{"id":"https://openalex.org/W2145006655","doi":"https://doi.org/10.1093/bioinformatics/btp387","title":"Efficient stochastic simulation of reaction\u2013diffusion processes via direct compilation","display_name":"Efficient stochastic simulation of reaction\u2013diffusion processes via direct compilation","publication_year":2009,"publication_date":"2009-07-03","ids":{"openalex":"https://openalex.org/W2145006655","doi":"https://doi.org/10.1093/bioinformatics/btp387","mag":"2145006655","pmid":"https://pubmed.ncbi.nlm.nih.gov/19578038"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp387","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp387","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2289/48994495/bioinformatics_25_17_2289.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/25/17/2289/48994495/bioinformatics_25_17_2289.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067207130","display_name":"Mieszko Lis","orcid":"https://orcid.org/0000-0003-3376-4384"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mieszko Lis","raw_affiliation_strings":["1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086311928","display_name":"Maxim N. Artyomov","orcid":"https://orcid.org/0000-0002-1133-4212"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maxim N. Artyomov","raw_affiliation_strings":["1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000525449","display_name":"Srinivas Devadas","orcid":"https://orcid.org/0000-0001-8253-7714"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srinivas Devadas","raw_affiliation_strings":["1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061654582","display_name":"Arup K. Chakraborty","orcid":"https://orcid.org/0000-0003-1268-9602"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arup K. Chakraborty","raw_affiliation_strings":["1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science and Artificial Intelligence Laboratory and the Departments of2 Chemistry, 3 Chemical Engineering and 4 Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5067207130"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.6535,"has_fulltext":true,"cited_by_count":59,"citation_normalized_percentile":{"value":0.93938618,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"17","first_page":"2289","last_page":"2291"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9889000058174133,"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/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9631999731063843,"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/computer-science","display_name":"Computer science","score":0.7920985221862793},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.7787331342697144},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.6583734750747681},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5979158282279968},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4984614849090576},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.48762765526771545},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.47814643383026123},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.440208375453949},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3965975344181061},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.39336636662483215},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10248991847038269},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07681256532669067}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7920985221862793},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.7787331342697144},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.6583734750747681},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5979158282279968},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4984614849090576},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.48762765526771545},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.47814643383026123},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.440208375453949},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3965975344181061},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.39336636662483215},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10248991847038269},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07681256532669067},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"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":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":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":"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":true},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","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":true},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btp387","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp387","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2289/48994495/bioinformatics_25_17_2289.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19578038","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19578038","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},{"id":"pmh:oai:dspace.mit.edu:1721.1/59816","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/59816","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"MIT web domain","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2734316","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2734316","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp387","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp387","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/17/2289/48994495/bioinformatics_25_17_2289.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G231554914","display_name":null,"funder_award_id":"P01AI-071195","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3461338524","display_name":null,"funder_award_id":"1P01/AI071195/01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G88596877","display_name":null,"funder_award_id":"AI071195","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2145006655.pdf","grobid_xml":"https://content.openalex.org/works/W2145006655.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1450823538","https://openalex.org/W1977290213","https://openalex.org/W1982903250","https://openalex.org/W1986649132","https://openalex.org/W1987003260","https://openalex.org/W1987129107","https://openalex.org/W2015045689","https://openalex.org/W2027733508","https://openalex.org/W2044859335","https://openalex.org/W2069941324","https://openalex.org/W2072077152","https://openalex.org/W2078734278","https://openalex.org/W2081098704","https://openalex.org/W2084924279","https://openalex.org/W2093179886","https://openalex.org/W2096234619","https://openalex.org/W2107919289","https://openalex.org/W2117792713","https://openalex.org/W2124236793","https://openalex.org/W2132898564","https://openalex.org/W2151251638","https://openalex.org/W2155418451","https://openalex.org/W2165700291","https://openalex.org/W2165714871","https://openalex.org/W2169193349","https://openalex.org/W2175715045","https://openalex.org/W2187198735","https://openalex.org/W2580666155","https://openalex.org/W4251141266","https://openalex.org/W4251538155","https://openalex.org/W6667917037","https://openalex.org/W6685665237","https://openalex.org/W6732216806"],"related_works":["https://openalex.org/W3096456556","https://openalex.org/W4240253816","https://openalex.org/W2169584677","https://openalex.org/W2979513934","https://openalex.org/W4232954277","https://openalex.org/W2020341030","https://openalex.org/W2749133591","https://openalex.org/W2367473450","https://openalex.org/W23346600","https://openalex.org/W2056396287"],"abstract_inverted_index":{"Abstract":[0],"We":[1],"present":[2],"the":[3,22],"Stochastic":[4],"Simulator":[5],"Compiler":[6],"(SSC),":[7],"a":[8,27],"tool":[9,24],"for":[10],"exact":[11],"stochastic":[12],"simulations":[13],"of":[14],"well-mixed":[15],"and":[16,36,64,68],"spatially":[17,32],"heterogeneous":[18,33],"systems.":[19],"SSC":[20,52,59],"is":[21,69],"first":[23],"to":[25,43,53],"allow":[26],"readable":[28],"high-level":[29],"description":[30],"with":[31],"simulation":[34],"algorithms":[35],"complex":[37],"geometries;":[38],"this":[39],"permits":[40],"large":[41],"systems":[42],"be":[44],"expressed":[45],"concisely.":[46],"Meanwhile,":[47],"direct":[48],"native-code":[49],"compilation":[50],"allows":[51],"generate":[54],"very":[55],"fast":[56],"simulations.":[57],"Availability:":[58],"currently":[60],"runs":[61],"on":[62],"Linux":[63],"Mac":[65],"OS":[66],"X,":[67],"freely":[70],"available":[71,81],"at":[72,82],"http://web.mit.edu/irc/ssc/.":[73],"Contact:":[74],"mieszko@csail.mit.edu":[75],"Supplementary":[76,78],"information:":[77],"data":[79],"are":[80],"Bioinformatics":[83],"online.":[84]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":12}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
