{"id":"https://openalex.org/W2980790673","doi":"https://doi.org/10.1186/s12859-019-3091-z","title":"doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows","display_name":"doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows","publication_year":2019,"publication_date":"2019-10-15","ids":{"openalex":"https://openalex.org/W2980790673","doi":"https://doi.org/10.1186/s12859-019-3091-z","mag":"2980790673","pmid":"https://pubmed.ncbi.nlm.nih.gov/31615395"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3091-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3091-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3091-z","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/track/pdf/10.1186/s12859-019-3091-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054638147","display_name":"Daniel Svensson","orcid":"https://orcid.org/0000-0002-4476-9255"},"institutions":[{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Daniel Svensson","raw_affiliation_strings":["Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden","institution_ids":["https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005308501","display_name":"Rickard Sj\u00f6gren","orcid":"https://orcid.org/0000-0001-7881-0968"},"institutions":[{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Rickard Sj\u00f6gren","raw_affiliation_strings":["Corporate Research, Sartorius AG, Ume\u00e5, Sweden","Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Corporate Research, Sartorius AG, Ume\u00e5, Sweden","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden","institution_ids":["https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033867338","display_name":"David Sundell","orcid":"https://orcid.org/0000-0002-6269-0217"},"institutions":[{"id":"https://openalex.org/I1291458624","display_name":"Swedish Defence Research Agency","ror":"https://ror.org/0470cgs30","country_code":"SE","type":"funder","lineage":["https://openalex.org/I1291458624"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"David Sundell","raw_affiliation_strings":["Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Ume\u00e5, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Ume\u00e5, Sweden","institution_ids":["https://openalex.org/I1291458624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034528790","display_name":"Andreas Sj\u00f6din","orcid":"https://orcid.org/0000-0001-5350-4219"},"institutions":[{"id":"https://openalex.org/I1291458624","display_name":"Swedish Defence Research Agency","ror":"https://ror.org/0470cgs30","country_code":"SE","type":"funder","lineage":["https://openalex.org/I1291458624"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Andreas Sj\u00f6din","raw_affiliation_strings":["Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Ume\u00e5, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of CBRN Security and Defence, FOI - Swedish Defence Research Agency, Ume\u00e5, Sweden","institution_ids":["https://openalex.org/I1291458624"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001681126","display_name":"Johan Trygg","orcid":"https://orcid.org/0000-0003-3799-6094"},"institutions":[{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Johan Trygg","raw_affiliation_strings":["Corporate Research, Sartorius AG, Ume\u00e5, Sweden. johan.trygg@umu.se","Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden. johan.trygg@umu.se","Corporate Research, Sartorius AG, Ume\u00e5, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-3799-6094","affiliations":[{"raw_affiliation_string":"Corporate Research, Sartorius AG, Ume\u00e5, Sweden. johan.trygg@umu.se","institution_ids":["https://openalex.org/I90267481"]},{"raw_affiliation_string":"Department of Chemistry, Computational Life Science Cluster (CLiC), Ume\u00e5 University, Ume\u00e5, Sweden. johan.trygg@umu.se","institution_ids":["https://openalex.org/I90267481"]},{"raw_affiliation_string":"Corporate Research, Sartorius AG, Ume\u00e5, Sweden","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5001681126"],"corresponding_institution_ids":["https://openalex.org/I90267481"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.171,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.5350798,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"1","first_page":"498","last_page":"498"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7132999897003174,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.7132999897003174,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.09480000287294388,"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/T10743","display_name":"Software Testing and Debugging Techniques","score":0.029999999329447746,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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/computer-science","display_name":"Computer