{"id":"https://openalex.org/W2045266982","doi":"https://doi.org/10.3390/computation2040246","title":"SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology","display_name":"SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology","publication_year":2014,"publication_date":"2014-12-18","ids":{"openalex":"https://openalex.org/W2045266982","doi":"https://doi.org/10.3390/computation2040246","mag":"2045266982","pmid":"https://pubmed.ncbi.nlm.nih.gov/32211200"},"language":"en","primary_location":{"id":"doi:10.3390/computation2040246","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation2040246","pdf_url":"https://www.mdpi.com/2079-3197/2/4/246/pdf?version=1418913224","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2079-3197/2/4/246/pdf?version=1418913224","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088021958","display_name":"Alexander D\u00f6rr","orcid":null},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Alexander D\u00f6rr","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111558148","display_name":"Roland Keller","orcid":null},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Roland Keller","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004958444","display_name":"Andreas Zell","orcid":"https://orcid.org/0000-0003-3299-2211"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Zell","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065854572","display_name":"Andreas Dr\u00e4ger","orcid":"https://orcid.org/0000-0002-1240-5553"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Andreas Dr\u00e4ger","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany","Systems Biology Research Group, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Systems Biology Research Group, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5088021958"],"corresponding_institution_ids":["https://openalex.org/I8087733"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.4268,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.63593422,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2","issue":"4","first_page":"246","last_page":"257"},"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9911999702453613,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7643547058105469},{"id":"https://openalex.org/keywords/parameter-space","display_name":"Parameter space","score":0.7320747375488281},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.6927148103713989},{"id":"https://openalex.org/keywords/calibration","display_name":"Calibration","score":0.6317890882492065},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6112727522850037},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5406103134155273},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5377289056777954},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5318084955215454},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.48213621973991394},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.4782223403453827},{"id":"https://openalex.org/keywords/model-parameter","display_name":"Model parameter","score":0.4328418970108032},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40159088373184204},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22576749324798584},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19871923327445984},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10354307293891907},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10269862413406372},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09251144528388977}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7643547058105469},{"id":"https://openalex.org/C73586568","wikidata":"https://www.wikidata.org/wiki/Q2600211","display_name":"Parameter space","level":2,"score":0.7320747375488281},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.6927148103713989},{"id":"https://openalex.org/C165838908","wikidata":"https://www.wikidata.org/wiki/Q736777","display_name":"Calibration","level":2,"score":0.6317890882492065},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6112727522850037},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5406103134155273},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5377289056777954},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5318084955215454},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.48213621973991394},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.4782223403453827},{"id":"https://openalex.org/C2983447341","wikidata":"https://www.wikidata.org/wiki/Q1413083","display_name":"Model parameter","level":2,"score":0.4328418970108032},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40159088373184204},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22576749324798584},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19871923327445984},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10354307293891907},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10269862413406372},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09251144528388977},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.3390/computation2040246","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation2040246","pdf_url":"https://www.mdpi.com/2079-3197/2/4/246/pdf?version=1418913224","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},{"id":"pmid:32211200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32211200","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":"Computation (Basel, Switzerland)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.664.6454","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.664.6454","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.mdpi.com/2079-3197/2/4/246/pdf/","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:5b2d3ead160d405a97dee45cc951a9d9","is_oa":true,"landing_page_url":"https://doaj.org/article/5b2d3ead160d405a97dee45cc951a9d9","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":"Computation, Vol 2, Iss 4, Pp 246-257 (2014)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2079-3197/2/4/246/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/computation2040246","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Computation","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7093077","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7093077","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computation (Basel)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/computation2040246","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation2040246","pdf_url":"https://www.mdpi.com/2079-3197/2/4/246/pdf?version=1418913224","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3005190885","display_name":null,"funder_award_id":"332020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2045266982.pdf","grobid_xml":"https://content.openalex.org/works/W2045266982.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W8761561","https://openalex.org/W174102300","https://openalex.org/W315572163","https://openalex.org/W1497256448","https://openalex.org/W1514875444","https://openalex.org/W1517923740","https://openalex.org/W1595159159","https://openalex.org/W1605961137","https://openalex.org/W1649408115","https://openalex.org/W1976811972","https://openalex.org/W2010632883","https://openalex.org/W2023395518","https://openalex.org/W2024060531","https://openalex.org/W2073293499","https://openalex.org/W2083108649","https://openalex.org/W2087360343","https://openalex.org/W2090120515","https://openalex.org/W2100525485","https://openalex.org/W2101168835","https://openalex.org/W2102434872","https://openalex.org/W2102653059","https://openalex.org/W2112036188","https://openalex.org/W2115343689","https://openalex.org/W2118258530","https://openalex.org/W2121697173","https://openalex.org/W2127130980","https://openalex.org/W2128782793","https://openalex.org/W2141059504","https://openalex.org/W2146696410","https://openalex.org/W2152195021","https://openalex.org/W2156730317","https://openalex.org/W2158622495","https://openalex.org/W2161088429","https://openalex.org/W2162144833","https://openalex.org/W2166071821","https://openalex.org/W2169245194","https://openalex.org/W2395301294","https://openalex.org/W2981264952","https://openalex.org/W3144526075","https://openalex.org/W4230073927","https://openalex.org/W4256451422","https://openalex.org/W6682642761"],"related_works":["https://openalex.org/W1998254728","https://openalex.org/W2069805373","https://openalex.org/W2023661646","https://openalex.org/W2369488043","https://openalex.org/W2066489961","https://openalex.org/W2905630886","https://openalex.org/W1987771408","https://openalex.org/W2612639608","https://openalex.org/W2087158431","https://openalex.org/W2793373094"],"abstract_inverted_index":{"The":[0],"identification":[1],"of":[2,40,68,119,134,146],"suitable":[3],"model":[4,45,98,111,142],"parameters":[5,41],"for":[6,65,94,127,139],"biochemical":[7,69],"reactions":[8],"has":[9],"been":[10],"recognized":[11],"as":[12,87,89],"a":[13,44,55,90,103,109],"quite":[14],"difficult":[15],"endeavor.":[16],"Parameter":[17],"values":[18],"from":[19],"literature":[20],"or":[21],"experiments":[22],"can":[23,36],"often":[24],"not":[25],"directly":[26],"be":[27],"combined":[28],"in":[29],"complex":[30],"reaction":[31],"systems.":[32],"Nature-inspired":[33],"optimization":[34,74],"techniques":[35],"find":[37],"appropriate":[38],"sets":[39],"that":[42,57],"calibrate":[43],"to":[46,121],"experimentally":[47],"obtained":[48],"time":[49],"series":[50],"data.":[51],"We":[52],"present":[53],"SBMLsimulator,":[54],"tool":[56],"combines":[58],"the":[59,72,117,129,135,140],"Systems":[60],"Biology":[61],"Simulation":[62],"Core":[63],"Library":[64],"dynamic":[66],"simulation":[67,99,131],"models":[70],"with":[71,84],"heuristic":[73],"framework":[75],"EvA2.":[76],"SBMLsimulator":[77,120,124],"provides":[78],"an":[79],"intuitive":[80],"graphical":[81],"user":[82],"interface":[83,93],"various":[85],"options":[86],"well":[88],"fully-featured":[91],"command-line":[92],"large-scale":[95,141],"and":[96,100,112,132,138,144],"script-based":[97],"calibration.":[101],"In":[102],"parameter":[104,136,148],"estimation":[105,145],"study":[106],"based":[107],"on":[108],"published":[110],"artificial":[113],"data":[114],"we":[115],"demonstrate":[116],"capability":[118],"identify":[122],"parameters.":[123],"is":[125],"useful":[126],"both,":[128],"interactive":[130],"exploration":[133],"space":[137],"calibration":[143],"uncertain":[147],"values.":[149]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}