openalex.org/I150468666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025611053","display_name":"James Taylor","orcid":"https://orcid.org/0000-0001-5079-840X"},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Taylor","raw_affiliation_strings":["Departments of Biology and Math & Computer Science, Emory University, Atlanta, GA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biology and Math & Computer Science, Emory University, Atlanta, GA, United States","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9993000030517578,"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":0.9993000030517578,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9947999715805054,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9916999936103821,"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/computer-science","display_name":"Computer science","score":0.6826026439666748},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5770576000213623},{"id":"https://openalex.org/keywords/galaxy","display_name":"Galaxy","score":0.5761051177978516},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5378628969192505},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5037123560905457},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4426715672016144},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.424545019865036},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4117484986782074},{"id":"https://openalex.org/keywords/astrophysics","display_name":"Astrophysics","score":0.23465165495872498},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.18500036001205444},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1708914041519165},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.15961319208145142},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13495096564292908},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.09139207005500793}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6826026439666748},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5770576000213623},{"id":"https://openalex.org/C98444146","wikidata":"https://www.wikidata.org/wiki/Q318","display_name":"Galaxy","level":2,"score":0.5761051177978516},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5378628969192505},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5037123560905457},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4426715672016144},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.424545019865036},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4117484986782074},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.23465165495872498},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.18500036001205444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1708914041519165},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.15961319208145142},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13495096564292908},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.09139207005500793},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/escience.2012.6404442","is_oa":false,"landing_page_url":"https://doi.org/10.1109/escience.2012.6404442","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 8th International Conference on E-Science","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.47999998927116394}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1583240815","https://openalex.org/W2001938458","https://openalex.org/W2057167586","https://openalex.org/W2059699217","https://openalex.org/W2126987356","https://openalex.org/W2136482257","https://openalex.org/W2140157849","https://openalex.org/W2140332639","https://openalex.org/W2154431984","https://openalex.org/W2158804744"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2081035100","https://openalex.org/W1968667271","https://openalex.org/W3206324740","https://openalex.org/W2497175360","https://openalex.org/W2181675095","https://openalex.org/W1549056443","https://openalex.org/W2379767673","https://openalex.org/W4376646135","https://openalex.org/W2363669182"],"abstract_inverted_index":{"High":[0],"throughput":[1],"sequencing":[2],"assays":[3],"have":[4],"given":[5],"rise":[6],"to":[7,21,92,109,131,136],"the":[8,22,76],"field":[9],"of":[10,25,48,78],"genomics":[11,26,106],"and":[12,54,64,70,111,125,127,133,144,150],"transformed":[13],"biomedical":[14],"research":[15,146,155],"into":[16],"a":[17,37,113],"computational":[18],"science.":[19],"Due":[20],"large":[23],"size":[24],"datasets,":[27],"high-performance":[28],"computing":[29],"is":[30,36],"essential":[31],"for":[32,45,116],"analysis.":[33],"Galaxy":[34,69,81,104,119,135,141,157],"(http://galaxyproject.org)":[35],"popular":[38],"Web-based":[39],"platform":[40,115],"that":[41,87],"can":[42,89],"be":[43,90],"used":[44],"all":[46],"facets":[47],"genomic":[49,145,154],"analyses,":[50],"including":[51],"data":[52],"retrieval":[53],"integration,":[55],"multi-step":[56],"analysis,":[57],"repeated":[58],"analyses":[59],"via":[60],"workflows,":[61],"visualization,":[62],"collaboration,":[63],"publication.":[65],"This":[66],"paper":[67],"describes":[68],"discusses":[71],"four":[72],"lessons":[73],"learned":[74],"from":[75],"development":[77,143],"Galaxy.":[79],"First,":[80],"uses":[82],"open,":[83],"extensible":[84],"frameworks":[85],"so":[86],"it":[88],"adapted":[91],"new":[93],"technologies":[94],"as":[95],"they":[96],"become":[97],"available.":[98],"Second,":[99],"by":[100],"leveraging":[101],"Web":[102],"technologies,":[103],"makes":[105],"tools":[107],"accessible":[108],"everyone":[110],"provides":[112],"common":[114],"collaboration.":[117],"Third,":[118],"fosters":[120],"community":[121,130],"amongst":[122],"both":[123],"developers":[124],"users":[126],"encourages":[128],"each":[129],"adapt":[132],"extend":[134],"meet":[137],"their":[138],"needs.":[139],"Finally,":[140],"software":[142],"are":[147],"closely":[148],"coupled,":[149],"challenges":[151],"encountered":[152],"during":[153],"drive":[156],"development.":[158]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
