{"id":"https://openalex.org/W3199089929","doi":"https://doi.org/10.1093/bioinformatics/btab649","title":"BioDynaMo: a modular platform for high-performance agent-based simulation","display_name":"BioDynaMo: a modular platform for high-performance agent-based simulation","publication_year":2021,"publication_date":"2021-09-13","ids":{"openalex":"https://openalex.org/W3199089929","doi":"https://doi.org/10.1093/bioinformatics/btab649","mag":"3199089929","pmid":"https://pubmed.ncbi.nlm.nih.gov/34529036"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab649","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab649","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/453/42039902/btab649.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/453/42039902/btab649.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038201375","display_name":"Lukas Breitwieser","orcid":"https://orcid.org/0000-0003-2265-8615"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I67311998","display_name":"European Organization for Nuclear Research","ror":"https://ror.org/01ggx4157","country_code":"CH","type":"facility","lineage":["https://openalex.org/I67311998"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Lukas Breitwieser","raw_affiliation_strings":["CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-2265-8615","affiliations":[{"raw_affiliation_string":"CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","institution_ids":["https://openalex.org/I67311998"]},{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035102250","display_name":"Ahmad Hesam","orcid":"https://orcid.org/0000-0001-7331-1000"},"institutions":[{"id":"https://openalex.org/I67311998","display_name":"European Organization for Nuclear Research","ror":"https://ror.org/01ggx4157","country_code":"CH","type":"facility","lineage":["https://openalex.org/I67311998"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["CH","NL"],"is_corresponding":true,"raw_author_name":"Ahmad Hesam","raw_affiliation_strings":["CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","Department of Quantum & Computer Engineering, Delft University of Technology , Delft 2628CD, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","institution_ids":["https://openalex.org/I67311998"]},{"raw_affiliation_string":"Department of Quantum & Computer Engineering, Delft University of Technology , Delft 2628CD, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087183311","display_name":"Jean de Montigny","orcid":"https://orcid.org/0000-0002-5832-5065"},"institutions":[{"id":"https://openalex.org/I67311998","display_name":"European Organization for Nuclear Research","ror":"https://ror.org/01ggx4157","country_code":"CH","type":"facility","lineage":["https://openalex.org/I67311998"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jean de Montigny","raw_affiliation_strings":["CERN openlab, IT Department, CERN, Geneva 1211, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","institution_ids":["https://openalex.org/I67311998"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036036733","display_name":"Vasileios Vavourakis","orcid":"https://orcid.org/0000-0002-4102-2084"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["CY","GB"],"is_corresponding":false,"raw_author_name":"Vasileios Vavourakis","raw_affiliation_strings":["Department of Mechanical & Manufacturing Engineering, University of Cyprus , Nicosia 2109, Cyprus","Department of Medical Physics & Biomedical Engineering, University College London , London WC1E 6BT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical & Manufacturing Engineering, University of Cyprus , Nicosia 2109, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"Department of Medical Physics & Biomedical Engineering, University College London , London WC1E 6BT, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015762893","display_name":"Alexandros Iosif","orcid":"https://orcid.org/0000-0002-5190-3766"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Alexandros Iosif","raw_affiliation_strings":["Department of Mechanical & Manufacturing Engineering, University of Cyprus , Nicosia 2109, Cyprus"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mechanical & Manufacturing Engineering, University of Cyprus , Nicosia 2109, Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040200473","display_name":"Jack Jennings","orcid":"https://orcid.org/0000-0002-6108-9155"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jack Jennings","raw_affiliation_strings":["School of Computing, Newcastle University , Newcastle upon Tyne NE4 5TG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, Newcastle University , Newcastle upon Tyne NE4 5TG, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005260652","display_name":"Marcus Kaiser","orcid":"https://orcid.org/0000-0002-4654-3110"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]},{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Marcus Kaiser","raw_affiliation_strings":["Department of Functional Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025, China","Precision Imaging Beacon, School of Medicine, University of Nottingham , Nottingham NG7 2UH, UK","School of Computing, Newcastle University , Newcastle upon Tyne NE4 5TG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Functional Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025, China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I2801556517"]},{"raw_affiliation_string":"Precision Imaging Beacon, School of Medicine, University of Nottingham , Nottingham NG7 2UH, UK","institution_ids":["https://openalex.org/I142263535"]},{"raw_affiliation_string":"School of Computing, Newcastle University , Newcastle upon Tyne NE4 5TG, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062206583","display_name":"Marco Manca","orcid":"https://orcid.org/0000-0002-7869-2620"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marco Manca","raw_affiliation_strings":["SCimPulse Foundation , Geleen 6162 BC, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-7869-2620","affiliations":[{"raw_affiliation_string":"SCimPulse Foundation , Geleen 6162 BC, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045880177","display_name":"Alberto Di Meglio","orcid":"https://orcid.org/0000-0001-6466-5413"},"institutions":[{"id":"https://openalex.org/I67311998","display_name":"European Organization for Nuclear Research","ror":"https://ror.org/01ggx4157","country_code":"CH","type":"facility","lineage":["https://openalex.org/I67311998"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Alberto