{"id":"https://openalex.org/W2077346271","doi":"https://doi.org/10.1186/1752-0509-6-36","title":"STEPS: efficient simulation of stochastic reaction\u2013diffusion models in realistic morphologies","display_name":"STEPS: efficient simulation of stochastic reaction\u2013diffusion models in realistic morphologies","publication_year":2012,"publication_date":"2012-05-10","ids":{"openalex":"https://openalex.org/W2077346271","doi":"https://doi.org/10.1186/1752-0509-6-36","mag":"2077346271","pmid":"https://pubmed.ncbi.nlm.nih.gov/22574658"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-36","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-36","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-36","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053167875","display_name":"Iain Hepburn","orcid":"https://orcid.org/0000-0003-2240-9918"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]}],"countries":["BE","JP"],"is_corresponding":false,"raw_author_name":"Iain Hepburn","raw_affiliation_strings":["Theoretical Neurobiology, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, Wilrijk 2610, Belgium. erik@oist.jp","Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Wilrijk, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Neurobiology, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, Wilrijk 2610, Belgium. erik@oist.jp","institution_ids":["https://openalex.org/I149213910"]},{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Wilrijk, Belgium","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030888030","display_name":"Weiliang Chen","orcid":"https://orcid.org/0000-0003-0304-583X"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Weiliang Chen","raw_affiliation_strings":["Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, 904-0411, Onna-son, Kunigami, Okinawa, Japan","Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, 904-0411, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017689140","display_name":"Stefan Wils","orcid":null},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]}],"countries":["BE","JP"],"is_corresponding":false,"raw_author_name":"Stefan Wils","raw_affiliation_strings":["Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, 904-0411, Onna-son, Kunigami, Okinawa, Japan","Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Universiteitsplein 1, Wilrijk, 2610, Belgium","Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Wilrijk, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, 904-0411, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Universiteitsplein 1, Wilrijk, 2610, Belgium","institution_ids":["https://openalex.org/I149213910"]},{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Wilrijk, Belgium","institution_ids":["https://openalex.org/I149213910"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089780814","display_name":"Erik De Schutter","orcid":"https://orcid.org/0000-0001-8618-5138"},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]}],"countries":["BE","JP"],"is_corresponding":true,"raw_author_name":"Erik De Schutter","raw_affiliation_strings":["Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, 904-0411, Onna-son, Kunigami, Okinawa, Japan","Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Universiteitsplein 1, Wilrijk, 2610, Belgium","Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Wilrijk, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Seaside House, 7542, Onna, 904-0411, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Universiteitsplein 1, Wilrijk, 2610, Belgium","institution_ids":["https://openalex.org/I149213910"]},{"raw_affiliation_string":"Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Onna-son, Kunigami, Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Theoretical Neurobiology, University of Antwerp Campus Drie Eiken, Wilrijk, Belgium","institution_ids":["https://openalex.org/I149213910"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5089780814"],"corresponding_institution_ids":["https://openalex.org/I142637625","https://openalex.org/I149213910"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":5.4886,"has_fulltext":true,"cited_by_count":162,"citation_normalized_percentile":{"value":0.96937062,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"6","issue":"1","first_page":"36","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.47999998927116394,"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":0.47999998927116394,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.0803999975323677,"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":0.03629999980330467,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7717905640602112},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.7625224590301514},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6812504529953003},{"id":"https://openalex.org/keywords/solver","display_name":"Solver","score":0.6026230454444885},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.507377564907074},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.4808710217475891},{"id":"https://openalex.org/keywords/polygon-mesh","display_name":"Polygon