{"id":"https://openalex.org/W3131510005","doi":"https://doi.org/10.1371/journal.pcbi.1008622","title":"Using prototyping to choose a bioinformatics workflow management system","display_name":"Using prototyping to choose a bioinformatics workflow management system","publication_year":2021,"publication_date":"2021-02-25","ids":{"openalex":"https://openalex.org/W3131510005","doi":"https://doi.org/10.1371/journal.pcbi.1008622","mag":"3131510005","pmid":"https://pubmed.ncbi.nlm.nih.gov/33630841"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008622","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008622","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008622&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008622&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042956066","display_name":"Michael Jackson","orcid":"https://orcid.org/0000-0002-1765-8234"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Michael Jackson","raw_affiliation_strings":["EPCC, The University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-1765-8234","affiliations":[{"raw_affiliation_string":"EPCC, The University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059197049","display_name":"Kostas Kavoussanakis","orcid":"https://orcid.org/0000-0001-9167-7145"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kostas Kavoussanakis","raw_affiliation_strings":["EPCC, The University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-9167-7145","affiliations":[{"raw_affiliation_string":"EPCC, The University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042990962","display_name":"Edward W. Wallace","orcid":"https://orcid.org/0000-0001-8025-6361"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Edward W. J. Wallace","raw_affiliation_strings":["Institute for Cell Biology and SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-8025-6361","affiliations":[{"raw_affiliation_string":"Institute for Cell Biology and SynthSys, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5042956066","https://openalex.org/A5042990962"],"corresponding_institution_ids":["https://openalex.org/I98677209"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":12.7041,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.98142167,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"2","first_page":"e1008622","last_page":"e1008622"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9970999956130981,"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":0.9835000038146973,"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":0.9038408398628235},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.8184223175048828},{"id":"https://openalex.org/keywords/workflow-technology","display_name":"Workflow technology","score":0.8164782524108887},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7461972832679749},{"id":"https://openalex.org/keywords/workflow-engine","display_name":"Workflow engine","score":0.740682065486908},{"id":"https://openalex.org/keywords/windows-workflow-foundation","display_name":"Windows Workflow Foundation","score":0.7109442949295044},{"id":"https://openalex.org/keywords/xpdl","display_name":"XPDL","score":0.6527000665664673},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5957691073417664},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.5392391085624695},{"id":"https://openalex.org/keywords/workflow-management-coalition","display_name":"Workflow Management Coalition","score":0.4772593677043915},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.35624194145202637},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21980851888656616}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.9038408398628235},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.8184223175048828},{"id":"https://openalex.org/C19612761","wikidata":"https://www.wikidata.org/wiki/Q8034836","display_name":"Workflow technology","level":3,"score":0.8164782524108887},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7461972832679749},{"id":"https://openalex.org/C188220564","wikidata":"https://www.wikidata.org/wiki/Q3325097","display_name":"Workflow engine","level":3,"score":0.740682065486908},{"id":"https://openalex.org/C163888707","wikidata":"https://www.wikidata.org/wiki/Q1154450","display_name":"Windows Workflow Foundation","level":4,"score":0.7109442949295044},{"id":"https://openalex.org/C130536060","wikidata":"https://www.wikidata.org/wiki/Q592375","display_name":"XPDL","level":4,"score":0.6527000665664673},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5957691073417664},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.5392391085624695},{"id":"https://openalex.org/C186533612","wikidata":"https://www.wikidata.org/wiki/Q471004","display_name":"Workflow Management Coalition","level":5,"score":0.4772593677043915},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.35624194145202637},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21980851888656616}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"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":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1008622","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008622","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008622&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:33630841","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33630841","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:4ebd3e4d325e46289fa70f8ed244a86a","is_oa":true,"landing_page_url":"https://doaj.org/article/4ebd3e4d325e46289fa70f8ed244a86a","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":"PLoS Computational Biology, Vol 17, Iss 2, p e1008622 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7906312","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7906312","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008622","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008622","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008622&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.6000000238418579,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G2059555639","display_name":"SSI: The UK Software Sustainability Institute","funder_award_id":"EP/H043160/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G2224711298","display_name":null,"funder_award_id":"EP/S021779/1","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"},{"id":"https://openalex.org/G2435155114","display_name":null,"funder_award_id":"208779/Z/17/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G2725021700","display_name":null,"funder_award_id":"EP/S021779/1","funder_id":"https://openalex.org/F4320326570","funder_display_name":"Software