{"id":"https://openalex.org/W2161088429","doi":"https://doi.org/10.1186/1752-0509-7-55","title":"The systems biology simulation core algorithm","display_name":"The systems biology simulation core algorithm","publication_year":2013,"publication_date":"2013-07-05","ids":{"openalex":"https://openalex.org/W2161088429","doi":"https://doi.org/10.1186/1752-0509-7-55","mag":"2161088429","pmid":"https://pubmed.ncbi.nlm.nih.gov/23826941"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-7-55","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-55","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-55","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-55","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","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":false,"raw_author_name":"Alexander D\u00f6rr","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041632412","display_name":"Akito Tabira","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akito Tabira","raw_affiliation_strings":["Graduate School of Science and Technology, Keio University, Yokohama, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Science and Technology, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008451312","display_name":"Akira Funahashi","orcid":"https://orcid.org/0000-0003-0605-239X"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akira Funahashi","raw_affiliation_strings":["Graduate School of Science and Technology, Keio University, Yokohama, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Science and Technology, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019319470","display_name":"Michael J. Ziller","orcid":"https://orcid.org/0000-0003-0781-7980"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael J Ziller","raw_affiliation_strings":["Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087335185","display_name":"Richard R. Adams","orcid":"https://orcid.org/0000-0003-1501-0941"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard Adams","raw_affiliation_strings":["SynthSys Edinburgh, CH Waddington Building, University of Edinburgh, Edinburgh, EH9 3JD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SynthSys Edinburgh, CH Waddington Building, University of Edinburgh, Edinburgh, EH9 3JD, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002460040","display_name":"Nicol\u00e1s Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-9290-7894"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicolas Rodriguez","raw_affiliation_strings":["European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112438594","display_name":"Nicolas Le Nov\u00e8re","orcid":null},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicolas Le Nov\u00e8re","raw_affiliation_strings":["Babraham Institute, Babraham, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Babraham Institute, Babraham, Cambridge, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089950523","display_name":"Noriko Hiroi","orcid":"https://orcid.org/0000-0002-0214-373X"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Noriko Hiroi","raw_affiliation_strings":["Graduate School of Science and Technology, Keio University, Yokohama, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Science and Technology, Keio University, Yokohama, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004102781","display_name":"Hannes Planatscher","orcid":"https://orcid.org/0000-0002-6536-0782"},"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":"Hannes Planatscher","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 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, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 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/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":"Andreas Dr\u00e4ger","raw_affiliation_strings":["Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5065854572"],"corresponding_institution_ids":["https://openalex.org/I8087733"],"apc_list":null,"apc_paid":{"value":1442,"currency":"EUR","value_usd":1555},"fwci":2.3939,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.89172404,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"7","issue":"1","first_page":"55","last_page":"55"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8325999975204468,"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":0.8325999975204468,"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":0.12630000710487366,"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/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.00570000009611249,"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/sbml","display_name":"SBML","score":0.9681222438812256},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7449159026145935},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5661588311195374},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.547431230545044},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.46894240379333496},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.46682044863700867},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4593845009803772},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.4461006820201874},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4283524751663208},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.41214677691459656},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.18496567010879517},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16583847999572754},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.14242780208587646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11070495843887329}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9681222438812256},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7449159026145935},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5661588311195374},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.547431230545044},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.46894240379333496},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.46682044863700867},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4593845009803772},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.4461006820201874},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4283524751663208},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.41214677691459656},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.18496567010879517},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16583847999572754},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.14242780208587646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11070495843887329},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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":"D000465","descriptor_name":"Algorithms","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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1186/1752-0509-7-55","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-55","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-55","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:23826941","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23826941","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pure.ed.ac.uk:openaire/15f9f4ee-c94c-4ca5-91ce-9c8add79a068","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/15f9f4ee-c94c-4ca5-91ce-9c8add79a068","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Keller, R, D\u00f6rr, A, Tabira, A, Funahashi, A, Ziller, M J, Adams, R, Rodriguez, N, Nov\u00e8re, N