{"id":"https://openalex.org/W2995326322","doi":"https://doi.org/10.1186/s12859-019-3181-y","title":"Parallelisation strategies for agent based simulation of immune systems","display_name":"Parallelisation strategies for agent based simulation of immune systems","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W2995326322","doi":"https://doi.org/10.1186/s12859-019-3181-y","mag":"2995326322","pmid":"https://pubmed.ncbi.nlm.nih.gov/31823716"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3181-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3181-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3181-y.pdf","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/s12859-019-3181-y.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084786722","display_name":"Mozhgan Kabiri Chimeh","orcid":"https://orcid.org/0000-0002-2561-7926"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Mozhgan Kabiri Chimeh","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, UK. m.kabiri-chimeh@sheffield.ac.uk","Department of Computer Science, University of Sheffield, Sheffield, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, UK. m.kabiri-chimeh@sheffield.ac.uk","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, UK","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039912522","display_name":"Peter Heywood","orcid":"https://orcid.org/0000-0001-9277-8394"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Heywood","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, UK","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003874484","display_name":"Marzio Pennisi","orcid":"https://orcid.org/0000-0003-0231-7653"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marzio Pennisi","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Catania, Catania, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Catania, Catania, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044340074","display_name":"Francesco Pappalardo","orcid":"https://orcid.org/0000-0003-1668-3320"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Pappalardo","raw_affiliation_strings":["Department of Drug Sciences, University of Catania, Catania, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Drug Sciences, University of Catania, Catania, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011413276","display_name":"Paul Richmond","orcid":"https://orcid.org/0000-0002-4657-5518"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Paul Richmond","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, UK","institution_ids":["https://openalex.org/I91136226"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5084786722"],"corresponding_institution_ids":["https://openalex.org/I91136226"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.4883,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.813497,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"S6","first_page":"579","last_page":"579"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12391","display_name":"Artificial Immune Systems Applications","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12391","display_name":"Artificial Immune Systems Applications","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9958999752998352,"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/T10482","display_name":"Mathematical and Theoretical Epidemiology and Ecology Models","score":0.9302999973297119,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6252180337905884},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.5310775637626648},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.47132423520088196},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45856013894081116},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3893941640853882},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.38382285833358765},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2775927186012268},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1288633942604065},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0846584141254425},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.06658244132995605},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.055004000663757324}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6252180337905884},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5310775637626648},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.47132423520088196},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45856013894081116},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3893941640853882},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.38382285833358765},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2775927186012268},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1288633942604065},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0846584141254425},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.06658244132995605},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.055004000663757324}],"mesh":[{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007107","descriptor_name":"Immune System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007107","descriptor_name":"Immune System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007107","descriptor_name":"Immune System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018448","descriptor_name":"Models, Immunological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-3181-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3181-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3181-y.pdf","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:31823716","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31823716","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:eprints.whiterose.ac.uk:155217","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:355edb4a3091481eb81874c06b01bbd4","is_oa":true,"landing_page_url":"https://doaj.org/article/355edb4a3091481eb81874c06b01bbd4","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S6, Pp 1-14 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5872233","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6905091","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3181-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3181-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3181-y.pdf","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":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G2309032329","display_name":null,"funder_award_id":"EP/N018869/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4726435050","display_name":null,"funder_award_id":"H2020-SC1-2017-CNECT-2, No. 777123","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G585938856","display_name":"Accelerating Scientific Discovery with Accelerated Computing","funder_award_id":"EP/N018869/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2995326322.pdf","grobid_xml":"https://content.openalex.org/works/W2995326322.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W2497774","https://openalex.org/W78789044","https://openalex.org/W778867002","https://openalex.org/W1504343806","https://openalex.org/W1512999284","https://openalex.org/W1765399862","https://openalex.org/W1978486653","https://openalex.org/W1980034145","https://openalex.org/W1994509201","https://openalex.org/W1997433991","https://openalex.org/W2011438811","https://openalex.org/W2028499920","https://openalex.org/W2041597162","https://openalex.org/W2070891817","https://openalex.org/W2081098704","https://openalex.org/W2086370911","https://openalex.org/W2091174660","https://openalex.org/W2096890314","https://openalex.org/W2102742832","https://openalex.org/W2124677924","https://openalex.org/W2133183093","https://openalex.org/W2154778014","https://openalex.org/W2159360750","https://openalex.org/W2161575244","https://openalex.org/W2165307608","https://openalex.org/W2169377408","https://openalex.org/W2170316986","https://openalex.org/W2172275426","https://openalex.org/W2186570571","https://openalex.org/W2338717024","https://openalex.org/W2477558360","https://openalex.org/W2541748267","https://openalex.org/W2575970083","https://openalex.org/W2595828237","https://openalex.org/W2603889387","https://openalex.org/W2756268336","https://openalex.org/W2793599788","https://openalex.org/W2797807751","https://openalex.org/W2800633717","https://openalex.org/W2802952608","https://openalex.org/W2913637406","https://openalex.org/W3121523601","https://openalex.org/W3138798301","https://openalex.org/W3145638023","https://openalex.org/W4205300089","https://openalex.org/W4249442404","https://openalex.org/W4294553758","https://openalex.org/W4294553893","https://openalex.org/W4300127459","https://openalex.org/W4301428739","https://openalex.org/W6806328399"],"related_works":["https://openalex.org/W4211132779","https://openalex.org/W1972945471","https://openalex.org/W2357948923","https://openalex.org/W4313472242","https://openalex.org/W2332159055","https://openalex.org/W2030500189","https://openalex.org/W2419188526","https://openalex.org/W2144422987","https://openalex.org/W2018938924","https://openalex.org/W3171722058"],"abstract_inverted_index":{"Our":[0],"performance":[1],"results":[2],"demonstrate":[3],"the":[4,37],"applicability":[5],"of":[6,13,26],"these":[7],"methods":[8],"to":[9,19],"a":[10],"broader":[11],"class":[12],"biological":[14],"systems":[15],"exhibiting":[16],"typical":[17],"cell":[18,20],"interactions.":[21],"The":[22],"advantage":[23],"and":[24],"disadvantage":[25],"each":[27,32],"implementation":[28],"is":[29],"discussed":[30],"showing":[31],"can":[33],"be":[34],"used":[35],"as":[36],"basis":[38],"for":[39],"developing":[40],"complete":[41],"immune":[42],"system":[43],"models":[44],"on":[45],"parallel":[46],"hardware.":[47]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