science","score":0.7233060598373413},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6492922306060791},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6323761343955994},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5932883024215698},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5847256183624268},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5549460649490356},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46812406182289124},{"id":"https://openalex.org/keywords/minion","display_name":"Minion","score":0.4557610750198364},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4041610658168793},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.31765836477279663},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1612616777420044},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12032368779182434},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11796370148658752},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1163228452205658}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7233060598373413},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6492922306060791},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6323761343955994},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5932883024215698},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5847256183624268},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5549460649490356},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46812406182289124},{"id":"https://openalex.org/C2779927696","wikidata":"https://www.wikidata.org/wiki/Q6865654","display_name":"Minion","level":5,"score":0.4557610750198364},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4041610658168793},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.31765836477279663},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1612616777420044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12032368779182434},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11796370148658752},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1163228452205658},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005604","descriptor_name":"Francisella tularensis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005604","descriptor_name":"Francisella tularensis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005604","descriptor_name":"Francisella tularensis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005604","descriptor_name":"Francisella tularensis","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-3091-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3091-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3091-z","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:31615395","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31615395","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:DiVA.org:umu-164986","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-164986","pdf_url":null,"source":{"id":"https://openalex.org/S4306400361","display_name":"DiVA at Ume\u00e5 University (Ume\u00e5 University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I90267481","host_organization_name":"Ume\u00e5 University","host_organization_lineage":["https://openalex.org/I90267481"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:cf8fcb2f6f8d4bdea6c88d2f2d16fcad","is_oa":true,"landing_page_url":"https://doaj.org/article/cf8fcb2f6f8d4bdea6c88d2f2d16fcad","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6794737","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6794737","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/s12859-019-3091-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3091-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3091-z","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":[{"display_name":"Decent work and economic growth","id":"https://metadata.un.org/sdg/8","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G3998057874","display_name":null,"funder_award_id":"B4662","funder_id":"https://openalex.org/F4320311328","funder_display_name":"Myndigheten f\u00f6r Samh\u00e4llsskydd och Beredskap"},{"id":"https://openalex.org/G8251056410","display_name":null,"funder_award_id":"2011.0042","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G8304598056","display_name":null,"funder_award_id":"2016-04376","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G8815752681","display_name":null,"funder_award_id":"2016\u201004376","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320311328","display_name":"Myndigheten f\u00f6r Samh\u00e4llsskydd och Beredskap","ror":"https://ror.org/04cz2yk65"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320325344","display_name":"Totalf\u00f6rsvarets Forskningsinstitut","ror":"https://ror.org/0470cgs30"},{"id":"https://openalex.org/F4320325677","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22"},{"id":"https://openalex.org/F4320336376","display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2980790673.pdf","grobid_xml":"https://content.openalex.org/works/W2980790673.