L, Hiroi, N, Planatscher, H, Zell, A & Dr\u00e4ger, A 2013, 'The systems biology simulation core algorithm', BMC Systems Biology, vol. 7, 55. https://doi.org/10.1186/1752-0509-7-55","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:dash.harvard.edu:1/11717551","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:11717551","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"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":"Journal Article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt5fb8350r","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/5fb8350r","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, vol 7, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2706472","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3707837","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3707837","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3707837","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":"BMC Syst Biol","raw_type":"Text"},{"id":"pmh:oai:pure.ed.ac.uk:publications/15f9f4ee-c94c-4ca5-91ce-9c8add79a068","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11820/15f9f4ee-c94c-4ca5-91ce-9c8add79a068","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:qt5fb8350r","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/5fb8350r","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Keller, Roland; D\u00c3\u00b6rr, Alexander; Tabira, Akito; Funahashi, Akira; Ziller, Michael J; Adams, Richard; \u00c2\u00a0et al.(2013). The systems biology simulation core algorithm. BMC Systems Biology, 7(1), 55. doi: http://dx.doi.org/10.1186/1752-0509-7-55. Retrieved from: http://www.escholarship.org/uc/item/5fb8350r","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-7-55","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-55","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-55","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2144373698","display_name":null,"funder_award_id":"BB/J019305/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2160003213","display_name":null,"funder_award_id":"BB/D019621/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6782187388","display_name":null,"funder_award_id":"0315756","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320309332","display_name":"Harvey Mudd College","ror":"https://ror.org/025ecfn45"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161088429.pdf","grobid_xml":"https://content.openalex.org/works/W2161088429.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W421502599","https://openalex.org/W1533710340","https://openalex.org/W1566102697","https://openalex.org/W1592132377","https://openalex.org/W1609175937","https://openalex.org/W1966506530","https://openalex.org/W1987242421","https://openalex.org/W1998125620","https://openalex.org/W2021747008","https://openalex.org/W2024060242","https://openalex.org/W2034375827","https://openalex.org/W2034463423","https://openalex.org/W2040155617","https://openalex.org/W2042388195","https://openalex.org/W2042880070","https://openalex.org/W2053289371","https://openalex.org/W2054024422","https://openalex.org/W2068930732","https://openalex.org/W2097319997","https://openalex.org/W2102653059","https://openalex.org/W2104759754","https://openalex.org/W2107062718","https://openalex.org/W2113777491","https://openalex.org/W2114124738","https://openalex.org/W2117364474","https://openalex.org/W2123783513","https://openalex.org/W2124236793","https://openalex.org/W2133938042","https://openalex.org/W2134221731","https://openalex.org/W2141058339","https://openalex.org/W2145435867","https://openalex.org/W2149570924","https://openalex.org/W2150386276","https://openalex.org/W2150599425","https://openalex.org/W2150908245","https://openalex.org/W2157529519","https://openalex.org/W2162144833","https://openalex.org/W2163518974","https://openalex.org/W2165610311","https://openalex.org/W2166751342","https://openalex.org/W2171745314","https://openalex.org/W2181917526","https://openalex.org/W2187198735","https://openalex.org/W2204394015","https://openalex.org/W2432517183","https://openalex.org/W2465447782","https://openalex.org/W2793328140","https://openalex.org/W2916475656","https://openalex.org/W2981264952","https://openalex.org/W4251141266","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2136043941","https://openalex.org/W2211443823","https://openalex.org/W2043776573","https://openalex.org/W2026725606","https://openalex.org/W2735157934","https://openalex.org/W2097410126","https://openalex.org/W2115343689","https://openalex.org/W2008016884","https://openalex.org/W1978435670"],"abstract_inverted_index":{"BACKGROUND:":[0],"With":[1],"the":[2,16,84,88,95,112,134,143,146,154,170,173,177,180,209,212,231],"increasing":[3],"availability":[4],"of":[5,19,27,71,83,87,94,111,125,136,145,162,169,179,211],"high":[6],"dimensional":[7],"time":[8],"course":[9],"data":[10],"for":[11,133,196],"metabolites,":[12],"genes,":[13],"and":[14,46,90,128,159,202],"fluxes,":[15],"mathematical":[17,85],"description":[18,168],"dynamical":[20],"systems":[21,30],"has":[22,150],"become":[23],"an":[24,59],"essential":[25],"aspect":[26],"research":[28],"in":[29,36,69,97],"biology.":[31],"Models":[32],"are":[33,67],"often":[34],"encoded":[35],"formats":[37],"such":[38],"as":[39,109,192],"SBML,":[40],"whose":[41],"structure":[42],"is":[43],"very":[44],"complex":[45],"difficult":[47],"to":[48,51,62,230],"evaluate":[49],"due":[50],"many":[52],"special":[53],"cases.":[54],"RESULTS:":[55],"This":[56],"article":[57],"describes":[58],"efficient":[60],"algorithm":[61,96,181],"solve":[63],"SBML":[64,156,174],"models":[65,89,161],"that":[66],"interpreted":[68],"terms":[70,210],"ordinary":[72],"differential":[73,138],"equations.":[74],"We":[75,103],"begin":[76],"our":[77],"consideration":[78],"with":[79,153],"a":[80,105,118,122,129,193],"formal":[81,167],"representation":[82],"form":[86],"explain":[91],"all":[92,160],"parts":[93],"detail,":[98],"including":[99],"several":[100],"preprocessing":[101],"steps.":[102],"provide":[104],"flexible":[106],"reference":[107,187],"implementation":[108,178,188],"part":[110],"Systems":[113],"Biology":[114],"Simulation":[115],"Core":[116],"Library,":[117],"community-driven":[119],"project":[120],"providing":[121],"large":[123],"collection":[124],"numerical":[126],"solvers":[127],"sophisticated":[130],"interface":[131],"hierarchy":[132],"definition":[135],"custom":[137],"equation":[139],"systems.":[140],"To":[141],"demonstrate":[142],"capabilities":[144],"new":[147],"algorithm,":[148],"it":[149],"been":[151],"tested":[152],"entire":[155],"Test":[157],"Suite":[158],"BioModels":[163],"Database.":[164],"CONCLUSIONS:":[165],"The":[166,186],"mathematics":[171],"behind":[172],"format":[175],"facilitates":[176],"within":[182],"specifically":[183],"tailored":[184],"programs.":[185,198],"can":[189,204,227],"be":[190,205,228],"used":[191],"simulation":[194],"backend":[195],"Java\u2122-based":[197],"Source":[199],"code,":[200],"binaries,":[201],"documentation":[203],"freely":[206],"obtained":[207],"under":[208],"LGPL":[213],"version":[214],"3":[215],"from":[216],"http://simulation-core.sourceforge.net.":[217],"Feature":[218],"requests,":[219],"bug":[220],"reports,":[221],"contributions,":[222],"or":[223],"any":[224],"further":[225],"discussion":[226],"directed":[229],"mailing":[232],"list":[233],"simulation-core-development@lists.sourceforge.net.":[234]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}