Sustainability Institute"},{"id":"https://openalex.org/G4518456141","display_name":"The UK Software Sustainability Institute: Phase 3","funder_award_id":"EP/S021779/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4722205739","display_name":"The Software Sustainability Institute: Phase 2","funder_award_id":"EP/N006410/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4999839975","display_name":"Collaborative Research: BBSRC:  RiboViz for reliable, reproducible and rigorous quantification of protein synthesis from ribosome profiling data","funder_award_id":"1936046","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5328447203","display_name":null,"funder_award_id":"EP/S021779/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5885757042","display_name":null,"funder_award_id":"BB/S018506/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7110065727","display_name":null,"funder_award_id":"EP/H043160/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G716340921","display_name":"BBSRC-NSF/BIO RiboViz for reliable, reproducible and rigorous quantification of protein synthesis from ribosome profiling data","funder_award_id":"BB/S018506/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7341832167","display_name":null,"funder_award_id":"EP/H043160/1","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7436348507","display_name":null,"funder_award_id":"EP/N006410/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8426425943","display_name":"Dynamic regulation of mRNA processing in adapting fungi","funder_award_id":"208779","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"},{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320332","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90"},{"id":"https://openalex.org/F4320326570","display_name":"Software Sustainability Institute","ror":"https://ror.org/0455awd29"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3131510005.pdf","grobid_xml":"https://content.openalex.org/works/W3131510005.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1827502043","https://openalex.org/W2013434113","https://openalex.org/W2036897871","https://openalex.org/W2078962046","https://openalex.org/W2102278945","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2110417468","https://openalex.org/W2131966673","https://openalex.org/W2185072450","https://openalex.org/W2310259903","https://openalex.org/W2539403003","https://openalex.org/W2605897695","https://openalex.org/W2607211817","https://openalex.org/W2751416425","https://openalex.org/W2902201297","https://openalex.org/W2917207851","https://openalex.org/W2950006067","https://openalex.org/W2952109315","https://openalex.org/W2971928433","https://openalex.org/W3006653136","https://openalex.org/W3013008564","https://openalex.org/W3040417797","https://openalex.org/W3047916956","https://openalex.org/W6697974936","https://openalex.org/W6901812552","https://openalex.org/W6901983125","https://openalex.org/W6931622787"],"related_works":["https://openalex.org/W2091596831","https://openalex.org/W2373541195","https://openalex.org/W2376410910","https://openalex.org/W2374818432","https://openalex.org/W2365658322","https://openalex.org/W291310304","https://openalex.org/W1545324131","https://openalex.org/W2166163080","https://openalex.org/W2370109655","https://openalex.org/W2370747980"],"abstract_inverted_index":{"Workflow":[0],"management":[1,73,92,106,198,204],"systems":[2,74,93,211],"represent,":[3],"manage,":[4],"and":[5,10,28,41,61,87,108,127,182,214,221,236,285],"execute":[6],"multistep":[7],"computational":[8],"analyses":[9],"offer":[11,263],"many":[12],"benefits":[13],"to":[14,26,29,44,62,96,103,115,135,143,166,179,183,275],"bioinformaticians.":[15],"They":[16,35],"provide":[17],"a":[18,49,67,133,161,196,202,206,230,246,264,269],"common":[19],"language":[20],"for":[21,169,249],"describing":[22],"analysis":[23,157],"workflows,":[24],"contributing":[25],"reproducibility":[27],"building":[30],"libraries":[31],"of":[32,48,54,81,147,153,176,187,209,232,260,267,273],"reusable":[33],"components.":[34],"can":[36,262],"support":[37],"both":[38],"incremental":[39],"build":[40,177],"re-entrancy-the":[42],"ability":[43],"selectively":[45],"re-execute":[46],"parts":[47],"workflow":[50,68,72,91,105,194,197,203],"in":[51,59,160],"the":[52,79,104,113,151,174,190,233,250,255],"presence":[53],"additional":[55],"inputs":[56],"or":[57],"changes":[58],"configuration":[60],"resume":[63],"execution":[64],"from":[65,139],"where":[66],"previously":[69],"stopped.":[70],"Many":[71],"enhance":[75],"portability":[76],"by":[77,227,287],"supporting":[78],"use":[80,175,259,276],"containers,":[82],"high-performance":[83],"computing":[84,171],"(HPC)":[85],"systems,":[86],"clouds.":[88],"Most":[89],"importantly,":[90],"allow":[94],"bioinformaticians":[95,114],"delegate":[97],"how":[98],"their":[99,124,129],"workflows":[100,120,181],"are":[101],"run":[102],"system":[107],"its":[109],"developers.":[110],"This":[111],"frees":[112],"focus":[116],"on":[117,123,128],"what":[118],"these":[119],"should":[121],"do,":[122],"data":[125,142],"analyses,":[126],"science.":[130],"RiboViz":[131,154,234],"is":[132,155],"package":[134],"extract":[136],"biological":[137],"insight":[138],"ribosome":[140],"profiling":[141],"help":[144],"advance":[145],"understanding":[146],"protein":[148],"synthesis.":[149],"At":[150],"heart":[152],"an":[156],"workflow,":[158,235],"implemented":[159],"Python":[162],"script.":[163],"To":[164,200],"conform":[165],"best":[167],"practices":[168],"scientific":[170],"which":[172],"recommend":[173],"tools":[178],"automate":[180],"reuse":[184],"code":[185],"instead":[186],"rewriting":[188],"it,":[189],"authors":[191],"reimplemented":[192],"this":[193],"within":[195,277],"system.":[199],"select":[201],"system,":[205],"rapid":[207],"survey":[208],"available":[210],"was":[212,225,238],"undertaken,":[213],"candidates":[215],"were":[216],"shortlisted:":[217],"Snakemake,":[218],"cwltool,":[219],"Toil,":[220],"Nextflow.":[222],"Each":[223],"candidate":[224],"evaluated":[226],"quickly":[228],"prototyping":[229,261],"subset":[231],"Nextflow":[237,253],"chosen.":[239],"The":[240,258],"selection":[241,272],"process":[242],"took":[243],"10":[244],"person-days,":[245],"small":[247],"cost":[248],"assurance":[251],"that":[252],"satisfied":[254],"authors'":[256],"requirements.":[257],"low-cost":[265],"way":[266],"making":[268],"more":[270],"informed":[271],"software":[274],"projects,":[278],"rather":[279],"than":[280],"relying":[281],"solely":[282],"upon":[283],"reviews":[284],"recommendations":[286],"others.":[288]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
