{"id":"https://openalex.org/W2106280788","doi":"https://doi.org/10.1093/bioinformatics/btv149","title":"Multiscale reaction-diffusion simulations with Smoldyn","display_name":"Multiscale reaction-diffusion simulations with Smoldyn","publication_year":2015,"publication_date":"2015-03-18","ids":{"openalex":"https://openalex.org/W2106280788","doi":"https://doi.org/10.1093/bioinformatics/btv149","mag":"2106280788","pmid":"https://pubmed.ncbi.nlm.nih.gov/25788627"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv149","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv149","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2406/49035046/bioinformatics_31_14_2406.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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2406/49035046/bioinformatics_31_14_2406.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060072866","display_name":"Martin Robinson","orcid":"https://orcid.org/0000-0002-1572-6782"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Martin Robinson","raw_affiliation_strings":["1 Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079267168","display_name":"Steven S. Andrews","orcid":"https://orcid.org/0000-0002-4576-8107"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven S. Andrews","raw_affiliation_strings":["2 Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, United States","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085919327","display_name":"Radek Erban","orcid":"https://orcid.org/0000-0001-8470-3763"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Radek Erban","raw_affiliation_strings":["1 Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060072866"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":3.3302,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.92978956,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"31","issue":"14","first_page":"2406","last_page":"2408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6324999928474426,"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":0.6324999928474426,"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":0.04820000007748604,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.03849999979138374,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7674890756607056},{"id":"https://openalex.org/keywords/lattice","display_name":"Lattice (music)","score":0.6079409718513489},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6077804565429688},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.565450131893158},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5222376585006714},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.4317641258239746},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4183283746242523},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3867788314819336},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3685532808303833},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.35144758224487305},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33327561616897583},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18066611886024475},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.13358789682388306},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10065534710884094}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7674890756607056},{"id":"https://openalex.org/C2781204021","wikidata":"https://www.wikidata.org/wiki/Q6497091","display_name":"Lattice (music)","level":2,"score":0.6079409718513489},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6077804565429688},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.565450131893158},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5222376585006714},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.4317641258239746},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4183283746242523},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3867788314819336},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3685532808303833},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.35144758224487305},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33327561616897583},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18066611886024475},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.13358789682388306},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10065534710884094},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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":"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":"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":"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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":5,"locations":[{"id":"doi:10.1093/bioinformatics/btv149","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv149","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2406/49035046/bioinformatics_31_14_2406.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:25788627","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25788627","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:ora.ox.ac.uk:uuid:e00a005b-dbfa-4e1d-b5ca-b9fbb4b466b6","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:e00a005b-dbfa-4e1d-b5ca-b9fbb4b466b6","pdf_url":"https://ora.ox.ac.uk/objects/uuid:e00a005b-dbfa-4e1d-b5ca-b9fbb4b466b6","source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"Journal article"},{"id":"pmh:oai:europepmc.org:3461083","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4495299","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:oai:open-archive.highwire.org:bioinfo:31/14/2406","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/14/2406","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv149","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv149","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/14/2406/49035046/bioinformatics_31_14_2406.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":0.4300000071525574,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G1393247254","display_name":null,"funder_award_id":"R01GM086615","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106280788.pdf","grobid_xml":"https://content.openalex.org/works/W2106280788.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1974341035","https://openalex.org/W1974974415","https://openalex.org/W1982903250","https://openalex.org/W1987659633","https://openalex.org/W1992487208","https://openalex.org/W1995867870","https://openalex.org/W2007134412","https://openalex.org/W2011619431","https://openalex.org/W2022333738","https://openalex.org/W2031220210","https://openalex.org/W2111107330","https://openalex.org/W2127732571","https://openalex.org/W2153969663","https://openalex.org/W2169509065","https://openalex.org/W2210900609","https://openalex.org/W3101708254"],"related_works":["https://openalex.org/W2384847609","https://openalex.org/W4242837953","https://openalex.org/W270927586","https://openalex.org/W2013531410","https://openalex.org/W283806354","https://openalex.org/W1556087793","https://openalex.org/W2965967938","https://openalex.org/W4233387348","https://openalex.org/W4243312585","https://openalex.org/W2289569302"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"Smoldyn":[2,69,94,165],"is":[3],"a":[4,39],"software":[5],"package":[6],"for":[7,52,123],"stochastic":[8],"modelling":[9,158],"of":[10,38,68,159],"spatial":[11,75],"biochemical":[12],"networks":[13],"and":[14,74,115,119,130,136,150,157],"intracellular":[15],"systems.":[16],"It":[17],"was":[18],"originally":[19],"developed":[20],"with":[21,35,82,92,103],"an":[22],"accurate":[23],"off-lattice":[24],"particle-based":[25],"model":[26,102,155],"at":[27,125,147],"its":[28],"core.":[29],"This":[30],"has":[31],"recently":[32],"been":[33],"enhanced":[34],"the":[36,66,99,164],"addition":[37],"computationally":[40],"efficient":[41],"on-lattice":[42,101],"model,":[43],"which":[44],"can":[45,78],"be":[46],"run":[47,98],"stand-alone":[48],"or":[49,107],"coupled":[50],"together":[51],"multiscale":[53],"simulations":[54],"using":[55],"both":[56],"models":[57,81],"in":[58,128],"regions":[59],"where":[60],"they":[61,110],"are":[62,145],"most":[63],"required,":[64],"increasing":[65],"applicability":[67],"to":[70,86,97,169],"larger":[71],"molecule":[72],"numbers":[73],"domains.":[76],"Simulations":[77],"switch":[79],"between":[80],"only":[83],"small":[84],"additions":[85],"their":[87],"configuration":[88,95,166],"file,":[89],"enabling":[90],"users":[91],"existing":[93],"files":[96],"new":[100],"any":[104],"reaction,":[105],"species":[106],"surface":[108],"descriptions":[109],"might":[111],"already":[112],"have.":[113],"Availability":[114],"Implementation:":[116],"Source":[117],"code":[118],"binaries":[120],"freely":[121],"available":[122,146],"download":[124],"www.smoldyn.org,":[126],"implemented":[127],"C/C++":[129],"supported":[131],"on":[132,154],"Linux,":[133],"Mac":[134],"OSX":[135],"MS":[137],"Windows.":[138],"Contact:":[139],"martin.robinson@maths.ox.ac.uk":[140],"Supplementary":[141,143],"Information:":[142],"data":[144],"Bioinformatics":[148],"online":[149],"include":[151],"additional":[152],"details":[153],"specification":[156],"surfaces,":[160],"as":[161,163],"well":[162],"file":[167],"used":[168],"generate":[170],"Figure":[171],"1.":[172]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