Di Meglio","raw_affiliation_strings":["CERN openlab, IT Department, CERN, Geneva 1211, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","institution_ids":["https://openalex.org/I67311998"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021955713","display_name":"Zaid Al-Ars","orcid":"https://orcid.org/0000-0001-7670-8572"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Zaid Al-Ars","raw_affiliation_strings":["Department of Quantum & Computer Engineering, Delft University of Technology , Delft 2628CD, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Quantum & Computer Engineering, Delft University of Technology , Delft 2628CD, The Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073843631","display_name":"Fons Rademakers","orcid":"https://orcid.org/0000-0002-3571-9635"},"institutions":[{"id":"https://openalex.org/I67311998","display_name":"European Organization for Nuclear Research","ror":"https://ror.org/01ggx4157","country_code":"CH","type":"facility","lineage":["https://openalex.org/I67311998"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Fons Rademakers","raw_affiliation_strings":["CERN openlab, IT Department, CERN, Geneva 1211, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CERN openlab, IT Department, CERN, Geneva 1211, Switzerland","institution_ids":["https://openalex.org/I67311998"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050695684","display_name":"Onur Mutlu","orcid":"https://orcid.org/0000-0002-0075-2312"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Onur Mutlu","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland","Department of Information Technology and Electrical Engineering , ETH Zurich, Zurich 8092, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Information Technology and Electrical Engineering , ETH Zurich, Zurich 8092, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033865614","display_name":"Roman Bauer","orcid":"https://orcid.org/0000-0002-7268-9359"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Roman Bauer","raw_affiliation_strings":["Department of Computer Science, University of Surrey , Guildford GU2 7XH, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Surrey , Guildford GU2 7XH, UK","institution_ids":["https://openalex.org/I28290843"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5033865614","https://openalex.org/A5035102250","https://openalex.org/A5038201375","https://openalex.org/A5050695684"],"corresponding_institution_ids":["https://openalex.org/I28290843","https://openalex.org/I35440088","https://openalex.org/I67311998","https://openalex.org/I98358874"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":3.1312,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.92580886,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"453","last_page":"460"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.21459999680519104,"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"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.21459999680519104,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.07639999687671661,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.0333000011742115,"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/modular-design","display_name":"Modular design","score":0.8544898629188538},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8127851486206055},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.6962199807167053},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.6409848928451538},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6196724772453308},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.49826502799987793},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4253637194633484},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.41982796788215637},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3605293035507202},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.335722953081131},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.32352638244628906},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.21093323826789856}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.8544898629188538},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8127851486206055},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.6962199807167053},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.6409848928451538},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6196724772453308},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.49826502799987793},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4253637194633484},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.41982796788215637},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3605293035507202},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.335722953081131},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.32352638244628906},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.21093323826789856},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btab649","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab649","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/453/42039902/btab649.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34529036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34529036","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/524389","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/524389","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, 38 (2)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8723141","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8723141","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:cds.cern.ch:2800211","is_oa":true,"landing_page_url":"http://cds.cern.ch/record/2800211","pdf_url":null,"source":{"id":"https://openalex.org/S4306400735","display_name":"International Linear Collider","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:nottingham-repository.worktribe.com:9085261","is_oa":true,"landing_page_url":"https://nottingham-repository.worktribe.com/output/9085261","pdf_url":null,"source":{"id":"https://openalex.org/S4306402483","display_name":"Repository@Nottingham (University of Nottingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142263535","host_organization_name":"University of Nottingham","host_organization_lineage":["https://openalex.org/I142263535"],"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":"Journal Article"},{"id":"pmh:oai:tudelft.nl:uuid:58dbf255-f719-45d2-a816-1cdb356285b4","is_oa":false,"landing_page_url":"http://resolver.tudelft.nl/uuid:58dbf255-f719-45d2-a816-1cdb356285b4","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},{"id":"doi:10.3929/ethz-b-000524389","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000524389","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","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","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab649","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab649","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/2/453/42039902/btab649.