{"id":"https://openalex.org/W7161011153","doi":"https://doi.org/10.1007/s42979-026-04947-0","title":"Right-Sizing Compute Resource Allocations for Bioinformatics Tools with Total Perspective Vortex","display_name":"Right-Sizing Compute Resource Allocations for Bioinformatics Tools with Total Perspective Vortex","publication_year":2026,"publication_date":"2026-05-13","ids":{"openalex":"https://openalex.org/W7161011153","doi":"https://doi.org/10.1007/s42979-026-04947-0"},"language":"en","primary_location":{"id":"doi:10.1007/s42979-026-04947-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s42979-026-04947-0","pdf_url":"https://link.springer.com/content/pdf/10.1007/s42979-026-04947-0.pdf","source":{"id":"https://openalex.org/S4210174798","display_name":"SN Computer Science","issn_l":"2661-8907","issn":["2661-8907","2662-995X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["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":"SN Computer Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s42979-026-04947-0.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136063493","display_name":"Nuwan Goonasekera","orcid":"https://orcid.org/0000-0002-3019-2934"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Nuwan Goonasekera","raw_affiliation_strings":["University of Melbourne, Melbourne, Australia"],"raw_orcid":"https://orcid.org/0000-0002-3019-2934","affiliations":[{"raw_affiliation_string":"University of Melbourne, Melbourne, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088630818","display_name":"Catherine Bromhead","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Catherine Bromhead","raw_affiliation_strings":["University of Melbourne, Melbourne, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Melbourne, Melbourne, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081097865","display_name":"Simon Gladman","orcid":null},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Simon Gladman","raw_affiliation_strings":["University of Melbourne, Melbourne, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Melbourne, Melbourne, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012038702","display_name":"Keith Suderman","orcid":"https://orcid.org/0000-0003-0502-4557"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keith Suderman","raw_affiliation_strings":["Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039419475","display_name":"Nathan Coraor","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan Coraor","raw_affiliation_strings":["Pennsylvania State University, State College, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, State College, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007199315","display_name":"B Gr\u00fcning","orcid":null},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bj\u00f6rn Gr\u00fcning","raw_affiliation_strings":["University of Freiburg, Freiburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Freiburg, Freiburg, Germany","institution_ids":["https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006951727","display_name":"Enis Afgan","orcid":"https://orcid.org/0000-0003-0922-6711"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enis Afgan","raw_affiliation_strings":["Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5136063493"],"corresponding_institution_ids":["https://openalex.org/I165779595"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":{"value":2290,"currency":"EUR","value_usd":2890},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.89353218,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.957099974155426,"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":0.957099974155426,"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/T11937","display_name":"Research Data Management Practices","score":0.008899999782443047,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.007400000002235174,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7867000102996826},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.642300009727478},{"id":"https://openalex.org/keywords/turnaround-time","display_name":"Turnaround time","score":0.5537999868392944},{"id":"https://openalex.org/keywords/queue","display_name":"Queue","score":0.5522000193595886},{"id":"https://openalex.org/keywords/job-queue","display_name":"Job queue","score":0.5493000149726868},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5235000252723694},{"id":"https://openalex.org/keywords/job-scheduler","display_name":"Job scheduler","score":0.5123999714851379},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4788999855518341}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7867000102996826},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.642300009727478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.619700014591217},{"id":"https://openalex.org/C176553487","wikidata":"https://www.wikidata.org/wiki/Q7855819","display_name":"Turnaround time","level":2,"score":0.5537999868392944},{"id":"https://openalex.org/C160403385","wikidata":"https://www.wikidata.org/wiki/Q220543","display_name":"Queue","level":2,"score":0.5522000193595886},{"id":"https://openalex.org/C171627638","wikidata":"https://www.wikidata.org/wiki/Q6206744","display_name":"Job queue","level":4,"score":0.5493000149726868},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5235000252723694},{"id":"https://openalex.org/C111873713","wikidata":"https://www.wikidata.org/wiki/Q1641413","display_name":"Job