mesh","score":0.4613302946090698},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44573357701301575},{"id":"https://openalex.org/keywords/tetrahedron","display_name":"Tetrahedron","score":0.43741440773010254},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.42416948080062866},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.42003726959228516},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3568806052207947},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32277441024780273},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17603576183319092},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.14855575561523438},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.13460448384284973},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1203036904335022},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.10219299793243408}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7717905640602112},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.7625224590301514},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6812504529953003},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.6026230454444885},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.507377564907074},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.4808710217475891},{"id":"https://openalex.org/C31487907","wikidata":"https://www.wikidata.org/wiki/Q1154597","display_name":"Polygon mesh","level":2,"score":0.4613302946090698},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44573357701301575},{"id":"https://openalex.org/C105239961","wikidata":"https://www.wikidata.org/wiki/Q160003","display_name":"Tetrahedron","level":2,"score":0.43741440773010254},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.42416948080062866},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.42003726959228516},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3568806052207947},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32277441024780273},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17603576183319092},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.14855575561523438},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.13460448384284973},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1203036904335022},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.10219299793243408},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"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":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-6-36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-36","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-36","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:22574658","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22574658","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 systems biology","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2471068","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3472240","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"},{"id":"pmh:c:irua:102224","is_oa":false,"landing_page_url":"https://hdl.handle.net/10067/1022240151162165141","pdf_url":null,"source":{"id":"https://openalex.org/S4377196495","display_name":"Anet (University of Antwerp)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149213910","host_organization_name":"University of Antwerp","host_organization_lineage":["https://openalex.org/I149213910"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-36","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-36","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-36","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313288","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52"},{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"},{"id":"https://openalex.org/F4320338291","display_name":"Sandia National Laboratories","ror":"https://ror.org/01apwpt12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2077346271.pdf","grobid_xml":"https://content.openalex.org/works/W2077346271.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W74971858","https://openalex.org/W648800387","https://openalex.org/W1497413361","https://openalex.org/W1591593323","https://openalex.org/W1598648881","https://openalex.org/W1599277155","https://openalex.org/W1964811412","https://openalex.org/W1966993727","https://openalex.org/W1973016141","https://openalex.org/W1974974415","https://openalex.org/W1976443948","https://openalex.org/W1981132987","https://openalex.org/W1983553517","https://openalex.org/W1986597140","https://openalex.org/W1986789040","https://openalex.org/W1987003260","https://openalex.org/W2005636685","https://openalex.org/W2008477808","https://openalex.org/W2015240388","https://openalex.org/W2016512924","https://openalex.org/W2022130011","https://openalex.org/W2022286642","https://openalex.org/W2026878536","https://openalex.org/W2031872736","https://openalex.org/W2032550351","https://openalex.org/W2038785086","https://openalex.org/W2042670485","https://openalex.org/W2044859335","https://openalex.org/W2046196975","https://openalex.org/W2046486910","https://openalex.org/W2060872711","https://openalex.org/W2061933976","https://openalex.org/W2063587638","https://openalex.org/W2067686344","https://openalex.org/W2067982358","https://openalex.org/W2077406048","https://openalex.org/W2078734278","https://openalex.org/W2082221311","https://openalex.org/W2084924279","https://openalex.org/W2090629368","https://openalex.org/W2095595785","https://openalex.org/W2095921114","https://openalex.org/W2097863660","https://openalex.org/W2099430463","https://openalex.org/W2100174069","https://openalex.org/W2109639508","https://openalex.org/W2112311198","https://openalex.org/W2113094198","https://openalex.org/W2114124738","https://openalex.org/W2117238525","https://openalex.org/W2132898564","https://openalex.org/W2142784661","https://openalex.org/W2147700328","https://openalex.org/W2150766477","https://openalex.org/W2150908245","https://openalex.org/W2151839418","https://openalex.org/W2155418451","https://openalex.org/W2156961733","https://openalex.org/W2161496609","https://openalex.org/W2167154952","https://openalex.org/W2176097705","https://openalex.org/W2326565381","https://openalex.org/W2432517183","https://openalex.org/W2488177635","https://openalex.org/W2610323627","https://openalex.org/W2981264952","https://openalex.org/W3098349557","https://openalex.org/W3214267983","https://openalex.org/W4212968535","https://openalex.org/W4229786028","https://openalex.org/W4255760236"],"related_works":["https://openalex.org/W1803737632","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2097410126","https://openalex.org/W2136043941","https://openalex.org/W2043776573","https://openalex.org/W2735157934","https://openalex.org/W3080133182","https://openalex.org/W1869813392","https://openalex.org/W2026725606"],"abstract_inverted_index":{"BACKGROUND:":[0],"Models":[1],"of":[2,32,42,56,75,166,206,260,268],"cellular":[3,269],"molecular":[4],"systems":[5,271],"are":[6,223],"built":[7],"from":[8],"components":[9],"such":[10,66,90],"as":[11,67],"biochemical":[12,106,126],"reactions":[13],"(including":[14],"interactions":[15],"between":[16,172],"ligands":[17],"and":[18,23,25,70,110,118,154,161,179,187,201,210,216,251,278,287,296],"membrane-bound":[19],"proteins),":[20],"conformational":[21],"changes":[22],"active":[24],"passive":[26],"transport.":[27],"A":[28],"discrete,":[29],"stochastic":[30,97],"description":[31],"the":[33,40,43,53,115,159,167,234,258,261],"kinetics":[34],"is":[35,86,192,196,239,292,297],"often":[36,240],"essential":[37],"to":[38,60,88,128,229,254],"capture":[39],"behavior":[41],"system":[44],"accurately.":[45],"Where":[46],"spatial":[47],"effects":[48],"play":[49],"a":[50,79,96,164,285],"prominent":[51],"role":[52],"complex":[54,273],"morphology":[55],"cells":[57],"may":[58],"have":[59],"be":[61,129,135],"represented,":[62],"along":[63],"with":[64,101,198,245,272,275],"aspects":[65],"chemical":[68],"localization":[69],"diffusion.":[71],"This":[72],"high":[73,276,279],"level":[74],"detail":[76],"makes":[77],"efficiency":[78,259],"particularly":[80],"important":[81],"consideration":[82],"for":[83,121,184,188,294],"software":[84],"that":[85],"designed":[87],"simulate":[89],"systems.":[91,212],"RESULTS:":[92],"We":[93],"describe":[94],"STEPS,":[95],"reaction-diffusion":[98,211,270],"simulator":[99],"developed":[100],"an":[102,176,199],"emphasis":[103],"on":[104,219],"simulating":[105],"signaling":[107],"pathways":[108],"accurately":[109,137],"efficiently.":[111],"STEPS":[112,157,238,262,265,291],"supports":[113],"all":[114],"above-mentioned":[116],"features,":[117],"well-validated":[119],"support":[120,183],"SBML":[122],"allows":[123],"many":[124],"existing":[125],"models":[127,267],"imported":[130,144],"reliably.":[131],"Complex":[132],"boundaries":[133,274],"can":[134],"represented":[136],"in":[138,225,237,248,281],"externally":[139],"generated":[140],"3D":[141],"tetrahedral":[142,173],"meshes":[143],"by":[145,252,284],"STEPS.":[146],"The":[147],"powerful":[148,286],"Python":[149,289],"interface":[150],"facilitates":[151],"model":[152,190],"construction":[153],"simulation":[155],"control.":[156],"implements":[158],"composition":[160],"rejection":[162],"method,":[163],"variation":[165],"Gillespie":[168],"SSA,":[169],"supporting":[170],"diffusion":[171,209],"elements":[174],"within":[175],"efficient":[177],"search":[178],"update":[180],"engine.":[181],"Additional":[182],"well-mixed":[185],"conditions":[186],"deterministic":[189],"solution":[191],"implemented.":[193],"Solver":[194],"accuracy":[195,277],"confirmed":[197],"original":[200],"extensive":[202],"validation":[203],"set":[204],"consisting":[205],"isolated":[207],"reaction,":[208],"Accuracy":[213],"imposes":[214],"upper":[215],"lower":[217],"limits":[218],"tetrahedron":[220],"sizes,":[221],"which":[222],"described":[224],"detail.":[226],"By":[227],"comparing":[228,253],"Smoldyn,":[230],"we":[231,256],"show":[232,257],"how":[233],"voxel-based":[235],"approach":[236],"faster":[241],"than":[242],"particle-based":[243],"methods,":[244],"increasing":[246],"advantage":[247],"larger":[249],"systems,":[250],"MesoRD":[255],"implementation.":[263],"CONCLUSION:":[264],"simulates":[266],"performance":[280],"C/C++,":[282],"controlled":[283],"user-friendly":[288],"interface.":[290],"free":[293],"use":[295],"available":[298],"at":[299],"http://steps.sourceforge.net/":[300]},"counts_by_year":[{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":13},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}