{"id":"https://openalex.org/W2113295049","doi":"https://doi.org/10.1186/1751-0473-9-20","title":"BioFlow: a web based workflow management software for design and execution of genomics pipelines","display_name":"BioFlow: a web based workflow management software for design and execution of genomics pipelines","publication_year":2014,"publication_date":"2014-09-18","ids":{"openalex":"https://openalex.org/W2113295049","doi":"https://doi.org/10.1186/1751-0473-9-20","mag":"2113295049"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-9-20","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-9-20","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-9-20","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-9-20","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054216133","display_name":"Harold R. Garner","orcid":"https://orcid.org/0000-0001-5359-5990"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]},{"id":"https://openalex.org/I4210137786","display_name":"Molecular Sciences Software Institute","ror":"https://ror.org/03x8p5f11","country_code":"US","type":"other","lineage":["https://openalex.org/I4210137786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Harold Garner","raw_affiliation_strings":["Virginia Bioinformatics Institute, Washington Street 0477, Blacksburg, 24061, VA, USA","Virginia Bioinformatics Institute, Blacksburg, USA"],"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Washington Street 0477, Blacksburg, 24061, VA, USA","institution_ids":["https://openalex.org/I859038795","https://openalex.org/I4210137786"]},{"raw_affiliation_string":"Virginia Bioinformatics Institute, Blacksburg, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032113716","display_name":"Ashwin Puthige","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137786","display_name":"Molecular Sciences Software Institute","ror":"https://ror.org/03x8p5f11","country_code":"US","type":"other","lineage":["https://openalex.org/I4210137786"]},{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashwin Puthige","raw_affiliation_strings":["Virginia Bioinformatics Institute, Washington Street 0477, Blacksburg, 24061, VA, USA","Virginia Bioinformatics Institute, Blacksburg, USA"],"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Washington Street 0477, Blacksburg, 24061, VA, USA","institution_ids":["https://openalex.org/I859038795","https://openalex.org/I4210137786"]},{"raw_affiliation_string":"Virginia Bioinformatics Institute, Blacksburg, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054216133"],"corresponding_institution_ids":["https://openalex.org/I4210137786","https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.183616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"9","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9951000213623047,"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":0.9781000018119812,"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":0.8660168647766113},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7834018468856812},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7053540945053101},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.6355538368225098},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5277265310287476},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4632365107536316},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.42378705739974976},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.41373297572135925},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32724928855895996},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.31085026264190674},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23694360256195068}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8660168647766113},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7834018468856812},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7053540945053101},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.6355538368225098},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5277265310287476},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4632365107536316},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.42378705739974976},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.41373297572135925},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32724928855895996},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.31085026264190674},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23694360256195068}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1751-0473-9-20","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-9-20","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-9-20","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4179862","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4179862","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Source Code Biol Med","raw_type":"Text"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/50545","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/50545","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-9-20","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-9-20","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-9-20","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113295049.pdf"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2097438318","https://openalex.org/W2123100726","https://openalex.org/W2136482257","https://openalex.org/W2168103533"],"related_works":["https://openalex.org/W2375304607","https://openalex.org/W2391168633","https://openalex.org/W2353477037","https://openalex.org/W2385499106","https://openalex.org/W2110462752","https://openalex.org/W1574425962","https://openalex.org/W4310820052","https://openalex.org/W2354357087","https://openalex.org/W2352774566","https://openalex.org/W4243836028"],"abstract_inverted_index":{"Bioinformatics":[0],"data":[1],"analysis":[2],"is":[3,46,112,175,240,264],"usually":[4],"done":[5],"sequentially":[6],"by":[7,15,154,162,242],"chaining":[8],"together":[9],"multiple":[10,34,244],"tools.":[11],"These":[12],"are":[13,160,171,208],"created":[14,225],"writing":[16],"scripts":[17,29],"and":[18,22,38,48,53,64,81,97,109,167,180,226,256],"tracking":[19],"the":[20,43,94,119,168,193,219,247,257,268,271],"inputs":[21],"outputs":[23,166,269],"of":[24,41,83,92,101,231,246,251],"all":[25,42,93,181],"stages.":[26],"Writing":[27],"such":[28],"require":[30],"programming":[31],"skills.":[32],"Executing":[33],"pipelines":[35,84,197],"in":[36,118,142],"parallel":[37,232],"keeping":[39],"track":[40,91],"generated":[44,96],"files":[45,95],"difficult":[47],"error":[49],"prone.":[50],"Checking":[51],"results":[52],"task":[54],"completion":[55],"requires":[56],"users":[57,212],"to":[58,61,67,139,195,213,218,266,270],"remotely":[59],"login":[60],"their":[62],"servers":[63],"run":[65],"commands":[66],"identify":[68],"process":[69],"status.":[70],"Users":[71,187],"would":[72],"benefit":[73],"from":[74],"a":[75,99,146],"web-based":[76],"tool":[77,87,106,174,179,194],"that":[78,207],"allows":[79],"creation":[80],"execution":[82,239],"remotely.":[85,186,228],"The":[86,115,129,165,173,221],"should":[88],"also":[89],"keep":[90],"maintain":[98],"history":[100,170],"user":[102],"activities.":[103],"A":[104,229],"software":[105,130,178],"for":[107,135,198],"building":[108],"executing":[110,199],"workflows":[111,120,150,206,222],"described":[113],"here.":[114],"individual":[116],"tools":[117,138,217],"can":[121,151,183,191,202,223,234,253],"be":[122,140,152,184,203,224,235,254,260],"any":[123],"command":[124],"line":[125],"executable":[126],"or":[127],"script.":[128],"has":[131],"an":[132],"intuitive":[133],"mechanism":[134],"adding":[136],"new":[137,216],"used":[141],"workflows.":[143],"It":[144],"contains":[145],"workflow":[147],"designer":[148],"where":[149],"creating":[153],"visually":[155],"connecting":[156],"various":[157],"components.":[158],"Workflows":[159],"executed":[161,227,255],"job":[163,169],"runners.":[164],"saved.":[172],"web":[176],"based":[177],"actions":[182],"performed":[185],"without":[188],"scripting":[189],"knowledge":[190],"utilize":[192],"build":[196],"tasks.":[200],"Pipelines":[201],"modeled":[204],"as":[205],"reusable.":[209],"BioFlow":[210],"enables":[211],"easily":[214,236],"add":[215],"database.":[220],"number":[230,250],"jobs":[233,272],"controlled.":[237],"Distributed":[238],"possible":[241],"running":[243],"instances":[245],"application.":[248],"Any":[249],"tasks":[252],"output":[258],"will":[259],"stored":[261],"making":[262],"it":[263],"easy":[265],"correlate":[267],"executed.":[273]},"counts_by_year":[{"year":2018,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