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1515242458","https://openalex.org/W1523412089","https://openalex.org/W1596936080","https://openalex.org/W1919257374","https://openalex.org/W1966822396","https://openalex.org/W1968098666","https://openalex.org/W2038872823","https://openalex.org/W2076163156","https://openalex.org/W2097126585","https://openalex.org/W2097998348","https://openalex.org/W2102532874","https://openalex.org/W2103441770","https://openalex.org/W2104677379","https://openalex.org/W2110417468","https://openalex.org/W2114074804","https://openalex.org/W2119180969","https://openalex.org/W2131241448","https://openalex.org/W2135361281","https://openalex.org/W2142449924","https://openalex.org/W2147733682","https://openalex.org/W2159954944","https://openalex.org/W2160969485","https://openalex.org/W2168133698","https://openalex.org/W2489506148","https://openalex.org/W2589379462","https://openalex.org/W2605897695","https://openalex.org/W2612836903","https://openalex.org/W2758005814","https://openalex.org/W2765745983","https://openalex.org/W2789843538","https://openalex.org/W2791837701","https://openalex.org/W2792286521","https://openalex.org/W2883524422","https://openalex.org/W2886761756","https://openalex.org/W2950964375","https://openalex.org/W2951501862","https://openalex.org/W2951529834","https://openalex.org/W3098304617","https://openalex.org/W4321515435"],"related_works":["https://openalex.org/W2749851556","https://openalex.org/W2765793069","https://openalex.org/W2550586733","https://openalex.org/W4200050032","https://openalex.org/W2515795842","https://openalex.org/W2324462508","https://openalex.org/W1855401909","https://openalex.org/W3138936383","https://openalex.org/W2601089939","https://openalex.org/W2907400852"],"abstract_inverted_index":{"BACKGROUND:":[0],"Selecting":[1],"the":[2,22,44,59,64,71,75,109,141,169,176,237,253],"proper":[3],"parameter":[4,16,65,153,227,270,279],"settings":[5,90,154,228],"for":[6,67,108,116,267,292],"bioinformatic":[7,117,133],"software":[8,134,269],"tools":[9,50,296],"is":[10,122,248,308],"challenging.":[11],"Not":[12],"only":[13],"will":[14],"each":[15,68],"have":[17],"an":[18],"individual":[19],"effect":[20],"on":[21,63,94,137],"outcome,":[23],"but":[24],"there":[25],"are":[26,85,155],"also":[27],"potential":[28],"interaction":[29],"effects":[30,36],"between":[31],"parameters.":[32],"Both":[33],"of":[34,74,79,114,140,143,201,210,295,301,306],"these":[35],"may":[37,51],"be":[38,52,315],"difficult":[39],"to":[40,131,189,236,242,274],"predict.":[41],"To":[42,106],"make":[43],"situation":[45],"even":[46],"more":[47],"complex,":[48],"multiple":[49],"run":[53],"in":[54,70,82,100,149,158,175,192,252,272,282,297],"a":[55,101,119,128,159,163,202,231,262,298],"sequential":[56],"pipeline":[57],"where":[58],"final":[60],"output":[61],"depends":[62],"configuration":[66],"tool":[69],"pipeline.":[72],"Because":[73],"complexity":[76],"and":[77,103,111,146,183,216,250,264,276,288,290,312],"difficulty":[78],"predicting":[80],"outcomes,":[81],"practice":[83],"parameters":[84,115,191],"often":[86],"left":[87],"at":[88,310],"default":[89,244],"or":[91,96],"set":[92],"based":[93,136],"personal":[95],"peer":[97],"experience":[98],"obtained":[99],"trial":[102],"error":[104],"fashion.":[105],"allow":[107],"reliable":[110],"efficient":[112],"selection":[113],"pipelines,":[118],"systematic":[120,263],"approach":[121,130,247],"needed.":[123],"RESULTS:":[124],"We":[125],"present":[126],"doepipeline,":[127],"novel":[129],"optimizing":[132,268],"parameters,":[135],"core":[138],"concepts":[139],"Design":[142],"Experiments":[144],"methodology":[145,260,286],"recent":[147],"advances":[148],"subset":[150,164],"designs.":[151],"Optimal":[152],"first":[156],"approximated":[157],"screening":[160],"phase":[161,178],"using":[162,179,243],"design":[165],"that":[166,229],"efficiently":[167],"spans":[168],"entire":[170],"search":[171],"space,":[172],"then":[173],"optimized":[174],"subsequent":[177],"response":[180],"surface":[181],"designs":[182],"OLS":[184],"modeling.":[185],"Doepipeline":[186],"was":[187],"used":[188],"optimize":[190],"four":[193,223],"use":[194],"cases;":[195],"1)":[196],"de-novo":[197],"assembly,":[198,205],"2)":[199],"scaffolding":[200],"fragmented":[203],"genome":[204],"3)":[206],"k-mer":[207],"taxonomic":[208],"classification":[209],"Oxford":[211],"Nanopore":[212],"Technologies":[213],"MinION":[214],"reads,":[215],"4)":[217],"genetic":[218],"variant":[219],"calling.":[220],"In":[221],"all":[222],"cases,":[224],"doepipeline":[225,283,307],"found":[226],"produced":[230],"better":[232],"outcome":[233],"with":[234],"respect":[235],"characteristic":[238],"measured":[239],"when":[240],"compared":[241],"values.":[245],"Our":[246,258],"implemented":[249],"available":[251,309],"Python":[254],"package":[255],"doepipeline.":[256],"CONCLUSIONS:":[257],"proposed":[259],"provides":[261],"robust":[265],"framework":[266],"settings,":[271],"contrast":[273],"labor-":[275],"time-intensive":[277],"manual":[278],"tweaking.":[280],"Implementation":[281],"makes":[284],"our":[285],"accessible":[287],"user-friendly,":[289],"allows":[291],"automatic":[293],"optimization":[294],"wide":[299],"range":[300],"cases.":[302],"The":[303],"source":[304],"code":[305],"https://github.com/clicumu/doepipeline":[311],"it":[313],"can":[314],"installed":[316],"through":[317],"conda-forge.":[318]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
