{"id":"https://openalex.org/W3208553257","doi":"https://doi.org/10.1186/s12859-021-04455-3","title":"FASTAFS: file system virtualisation of random access compressed FASTA files","display_name":"FASTAFS: file system virtualisation of random access compressed FASTA files","publication_year":2021,"publication_date":"2021-11-01","ids":{"openalex":"https://openalex.org/W3208553257","doi":"https://doi.org/10.1186/s12859-021-04455-3","mag":"3208553257","pmid":"https://pubmed.ncbi.nlm.nih.gov/34724897"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04455-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04455-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04455-3","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/s12859-021-04455-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081979091","display_name":"Youri Hoogstrate","orcid":"https://orcid.org/0000-0003-2166-0676"},"institutions":[{"id":"https://openalex.org/I2801952686","display_name":"Erasmus MC","ror":"https://ror.org/018906e22","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2801952686"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Youri Hoogstrate","raw_affiliation_strings":["Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl","Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl","Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl","Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl","institution_ids":[]},{"raw_affiliation_string":"Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl","institution_ids":[]},{"raw_affiliation_string":"Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands. yhoogstrate@erasmusmc.nl","institution_ids":[]},{"raw_affiliation_string":"Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I2801952686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034635531","display_name":"Guido Jenster","orcid":"https://orcid.org/0000-0002-8658-2552"},"institutions":[{"id":"https://openalex.org/I4210149908","display_name":"Erasmus MC Cancer Institute","ror":"https://ror.org/03r4m3349","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686","https://openalex.org/I4210149908"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Guido W. Jenster","raw_affiliation_strings":["Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I4210149908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008299051","display_name":"Harmen J.G. van de Werken","orcid":"https://orcid.org/0000-0002-9794-1477"},"institutions":[{"id":"https://openalex.org/I4210149908","display_name":"Erasmus MC Cancer Institute","ror":"https://ror.org/03r4m3349","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I2801952686","https://openalex.org/I4210149908"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Harmen J. G. van de Werken","raw_affiliation_strings":["Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands","Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands","Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I4210149908"]},{"raw_affiliation_string":"Department of Immunology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I4210149908"]},{"raw_affiliation_string":"Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands","institution_ids":["https://openalex.org/I4210149908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081979091"],"corresponding_institution_ids":["https://openalex.org/I2801952686"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4058,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.59951016,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"22","issue":"1","first_page":"535","last_page":"535"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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":0.9973999857902527,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9969000220298767,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9886999726295471,"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/computer-science","display_name":"Computer science","score":0.7959949970245361},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6462445855140686},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.5871772170066833},{"id":"https://openalex.org/keywords/random-access","display_name":"Random access","score":0.575171172618866},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.5546016693115234},{"id":"https://openalex.org/keywords/versioning-file-system","display_name":"Versioning file system","score":0.5220556259155273},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4781566560268402},{"id":"https://openalex.org/keywords/data-file","display_name":"Data file","score":0.47534772753715515},{"id":"https://openalex.org/keywords/computer-file","display_name":"Computer file","score":0.45846426486968994},{"id":"https://openalex.org/keywords/sync","display_name":"sync","score":0.4249059557914734},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.33909159898757935},{"id":"https://openalex.org/keywords/stub-file","display_name":"Stub file","score":0.16943636536598206},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.10923588275909424}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7959949970245361},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6462445855140686},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5871772170066833},{"id":"https://openalex.org/C101722063","wikidata":"https://www.wikidata.org/wiki/Q218825","display_name":"Random access","level":2,"score":0.575171172618866},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.5546016693115234},{"id":"https://openalex.org/C166807848","wikidata":"https://www.wikidata.org/wiki/Q3445065","display_name":"Versioning file system","level":4,"score":0.5220556259155273},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4781566560268402},{"id":"https://openalex.org/C171730128","wikidata":"https://www.wikidata.org/wiki/Q5227290","display_name":"Data file","level":2,"score":0.47534772753715515},{"id":"https://openalex.org/C95637964","wikidata":"https://www.wikidata.org/wiki/Q82753","display_name":"Computer file","level":2,"score":0.45846426486968994},{"id":"https://openalex.org/C3913047","wikidata":"https://www.wikidata.org/wiki/Q1956265","display_name":"sync","level":3,"score":0.4249059557914734},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.33909159898757935},{"id":"https://openalex.org/C13674803","wikidata":"https://www.wikidata.org/wiki/Q7627301","display_name":"Stub file","level":3,"score":0.16943636536598206},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.10923588275909424},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-021-04455-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04455-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04455-3","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:34724897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34724897","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:eur:oai:pure.eur.nl:publications/11e5b014-6a2f-4c9a-9704-0e9a5a8e7dc1","is_oa":true,"landing_page_url":"https://pure.eur.nl/en/publications/11e5b014-6a2f-4c9a-9704-0e9a5a8e7dc1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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, 22(1):535. BioMed Central Ltd.","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:fbb2aed2325b447aa3f461d033a7c2f8","is_oa":true,"landing_page_url":"https://doaj.org/article/fbb2aed2325b447aa3f461d033a7c2f8","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-12 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7450381","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8558547","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8558547","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8558547","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/s12859-021-04455-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04455-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04455-3","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3208553257.pdf","grobid_xml":"https://content.openalex.org/works/W3208553257.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1978939618","https://openalex.org/W2014677321","https://openalex.org/W2034285706","https://openalex.org/W2110417468","https://openalex.org/W2110905563","https://openalex.org/W2114792961","https://openalex.org/W2119180969","https://openalex.org/W2124799197","https://openalex.org/W2154139219","https://openalex.org/W2155943701","https://openalex.org/W2158678815","https://openalex.org/W2169456326","https://openalex.org/W2336957559","https://openalex.org/W2529838505","https://openalex.org/W2605897695","https://openalex.org/W2898440040","https://openalex.org/W2951893579","https://openalex.org/W4233120011","https://openalex.org/W4255738661"],"related_works":["https://openalex.org/W1988281752","https://openalex.org/W3032858184","https://openalex.org/W2157319784","https://openalex.org/W2375081845","https://openalex.org/W3209230099","https://openalex.org/W1977082847","https://openalex.org/W2625128489","https://openalex.org/W2090798606","https://openalex.org/W2356613511","https://openalex.org/W96486943"],"abstract_inverted_index":{"FASTAFS":[0],"is":[1],"a":[2],"user-friendly":[3],"and":[4,15],"easy":[5],"to":[6,13,26,50],"deploy":[7],"backwards":[8],"compatible":[9],"generic":[10],"purpose":[11],"solution":[12],"store":[14],"access":[16,25],"compressed":[17],"FASTA":[18,27],"files,":[19],"since":[20],"it":[21],"offers":[22,44],"file":[23,36],"system":[24],"files":[28,34],"as":[29,31,41],"well":[30],"in-sync":[32],"metadata":[33],"through":[35],"virtualisation.":[37],"Using":[38],"virtual":[39],"filesystems":[40],"in-between":[42],"layer":[43],"format":[45],"conversion":[46],"without":[47],"the":[48],"need":[49],"rewrite":[51],"code":[52],"into":[53],"different":[54],"programming":[55],"languages":[56],"while":[57],"preserving":[58],"compatibility.":[59]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
