{"id":"https://openalex.org/W2775310880","doi":"https://doi.org/10.1155/2017/1232868","title":"HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks","display_name":"HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2775310880","doi":"https://doi.org/10.1155/2017/1232868","mag":"2775310880"},"language":"en","primary_location":{"id":"doi:10.1155/2017/1232868","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2017/1232868","pdf_url":"http://downloads.hindawi.com/journals/complexity/2017/1232868.pdf","source":{"id":"https://openalex.org/S207319443","display_name":"Complexity","issn_l":"1076-2787","issn":["1076-2787","1099-0526"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Complexity","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://downloads.hindawi.com/journals/complexity/2017/1232868.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052320095","display_name":"Luca Marchetti","orcid":"https://orcid.org/0000-0001-9043-7705"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Luca Marchetti","raw_affiliation_strings":["The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy"],"raw_orcid":"https://orcid.org/0000-0001-9043-7705","affiliations":[{"raw_affiliation_string":"The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003291433","display_name":"Rosario Lombardo","orcid":"https://orcid.org/0000-0003-4517-3004"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rosario Lombardo","raw_affiliation_strings":["The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy"],"raw_orcid":"https://orcid.org/0000-0003-4517-3004","affiliations":[{"raw_affiliation_string":"The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028775661","display_name":"Corrado Priami","orcid":"https://orcid.org/0000-0002-3261-6235"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]},{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Corrado Priami","raw_affiliation_strings":["Department of Computer Science, University of Pisa, Pisa, Italy","The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy"],"raw_orcid":"https://orcid.org/0000-0002-3261-6235","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Pisa, Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, No. 1, 38068 Rovereto, Italy","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052320095"],"corresponding_institution_ids":["https://openalex.org/I193223587","https://openalex.org/I2802934434"],"apc_list":{"value":2300,"currency":"USD","value_usd":2300},"apc_paid":{"value":2300,"currency":"USD","value_usd":2300},"fwci":0.1093,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.51647155,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"2017","issue":null,"first_page":"1","last_page":"12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9962000250816345,"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":0.9902999997138977,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8235151767730713},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.7405968904495239},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6924352645874023},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5739015936851501},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5191625356674194},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47042298316955566},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4425068795681},{"id":"https://openalex.org/keywords/simulation-software","display_name":"Simulation software","score":0.43508678674697876},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.42400062084198},{"id":"https://openalex.org/keywords/modeling-and-simulation","display_name":"Modeling and simulation","score":0.4143002927303314},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34886541962623596},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.34374499320983887},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23174241185188293},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12475910782814026},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07575353980064392}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8235151767730713},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.7405968904495239},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6924352645874023},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5739015936851501},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5191625356674194},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47042298316955566},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4425068795681},{"id":"https://openalex.org/C91757755","wikidata":"https://www.wikidata.org/wiki/Q11121294","display_name":"Simulation software","level":3,"score":0.43508678674697876},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.42400062084198},{"id":"https://openalex.org/C167343916","wikidata":"https://www.wikidata.org/wiki/Q6888384","display_name":"Modeling and simulation","level":2,"score":0.4143002927303314},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34886541962623596},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.34374499320983887},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23174241185188293},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12475910782814026},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07575353980064392},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1155/2017/1232868","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2017/1232868","pdf_url":"http://downloads.hindawi.com/journals/complexity/2017/1232868.pdf","source":{"id":"https://openalex.org/S207319443","display_name":"Complexity","issn_l":"1076-2787","issn":["1076-2787","1099-0526"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Complexity","raw_type":"journal-article"},{"id":"pmh:oai:zenodo.org:48960","is_oa":true,"landing_page_url":"https://www.openaccessrepository.it/record/48960","pdf_url":"https://zenodo.org/record/48960","source":{"id":"https://openalex.org/S4306402478","display_name":"INFM-OAR (INFN Catania)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210116497","host_organization_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Catania","host_organization_lineage":["https://openalex.org/I4210116497"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:hin:complx:1232868","is_oa":false,"landing_page_url":"http://downloads.hindawi.com/journals/8503/2017/1232868.xml","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:arpi.unipi.it:11568/886999","is_oa":true,"landing_page_url":"https://www.hindawi.com/journals/complexity/2017/1232868/","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:04c4bbb788ec4bfc8fa861a7a29e9702","is_oa":true,"landing_page_url":"https://doaj.org/article/04c4bbb788ec4bfc8fa861a7a29e9702","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Complexity, Vol 2017 (2017)","raw_type":"article"},{"id":"pmh:oai:iris.unitn.it:11572/326036","is_oa":true,"landing_page_url":"http://hdl.handle.net/11572/326036","pdf_url":null,"source":{"id":"https://openalex.org/S4377196320","display_name":"Iris (University of Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1155/2017/1232868","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2017/1232868","pdf_url":"http://downloads.hindawi.com/journals/complexity/2017/1232868.pdf","source":{"id":"https://openalex.org/S207319443","display_name":"Complexity","issn_l":"1076-2787","issn":["1076-2787","1099-0526"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Complexity","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8768433972","display_name":null,"funder_award_id":"S503/2015/664730","funder_id":"https://openalex.org/F4320326086","funder_display_name":"Provincia Autonoma di Trento"}],"funders":[{"id":"https://openalex.org/F4320324120","display_name":"Universit\u00e0 degli Studi di Verona","ror":"https://ror.org/039bp8j42"},{"id":"https://openalex.org/F4320326086","display_name":"Provincia Autonoma di Trento","ror":"https://ror.org/017e99q89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2775310880.pdf","grobid_xml":"https://content.openalex.org/works/W2775310880.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1559256881","https://openalex.org/W1589828999","https://openalex.org/W1965853004","https://openalex.org/W1974161639","https://openalex.org/W1975075402","https://openalex.org/W1975586684","https://openalex.org/W1978486653","https://openalex.org/W1996405087","https://openalex.org/W2002083262","https://openalex.org/W2004685742","https://openalex.org/W2027506430","https://openalex.org/W2046039809","https://openalex.org/W2046451925","https://openalex.org/W2058943257","https://openalex.org/W2078027626","https://openalex.org/W2078734278","https://openalex.org/W2084924279","https://openalex.org/W2102653059","https://openalex.org/W2135249635","https://openalex.org/W2143784594","https://openalex.org/W2148626278","https://openalex.org/W2155418451","https://openalex.org/W2285943646","https://openalex.org/W2342443391","https://openalex.org/W2484307026","https://openalex.org/W2593879581","https://openalex.org/W2741871742","https://openalex.org/W4300831640"],"related_works":["https://openalex.org/W2606446052","https://openalex.org/W2036021480","https://openalex.org/W2381376639","https://openalex.org/W2122372697","https://openalex.org/W3128885716","https://openalex.org/W2372222640","https://openalex.org/W120587663","https://openalex.org/W2129865864","https://openalex.org/W2380107159","https://openalex.org/W2105908646"],"abstract_inverted_index":{"HSimulator":[0,15,78,119],"is":[1,79,120],"a":[2,12,20,66,97,108],"multithread":[3],"simulator":[4],"for":[5,53,100],"mass-action":[6],"biochemical":[7],"reaction":[8,70],"systems":[9],"placed":[10],"in":[11],"well-mixed":[13],"environment.":[14],"provides":[16],"optimized":[17],"implementation":[18,36],"of":[19,22,37,57,65,68,116],"set":[21],"widespread":[23],"state-of-the-art":[24],"stochastic,":[25],"deterministic,":[26],"and":[27,102,107],"hybrid":[28,48],"simulation":[29,56,64,98],"strategies":[30],"including":[31],"the":[32,38,46,58,62,69,84,114,123],"first":[33],"publicly":[34],"available":[35],"Hybrid":[39],"Rejection-based":[40],"Stochastic":[41],"Simulation":[42],"Algorithm":[43],"(HRSSA).":[44],"HRSSA,":[45],"fastest":[47],"algorithm":[49],"to":[50,112],"date,":[51],"allows":[52],"an":[54],"efficient":[55],"models":[59],"while":[60],"ensuring":[61],"exact":[63],"subset":[67],"network":[71],"modeling":[72,101],"slow":[73],"reactions.":[74],"Benchmarks":[75],"show":[76],"that":[77],"often":[80],"considerably":[81],"faster":[82],"than":[83],"other":[85],"considered":[86],"simulators.":[87],"The":[88],"software,":[89],"running":[90],"on":[91],"Java":[92,110],"v6.0":[93],"or":[94],"higher,":[95],"offers":[96],"GUI":[99],"visually":[103],"exploring":[104],"biological":[105],"processes":[106],"Javadoc-documented":[109],"library":[111],"support":[113],"development":[115],"custom":[117],"applications.":[118],"released":[121],"under":[122],"COSBI":[124],"Shared":[125],"Source":[126],"license":[127],"agreement":[128],"(COSBI-SSLA).":[129]},"counts_by_year":[{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
