{"id":"https://openalex.org/W4409505244","doi":"https://doi.org/10.1186/s12859-025-06108-1","title":"DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes","display_name":"DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes","publication_year":2025,"publication_date":"2025-04-16","ids":{"openalex":"https://openalex.org/W4409505244","doi":"https://doi.org/10.1186/s12859-025-06108-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/40240939"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06108-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06108-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06108-1","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/s12859-025-06108-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110919886","display_name":"Daniel Ortiz-Mart\u00ednez","orcid":null},"institutions":[{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Daniel Ortiz-Mart\u00ednez","raw_affiliation_strings":["Department of Mathematics and Computer Science, Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain. daniel.ortiz@ub.edu"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain. daniel.ortiz@ub.edu","institution_ids":["https://openalex.org/I71999127"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5110919886"],"corresponding_institution_ids":["https://openalex.org/I71999127"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08144291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"106","last_page":"106"},"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":0.9991999864578247,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9940000176429749,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8721438646316528},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8478684425354004},{"id":"https://openalex.org/keywords/workflow-technology","display_name":"Workflow technology","score":0.5684775710105896},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.5527452826499939},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.5442521572113037},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.47933730483055115},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.44605591893196106},{"id":"https://openalex.org/keywords/control-flow","display_name":"Control flow","score":0.43486297130584717},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4237102270126343},{"id":"https://openalex.org/keywords/interactivity","display_name":"Interactivity","score":0.41217151284217834},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3526669144630432},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2811576724052429},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1712484359741211}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8721438646316528},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8478684425354004},{"id":"https://openalex.org/C19612761","wikidata":"https://www.wikidata.org/wiki/Q8034836","display_name":"Workflow technology","level":3,"score":0.5684775710105896},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.5527452826499939},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5442521572113037},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.47933730483055115},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.44605591893196106},{"id":"https://openalex.org/C160191386","wikidata":"https://www.wikidata.org/wiki/Q868299","display_name":"Control flow","level":2,"score":0.43486297130584717},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4237102270126343},{"id":"https://openalex.org/C144430266","wikidata":"https://www.wikidata.org/wiki/Q839721","display_name":"Interactivity","level":2,"score":0.41217151284217834},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3526669144630432},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2811576724052429},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1712484359741211},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"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":"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":"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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-025-06108-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06108-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06108-1","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:40240939","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40240939","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:diposit.ub.edu:2445/227061","is_oa":true,"landing_page_url":"https://hdl.handle.net/2445/227061","pdf_url":null,"source":{"id":"https://openalex.org/S4306401653","display_name":"Dip\u00f2sit Digital de la Universitat de Barcelona (Universitat de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71999127","host_organization_name":"Universitat de Barcelona","host_organization_lineage":["https://openalex.org/I71999127"],"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":"Articles publicats en revistes (Matem\u00e0tiques i Inform\u00e0tica)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:doaj.org/article:c25dcfbc0fa245fb906b7b666f534600","is_oa":true,"landing_page_url":"https://doaj.org/article/c25dcfbc0fa245fb906b7b666f534600","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-25 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12004750","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12004750","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06108-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06108-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06108-1","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":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.550000011920929}],"awards":[{"id":"https://openalex.org/G2966929935","display_name":null,"funder_award_id":"2023PMD-UB/021","funder_id":"https://openalex.org/F4320323428","funder_display_name":"Universitat de Barcelona"}],"funders":[{"id":"https://openalex.org/F4320323428","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409505244.pdf","grobid_xml":"https://content.openalex.org/works/W4409505244.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1548178570","https://openalex.org/W1913040451","https://openalex.org/W2103363198","https://openalex.org/W2110417468","https://openalex.org/W2111350087","https://openalex.org/W2146005104","https://openalex.org/W2152956782","https://openalex.org/W2162041888","https://openalex.org/W2235737683","https://openalex.org/W2337209831","https://openalex.org/W2405513305","https://openalex.org/W2485599059","https://openalex.org/W2509439934","https://openalex.org/W2520518019","https://openalex.org/W2587995914","https://openalex.org/W2605897695","https://openalex.org/W2607211817","https://openalex.org/W2867868648","https://openalex.org/W2883743899","https://openalex.org/W2911625174","https://openalex.org/W2949297597","https://openalex.org/W3010653800","https://openalex.org/W3200776886","https://openalex.org/W3207572846","https://openalex.org/W3209541830","https://openalex.org/W4283647069","https://openalex.org/W4387646069","https://openalex.org/W4388581286","https://openalex.org/W4398182689","https://openalex.org/W6630405334","https://openalex.org/W6921522649"],"related_works":["https://openalex.org/W2391168633","https://openalex.org/W2385499106","https://openalex.org/W2035995658","https://openalex.org/W2376671203","https://openalex.org/W2375304607","https://openalex.org/W2049143847","https://openalex.org/W1574425962","https://openalex.org/W2354357087","https://openalex.org/W2353477037","https://openalex.org/W2387628393"],"abstract_inverted_index":{"DeBasher":[0],"is":[1,33],"an":[2],"FBP":[3],"Bash":[4],"extension":[5],"that":[6],"can":[7],"be":[8],"useful":[9],"in":[10,17],"a":[11,30],"wide":[12],"range":[13],"of":[14],"situations":[15],"and":[16],"particular":[18],"when":[19,29],"implementing":[20],"complex":[21],"workflows,":[22],"workflows":[23],"with":[24],"interactivity":[25],"or":[26,28],"triggers,":[27],"high":[31],"scalability":[32],"required.":[34]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
