{"id":"https://openalex.org/W2593960650","doi":"https://doi.org/10.1093/bioinformatics/btw700","title":"Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface","display_name":"Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface","publication_year":2016,"publication_date":"2016-11-02","ids":{"openalex":"https://openalex.org/W2593960650","doi":"https://doi.org/10.1093/bioinformatics/btw700","mag":"2593960650","pmid":"https://pubmed.ncbi.nlm.nih.gov/28365760"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/710/25148518/btw700.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/710/25148518/btw700.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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"]},{"id":"https://openalex.org/I182145113","display_name":"Isaac Newton Institute for Mathematical Sciences","ror":"https://ror.org/007vkej58","country_code":"GB","type":"facility","lineage":["https://openalex.org/I182145113"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Steven S Andrews","raw_affiliation_strings":["Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA","Isaac Newton Institute for Mathematical Sciences, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Isaac Newton Institute for Mathematical Sciences, Cambridge, UK","institution_ids":["https://openalex.org/I182145113"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5079267168"],"corresponding_institution_ids":["https://openalex.org/I182145113","https://openalex.org/I4210089486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":7.1468,"has_fulltext":true,"cited_by_count":135,"citation_normalized_percentile":{"value":0.97544032,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"33","issue":"5","first_page":"710","last_page":"717"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9896000027656555,"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"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9805999994277954,"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/interface","display_name":"Interface (matter)","score":0.7015733122825623},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6886340379714966},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5519416928291321},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5272128582000732},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5259835124015808},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.49549806118011475},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4840652048587799},{"id":"https://openalex.org/keywords/tracking","display_name":"Tracking (education)","score":0.4802401661872864},{"id":"https://openalex.org/keywords/particle","display_name":"Particle (ecology)","score":0.4412556290626526},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.439511239528656},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3613720238208771},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3610525131225586},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3282562494277954},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.25537392497062683},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1995333433151245},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.08725723624229431}],"concepts":[{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.7015733122825623},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6886340379714966},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5519416928291321},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5272128582000732},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5259835124015808},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.49549806118011475},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4840652048587799},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.4802401661872864},{"id":"https://openalex.org/C2778517922","wikidata":"https://www.wikidata.org/wiki/Q7140482","display_name":"Particle (ecology)","level":2,"score":0.4412556290626526},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.439511239528656},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3613720238208771},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3610525131225586},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3282562494277954},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.25537392497062683},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1995333433151245},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.08725723624229431},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","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/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C111368507","wikidata":"https://www.wikidata.org/wiki/Q43518","display_name":"Oceanography","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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D046609","descriptor_name":"Libraries, Digital","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046609","descriptor_name":"Libraries, Digital","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046609","descriptor_name":"Libraries, Digital","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/710/25148518/btw700.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28365760","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28365760","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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw700","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw700","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/5/710/25148518/btw700.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3728093668","display_name":"Isaac Newton Institute for Mathematical Sciences","funder_award_id":"EP/K032208/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4421442999","display_name":null,"funder_award_id":"EP/K032208","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4984718776","display_name":null,"funder_award_id":"P/K032208/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5128091834","display_name":null,"funder_award_id":"EP/K032208/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5578800588","display_name":null,"funder_award_id":"EP/K032208/1","funder_id":"https://openalex.org/F4320313284","funder_display_name":"Isaac Newton Institute for Mathematical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320308793","display_name":"Fred Hutchinson Cancer Research Center","ror":"https://ror.org/007ps6h72"},{"id":"https://openalex.org/F4320313284","display_name":"Isaac Newton Institute for Mathematical Sciences","ror":null},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320337380","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2593960650.pdf","grobid_xml":"https://content.openalex.org/works/W2593960650.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W205153889","https://openalex.org/W1542466803","https://openalex.org/W1563071114","https://openalex.org/W1636338970","https://openalex.org/W1915252789","https://openalex.org/W1966886240","https://openalex.org/W1967690208","https://openalex.org/W1969369091","https://openalex.org/W1971117579","https://openalex.org/W1971644094","https://openalex.org/W1974974415","https://openalex.org/W1977290213","https://openalex.org/W1978408051","https://openalex.org/W1981390104","https://openalex.org/W1984441765","https://openalex.org/W1986419282","https://openalex.org/W1986649132","https://openalex.org/W1988498168","https://openalex.org/W1989737071","https://openalex.org/W1990031169","https://openalex.org/W2000836754","https://openalex.org/W2002505185","https://openalex.org/W2005524843","https://openalex.org/W2010016922","https://openalex.org/W2025828073","https://openalex.org/W2031220210","https://openalex.org/W2041715593","https://openalex.org/W2046473711","https://openalex.org/W2047331390","https://openalex.org/W2049445311","https://openalex.org/W2052360207","https://openalex.org/W2056370235","https://openalex.org/W2061279689","https://openalex.org/W2067386221","https://openalex.org/W2068359975","https://openalex.org/W2076737014","https://openalex.org/W2082710031","https://openalex.org/W2084451754","https://openalex.org/W2097863660","https://openalex.org/W2099015579","https://openalex.org/W2106280788","https://openalex.org/W2117195816","https://openalex.org/W2121490181","https://openalex.org/W2124065115","https://openalex.org/W2132898564","https://openalex.org/W2134542242","https://openalex.org/W2151665622","https://openalex.org/W2155418451","https://openalex.org/W2159629828","https://openalex.org/W2163126094","https://openalex.org/W2163493106","https://openalex.org/W2167185762","https://openalex.org/W2169509065","https://openalex.org/W2193304014","https://openalex.org/W2210900609","https://openalex.org/W2271421556","https://openalex.org/W2327756257","https://openalex.org/W2594389897","https://openalex.org/W2963297730","https://openalex.org/W3034081432","https://openalex.org/W6667429390","https://openalex.org/W6734533521"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W2329643025","https://openalex.org/W2002770077","https://openalex.org/W3131163342","https://openalex.org/W2092256833","https://openalex.org/W2142369114","https://openalex.org/W2361728394","https://openalex.org/W2166271660","https://openalex.org/W2352631095","https://openalex.org/W3081644756"],"abstract_inverted_index":{"steven.s.andrews@gmail.com.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":34},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