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G2538110292","display_name":"Controlling Abnormal Network Dynamics with Optogenetics (CANDO)","funder_award_id":"102037","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G262539850","display_name":null,"funder_award_id":"A000026","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4249494967","display_name":null,"funder_award_id":"NS/A000026/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4475059929","display_name":"Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies","funder_award_id":"EP/N031962/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5297830449","display_name":"Innovation Fellowship: Computational modelling of cryopreservation of biological tissue","funder_award_id":"EP/S001433/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G566283901","display_name":null,"funder_award_id":"MR/N015037/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7047248673","display_name":"Computational modeling of retinal development","funder_award_id":"MR/N015037/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7113140588","display_name":"Innovation Fellowship: Computational modelling of cryopreservation of biological tissue","funder_award_id":"EP/S001433/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7928544064","display_name":null,"funder_award_id":"MR/T004347/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8035887905","display_name":null,"funder_award_id":"EP/N031962/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8171038970","display_name":null,"funder_award_id":"MR/T004347/2","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8699219344","display_name":null,"funder_award_id":"N031962","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320313559","display_name":"CERN","ror":"https://ror.org/01ggx4157"},{"id":"https://openalex.org/F4320316785","display_name":"VMware","ror":null},{"id":"https://openalex.org/F4320320295","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70"},{"id":"https://openalex.org/F4320330117","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30"},{"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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3199089929.pdf","grobid_xml":"https://content.openalex.org/works/W3199089929.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1548644314","https://openalex.org/W1795050634","https://openalex.org/W1967324141","https://openalex.org/W1967961367","https://openalex.org/W1985449099","https://openalex.org/W1997338027","https://openalex.org/W2010478558","https://openalex.org/W2025516544","https://openalex.org/W2102667107","https://openalex.org/W2103900801","https://openalex.org/W2112682311","https://openalex.org/W2112745564","https://openalex.org/W2117899937","https://openalex.org/W2124677924","https://openalex.org/W2130071305","https://openalex.org/W2132729131","https://openalex.org/W2147270524","https://openalex.org/W2148301044","https://openalex.org/W2157999920","https://openalex.org/W2160135160","https://openalex.org/W2171895829","https://openalex.org/W2272546316","https://openalex.org/W2288506358","https://openalex.org/W2465605447","https://openalex.org/W2543459117","https://openalex.org/W2595828237","https://openalex.org/W2623066589","https://openalex.org/W2739789502","https://openalex.org/W2898416763","https://openalex.org/W2949797623","https://openalex.org/W3002265756","https://openalex.org/W6632585931","https://openalex.org/W6656594533","https://openalex.org/W6682044371"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W4384009753","https://openalex.org/W2791776396","https://openalex.org/W4286531993","https://openalex.org/W3081674575","https://openalex.org/W4287673983"],"abstract_inverted_index":{"MOTIVATION:":[0],"Agent-based":[1],"modeling":[2],"is":[3,135,145],"an":[4,83,136],"indispensable":[5],"tool":[6],"for":[7,127],"studying":[8],"complex":[9],"biological":[10],"systems.":[11],"However,":[12],"existing":[13],"simulation":[14,37,53],"platforms":[15],"do":[16],"not":[17],"always":[18],"take":[19],"full":[20],"advantage":[21],"of":[22,44,97],"modern":[23],"hardware":[24],"and":[25,51,69,144],"often":[26],"have":[27],"a":[28,35,49,119],"field-specific":[29],"software":[30],"design.":[31],"RESULTS:":[32],"We":[33,55],"present":[34],"novel":[36],"platform":[38],"called":[39],"BioDynaMo":[40,47,58,91,125,134],"that":[41,57,90],"alleviates":[42],"both":[43],"these":[45],"problems.":[46],"features":[48],"modular":[50],"high-performance":[52],"engine.":[54],"demonstrate":[56],"can":[59],"be":[60],"used":[61],"to":[62,94,109,150],"simulate":[63,110],"use":[64,73,112],"cases":[65],"in:":[66],"neuroscience,":[67],"oncology":[68],"epidemiology.":[70],"For":[71],"each":[72,111],"case,":[74],"we":[75],"validate":[76],"our":[77],"findings":[78],"with":[79,114],"experimental":[80],"data":[81],"or":[82],"analytical":[84],"solution.":[85],"Our":[86],"performance":[87],"results":[88,153],"show":[89],"performs":[92],"up":[93],"three":[95],"orders":[96],"magnitude":[98],"faster":[99],"than":[100],"the":[101,123,140,152,157],"state-of-the-art":[102],"baselines.":[103],"This":[104],"improvement":[105],"makes":[106],"it":[107],"feasible":[108],"case":[113],"one":[115],"billion":[116],"agents":[117],"on":[118],"single":[120],"server,":[121],"showcasing":[122],"potential":[124],"has":[126],"computational":[128],"biology":[129],"research.":[130],"AVAILABILITY":[131],"AND":[132],"IMPLEMENTATION:":[133],"open-source":[137],"project":[138],"under":[139],"Apache":[141],"2.0":[142],"license":[143],"available":[146,155],"at":[147,163],"www.biodynamo.org.":[148],"Instructions":[149],"reproduce":[151],"are":[154],"in":[156],"supplementary":[158],"information.":[159],"SUPPLEMENTARY":[160],"INFORMATION:":[161],"Available":[162],"https://doi.org/10.5281/zenodo.5121618.":[164]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
