{"id":"https://openalex.org/W2164055371","doi":"https://doi.org/10.1093/bioinformatics/btg376","title":"Adaptive stochastic-deterministic chemical kinetic simulations","display_name":"Adaptive stochastic-deterministic chemical kinetic simulations","publication_year":2003,"publication_date":"2003-12-23","ids":{"openalex":"https://openalex.org/W2164055371","doi":"https://doi.org/10.1093/bioinformatics/btg376","mag":"2164055371","pmid":"https://pubmed.ncbi.nlm.nih.gov/14693812"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg376","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/1/78/618240/btg376.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/20/1/78/618240/btg376.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090300707","display_name":"Karan Vasudeva","orcid":null},"institutions":[{"id":"https://openalex.org/I194223965","display_name":"National Centre for Biological Sciences","ror":"https://ror.org/03gf8rp76","country_code":"IN","type":"facility","lineage":["https://openalex.org/I11947397","https://openalex.org/I194223965","https://openalex.org/I2799351866","https://openalex.org/I3149292468"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Karan Vasudeva","raw_affiliation_strings":["National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560065, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore 560065, India","institution_ids":["https://openalex.org/I194223965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066858212","display_name":"Upinder S. Bhalla","orcid":"https://orcid.org/0000-0003-1722-5188"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Upinder S. Bhalla","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090300707"],"corresponding_institution_ids":["https://openalex.org/I194223965"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.6039,"has_fulltext":false,"cited_by_count":67,"citation_normalized_percentile":{"value":0.90182301,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"20","issue":"1","first_page":"78","last_page":"84"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.930400013923645,"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":0.930400013923645,"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/T13187","display_name":"Diffusion and Search Dynamics","score":0.013100000098347664,"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/T12653","display_name":"Cyclization and Aryne Chemistry","score":0.006200000178068876,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6053398251533508},{"id":"https://openalex.org/keywords/kinetic-energy","display_name":"Kinetic energy","score":0.48052510619163513},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3756599426269531},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35340988636016846},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3498435318470001},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19962522387504578},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12688329815864563},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10829567909240723}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6053398251533508},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.48052510619163513},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3756599426269531},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35340988636016846},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3498435318470001},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19962522387504578},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12688329815864563},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10829567909240723},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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":"D005246","descriptor_name":"Feedback","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005246","descriptor_name":"Feedback","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005246","descriptor_name":"Feedback","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":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009097","descriptor_name":"Multienzyme Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","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":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020650","descriptor_name":"Combinatorial Chemistry Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020650","descriptor_name":"Combinatorial Chemistry Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020650","descriptor_name":"Combinatorial Chemistry Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg376","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/1/78/618240/btg376.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:14693812","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14693812","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/btg376","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg376","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/1/78/618240/btg376.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/G808707995","display_name":null,"funder_award_id":"GM54508","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W74971858","https://openalex.org/W1502029496","https://openalex.org/W1564150153","https://openalex.org/W1644749979","https://openalex.org/W1797216850","https://openalex.org/W1946177469","https://openalex.org/W1969621260","https://openalex.org/W1976443948","https://openalex.org/W1978726508","https://openalex.org/W1988791304","https://openalex.org/W2001072557","https://openalex.org/W2021767976","https://openalex.org/W2049445311","https://openalex.org/W2071902635","https://openalex.org/W2074401358","https://openalex.org/W2078734278","https://openalex.org/W2084924279","https://openalex.org/W2086611351","https://openalex.org/W2087445908","https://openalex.org/W2101744311","https://openalex.org/W2111682035","https://openalex.org/W2133658130","https://openalex.org/W2133667940","https://openalex.org/W2134895233","https://openalex.org/W2155418451","https://openalex.org/W2158691076","https://openalex.org/W2171458571"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W1974744264","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2359412950","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Biochemical":[2],"signaling":[3,15,38],"pathways":[4],"and":[5,59,66,76,166,178],"genetic":[6],"circuits":[7],"often":[8,31],"involve":[9],"very":[10],"small":[11],"numbers":[12,36],"of":[13,37,68,85,109,136,143,164],"key":[14],"molecules.":[16],"Computationally":[17],"expensive":[18],"stochastic":[19,52,60,90,123],"methods":[20,124],"are":[21,174],"necessary":[22],"to":[23,139],"simulate":[24],"such":[25],"chemical":[26,29,103],"situations.":[27],"Single-molecule":[28],"events":[30],"co-exist":[32],"with":[33,88],"much":[34],"larger":[35],"molecules":[39],"where":[40],"mass-action":[41],"kinetics":[42],"is":[43,73,154],"a":[44,133],"reasonable":[45],"approximation.":[46],"Here,":[47],"we":[48],"describe":[49],"an":[50,96,106],"adaptive":[51,97],"method":[53,72,87,101,112],"that":[54],"dynamically":[55],"chooses":[56],"between":[57],"deterministic":[58],"calculations":[61],"depending":[62],"on":[63],"molecular":[64],"count":[65],"propensity":[67],"forward":[69],"reactions.":[70],"The":[71],"fixed":[74],"timestep":[75],"has":[77],"first":[78],"order":[79],"accuracy.":[80],"We":[81,93,130],"compare":[82],"the":[83,111,141,152,167,181],"efficiency":[84],"this":[86,172],"exact":[89,122],"methods.":[91,146],"Results:":[92],"have":[94,131],"implemented":[95],"stochastic-deterministic":[98],"approximate":[99],"simulation":[100,145],"for":[102,125],"kinetics.":[104],"With":[105],"error":[107],"margin":[108],"5%,":[110],"solves":[113],"typical":[114],"biologically":[115],"constrained":[116],"reaction":[117,126,137],"schemes":[118],"more":[119],"rapidly":[120],"than":[121],"volumes":[127],"&amp;gt;1\u201310":[128],"\u00b5m3.":[129],"developed":[132],"test":[134,140,168],"suite":[135,169],"cases":[138],"accuracy":[142],"mixed":[144],"Availability:":[147],"Simulation":[148],"software":[149],"used":[150,170],"in":[151,171],"paper":[153,173],"freely":[155],"available":[156,175],"from":[157,176,180],"http://www.ncbs.res.in/kinetikit/download.html":[158,177],"Supplementary":[159],"information:":[160],"A":[161],"GENESIS/Kinetikit":[162],"implementation":[163],"models":[165],"also":[179],"DOQCS":[182],"database,":[183],"http://doqcs.ncbs.res.in":[184]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
