{"id":"https://openalex.org/W3209924522","doi":"https://doi.org/10.1109/mcse.2022.3226602","title":"OpenACC Acceleration of an Agent-Based Biological Simulation Framework","display_name":"OpenACC Acceleration of an Agent-Based Biological Simulation Framework","publication_year":2022,"publication_date":"2022-09-01","ids":{"openalex":"https://openalex.org/W3209924522","doi":"https://doi.org/10.1109/mcse.2022.3226602","mag":"3209924522"},"language":"en","primary_location":{"id":"doi:10.1109/mcse.2022.3226602","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcse.2022.3226602","pdf_url":null,"source":{"id":"https://openalex.org/S107923245","display_name":"Computing in Science & Engineering","issn_l":"1521-9615","issn":["1521-9615","1558-366X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320061","host_organization_name":"AIP Publishing","host_organization_lineage":["https://openalex.org/P4310320061","https://openalex.org/P4310320257"],"host_organization_lineage_names":["AIP Publishing","American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in Science &amp; Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019954695","display_name":"Matt Stack","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matt Stack","raw_affiliation_strings":["NVIDIA Corporation, Santa Clara, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NVIDIA Corporation, Santa Clara, CA, USA","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052380564","display_name":"Paul Macklin","orcid":"https://orcid.org/0000-0002-9925-0151"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Macklin","raw_affiliation_strings":["Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102797544","display_name":"Robert Searles","orcid":"https://orcid.org/0000-0001-9309-148X"},"institutions":[{"id":"https://openalex.org/I4210127875","display_name":"Nvidia (United States)","ror":"https://ror.org/03jdj4y14","country_code":"US","type":"company","lineage":["https://openalex.org/I4210127875"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Searles","raw_affiliation_strings":["NVIDIA Corporation, Santa Clara, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9309-148X","affiliations":[{"raw_affiliation_string":"NVIDIA Corporation, Santa Clara, CA, USA","institution_ids":["https://openalex.org/I4210127875"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009614578","display_name":"Sunita Chandrasekaran","orcid":"https://orcid.org/0000-0002-3560-9428"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sunita Chandrasekaran","raw_affiliation_strings":["University of Delaware, Newark, 19716, DE, USA"],"raw_orcid":"https://orcid.org/0000-0002-3560-9428","affiliations":[{"raw_affiliation_string":"University of Delaware, Newark, 19716, DE, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019954695"],"corresponding_institution_ids":["https://openalex.org/I4210127875"],"apc_list":null,"apc_paid":null,"fwci":0.6944,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.65510546,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"5","first_page":"53","last_page":"63"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.991100013256073,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.991100013256073,"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/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9850000143051147,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9707000255584717,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.663684070110321},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6045268177986145},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12232565879821777}],"concepts":[{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.663684070110321},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6045268177986145},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12232565879821777},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/mcse.2022.3226602","is_oa":false,"landing_page_url":"https://doi.org/10.1109/mcse.2022.3226602","pdf_url":null,"source":{"id":"https://openalex.org/S107923245","display_name":"Computing in Science & Engineering","issn_l":"1521-9615","issn":["1521-9615","1558-366X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320061","host_organization_name":"AIP Publishing","host_organization_lineage":["https://openalex.org/P4310320061","https://openalex.org/P4310320257"],"host_organization_lineage_names":["AIP Publishing","American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computing in Science &amp; Engineering","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5219964443","display_name":null,"funder_award_id":"1814609","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W2081347187","https://openalex.org/W2127112348","https://openalex.org/W2152246075","https://openalex.org/W2256248976","https://openalex.org/W2294178969","https://openalex.org/W2530996262","https://openalex.org/W2618506555","https://openalex.org/W2739107310","https://openalex.org/W2750212803","https://openalex.org/W2759656827","https://openalex.org/W2792539412","https://openalex.org/W2889169257","https://openalex.org/W2908975485","https://openalex.org/W2911948847","https://openalex.org/W2913957157","https://openalex.org/W2949797623","https://openalex.org/W2951213949","https://openalex.org/W2951856423","https://openalex.org/W2953317739","https://openalex.org/W2970909703","https://openalex.org/W3014308616","https://openalex.org/W3025028558","https://openalex.org/W3048573030","https://openalex.org/W3092921513","https://openalex.org/W3100533031","https://openalex.org/W3120951142","https://openalex.org/W3121642227","https://openalex.org/W3127269190","https://openalex.org/W3157590335","https://openalex.org/W3159287961","https://openalex.org/W3160105984","https://openalex.org/W3164615498","https://openalex.org/W3184809620","https://openalex.org/W3190433214","https://openalex.org/W3199639156","https://openalex.org/W3200584885","https://openalex.org/W3203423444"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Computational":[0],"biology":[1],"has":[2],"increasingly":[3],"turned":[4],"to":[5,8,43,59,85],"agent-based":[6,49,68],"modeling":[7,51],"explore":[9],"complex":[10],"biological":[11,25,45,50],"systems.":[12],"Biological":[13],"diffusion":[14,33,62],"(diffusion,":[15],"decay,":[16],"secretion,":[17],"and":[18,34,113],"uptake)":[19],"is":[20],"a":[21,66,86,118,125],"key":[22],"driver":[23],"of":[24,64],"tissues.":[26],"GPU":[27,83],"computing":[28],"can":[29,140],"vastly":[30],"accelerate":[31,60],"the":[32,38,61,78,99,111,114,131],"decay":[35],"operators":[36],"in":[37,47],"partial":[39],"differential":[40],"equations":[41],"used":[42],"represent":[44],"transport":[46],"an":[48,73],"system.":[52],"In":[53],"this":[54],"article,":[55],"we":[56,116,139],"utilize":[57],"OpenACC":[58,108],"portion":[63],"PhysiCell,":[65],"cross-platform":[67],"biosimulation":[69],"framework.":[70],"We":[71,93],"demonstrate":[72,95],"almost":[74],"40\u00d7":[75],"speedup":[76,97],"on":[77,89,98],"state-of-the-art":[79],"NVIDIA":[80],"Ampere":[81],"100":[82],"compared":[84],"serial":[87],"run":[88],"AMD\u2019s":[90],"EPYC":[91,102],"7742.":[92],"also":[94],"9\u00d7":[96],"64-core":[100],"AMD":[101],"7742":[103],"multicore":[104],"platform.":[105],"By":[106],"using":[107],"for":[109],"both":[110],"CPUs":[112],"GPUs,":[115],"maintain":[117],"single":[119],"source":[120],"code":[121],"base,":[122],"thus":[123],"creating":[124],"portable":[126],"yet":[127],"performant":[128],"solution.":[129],"With":[130],"simulator\u2019s":[132],"most":[133],"significant":[134],"computational":[135],"bottleneck":[136],"significantly":[137],"reduced,":[138],"continue":[141],"cancer":[142],"simulations":[143],"over":[144],"much":[145],"longer":[146],"times.":[147]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