scheduler","level":3,"score":0.5123999714851379},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4788999855518341},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4693000018596649},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.4494999945163727},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.41440001130104065},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.3840999901294708},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3610999882221222},{"id":"https://openalex.org/C66204764","wikidata":"https://www.wikidata.org/wiki/Q219416","display_name":"Sustainability","level":2,"score":0.3276999890804291},{"id":"https://openalex.org/C42475967","wikidata":"https://www.wikidata.org/wiki/Q194292","display_name":"Operations research","level":1,"score":0.3215999901294708},{"id":"https://openalex.org/C29202148","wikidata":"https://www.wikidata.org/wiki/Q287260","display_name":"Resource allocation","level":2,"score":0.30979999899864197},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.2935999929904938},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C2780609101","wikidata":"https://www.wikidata.org/wiki/Q17156588","display_name":"Resource management (computing)","level":2,"score":0.2750000059604645}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s42979-026-04947-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s42979-026-04947-0","pdf_url":"https://link.springer.com/content/pdf/10.1007/s42979-026-04947-0.pdf","source":{"id":"https://openalex.org/S4210174798","display_name":"SN Computer Science","issn_l":"2661-8907","issn":["2661-8907","2662-995X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["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":"SN Computer Science","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s42979-026-04947-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s42979-026-04947-0","pdf_url":"https://link.springer.com/content/pdf/10.1007/s42979-026-04947-0.pdf","source":{"id":"https://openalex.org/S4210174798","display_name":"SN Computer Science","issn_l":"2661-8907","issn":["2661-8907","2662-995X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["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":"SN Computer Science","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6815854907035828,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320974","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7161011153.pdf","grobid_xml":"https://content.openalex.org/works/W7161011153.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1596936080","https://openalex.org/W2078962046","https://openalex.org/W2102278945","https://openalex.org/W2110417468","https://openalex.org/W2141458291","https://openalex.org/W2605897695","https://openalex.org/W2808343649","https://openalex.org/W2898099374","https://openalex.org/W2912228103","https://openalex.org/W2917207851","https://openalex.org/W2955703013","https://openalex.org/W4210302214","https://openalex.org/W4319017910","https://openalex.org/W4380325188","https://openalex.org/W4382055832","https://openalex.org/W4386585065","https://openalex.org/W4398182689","https://openalex.org/W4401736248","https://openalex.org/W4416544020"],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"The":[1],"rapid":[2],"growth":[3],"of":[4,23,74,96,119,127,129,180],"data-driven":[5],"biomedical":[6],"research":[7],"has":[8,124],"increased":[9],"pressure":[10],"on":[11],"shared":[12,164],"compute":[13],"infrastructure,":[14],"where":[15],"a":[16,52,61,93,151],"persistent":[17],"challenge":[18],"is":[19],"the":[20,66,111,163,198],"widespread":[21],"over-allocation":[22],"resources.":[24],"This":[25,35],"practice":[26],"increases":[27],"queue":[28,145],"wait":[29,146],"times,":[30,189],"costs,":[31],"and":[32,46,77,91,110,116,121,166,178,190],"carbon":[33],"emissions.":[34],"study":[36],"investigates":[37],"whether":[38],"job":[39,187],"resource":[40,98],"requests":[41],"can":[42],"be":[43],"automatically":[44],"right-sized":[45],"efficiently":[47],"scheduled":[48,125],"at":[49],"scale":[50],"within":[51],"science":[53],"gateway.":[54],"We":[55],"developed":[56,195],"Total":[57],"Perspective":[58],"Vortex":[59],"(TPV),":[60],"software":[62],"library":[63],"integrated":[64],"into":[65],"Galaxy":[67,107,140],"platform.":[68],"TPV":[69,123,142,175],"introduces":[70],"(i)":[71],"dynamic":[72],"adjustment":[73],"CPU,":[75],"memory,":[76],"GPU":[78],"requirements":[79,99],"for":[80,100,172,196],"individual":[81],"jobs,":[82],"(ii)":[83],"meta-scheduling":[84],"across":[85,106],"heterogeneous":[86],"resources":[87],"using":[88],"configurable":[89],"rules,":[90],"(iii)":[92],"community-curated":[94],"database":[95,165],"default":[97],"nearly":[101],"1,000":[102],"bioinformatics":[103],"tools.":[104],"Deployments":[105],"Australia,":[108,141],"Europe,":[109],"United":[112],"States":[113],"provided":[114],"quantitative":[115],"qualitative":[117],"evidence":[118],"performance":[120],"usability.":[122],"tens":[126],"millions":[128],"jobs":[130],"in":[131,137,154],"production,":[132],"with":[133],"scheduling":[134],"decisions":[135],"executed":[136],"milliseconds.":[138],"At":[139],"reduced":[143],"average":[144],"times":[147],"by":[148,183],"15%":[149],"despite":[150],"27%":[152],"increase":[153],"workload.":[155],"Administrators":[156],"reported":[157],"major":[158],"time":[159],"savings":[160],"due":[161],"to":[162,201],"simplified":[167],"configuration,":[168],"while":[169],"retaining":[170],"flexibility":[171],"local":[173],"customization.":[174],"improves":[176],"efficiency":[177],"sustainability":[179],"scientific":[181],"gateways":[182],"reducing":[184],"waste,":[185],"shortening":[186],"turnaround":[188],"lowering":[191],"administrative":[192],"burden.":[193],"While":[194],"Galaxy,":[197],"approach":[199],"generalizes":[200],"other":[202],"workflow":[203],"systems.":[204]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2026-05-14T00:00:00"}
