{"id":"https://openalex.org/W66143020","doi":null,"title":"SBML ODE Solver Library: a command-line tool and library for numerical analysis of reaction networks","display_name":"SBML ODE Solver Library: a command-line tool and library for numerical analysis of reaction networks","publication_year":2005,"publication_date":"2005-01-01","ids":{"openalex":"https://openalex.org/W66143020","mag":"66143020"},"language":"en","primary_location":{"id":"mag:66143020","doi":null,"is_oa":false,"landing_page_url":"https://www.tbi.univie.ac.at/papers/PREPRINTS/05-03-002.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046792401","display_name":"Rainer Machn","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rainer Machn","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090126272","display_name":"Andrew Finney","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrew Finney","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073288820","display_name":"Stefanie Widder A","orcid":"https://orcid.org/0000-0003-0733-5666","observed_orcids":["https://orcid.org/0000-0003-0733-5666"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stefanie Widder","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-0733-5666","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065863676","display_name":"Melanie I. Stefan","orcid":"https://orcid.org/0000-0002-6086-7357","observed_orcids":["https://orcid.org/0000-0002-6086-7357"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Melanie I. Stefan","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6086-7357","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5005564950","display_name":"Christoph Flamm","orcid":"https://orcid.org/0000-0001-5500-2415","observed_orcids":["https://orcid.org/0000-0001-5500-2415"]},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Christoph Flamm","raw_affiliation_strings":["Univ. of Vienna#TAB#"],"raw_orcid":"https://orcid.org/0000-0001-5500-2415","affiliations":[{"raw_affiliation_string":"Univ. of Vienna#TAB#","institution_ids":["https://openalex.org/I129774422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1032,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.36913696,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9179999828338623,"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":0.9179999828338623,"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/T13286","display_name":"Modeling and Simulation Systems","score":0.05009999871253967,"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"}},{"id":"https://openalex.org/T11416","display_name":"Numerical Solvers for Ordinary Differential Equations","score":0.006599999964237213,"subfield":{"id":"https://openalex.org/subfields/2612","display_name":"Numerical Analysis"},"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/systems-biology-markup-language","display_name":"SBML","score":0.800000011920929},{"id":"https://openalex.org/keywords/chemical-reaction-networks","display_name":"chemical reaction networks","score":0.8920000195503235},{"id":"https://openalex.org/keywords/ordinary-differential-equations","display_name":"ordinary differential equations","score":0.9890000224113464},{"id":"https://openalex.org/keywords/numerical-integration","display_name":"numerical integration","score":0.972000002861023},{"id":"https://openalex.org/keywords/libsbml","display_name":"libSBML","score":0.9750000238418579},{"id":"https://openalex.org/keywords/command-line-tool","display_name":"command-line tool","score":0.8259999752044678},{"id":"https://openalex.org/keywords/programming-libraries","display_name":"programming libraries","score":0.5649999976158142},{"id":"https://openalex.org/keywords/data-visualization","display_name":"data visualization","score":0.6940000057220459},{"id":"https://openalex.org/keywords/graphviz","display_name":"Graphviz","score":0.9779999852180481},{"id":"https://openalex.org/keywords/educational-software","display_name":"educational software","score":0.33399999141693115}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9870771169662476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7259461879730225},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.64732825756073},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6411378383636475},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.6184139251708984},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5519018173217773},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5007033348083496},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35501331090927124},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.20750799775123596},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1584775745868683},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12582498788833618},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.1219111979007721}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:66143020","doi":null,"is_oa":false,"landing_page_url":"https://www.tbi.univie.ac.at/papers/PREPRINTS/05-03-002.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1576664335","https://openalex.org/W1979565917","https://openalex.org/W2042880070","https://openalex.org/W2044889656","https://openalex.org/W2065782501","https://openalex.org/W2117364474","https://openalex.org/W2150908245"],"related_works":["https://openalex.org/W7097141701","https://openalex.org/W2117344541","https://openalex.org/W7101279161","https://openalex.org/W7099798349","https://openalex.org/W7098282531","https://openalex.org/W2974115398","https://openalex.org/W2104759754","https://openalex.org/W2272767959","https://openalex.org/W3165512191","https://openalex.org/W7098470946"],"abstract_inverted_index":{"The":[0,60],"SBML":[1,64,69,107],"ODE":[2,74],"Solver":[3],"Library":[4],"(SOSlib)":[5],"is":[6,41,55,110],"a":[7,20,28,49,91,101],"command-line":[8],"oriented":[9],"tool":[10],"and":[11,16,54,71,76,88,98,103],"programming":[12],"library":[13,65],"for":[14,48,67,78,113],"construction":[15,72],"numerical":[17,79],"integration":[18],"of":[19,22,51,73,94],"system":[21],"ordinary":[23],"differential":[24],"equations":[25],"(ODE)":[26],"from":[27],"chemical":[29],"reaction":[30],"network":[31],"encoded":[32],"in":[33,43],"the":[34,63,95],"Systems":[35],"Biology":[36],"Markup":[37],"Language":[38],"(SBML).":[39],"It":[40],"written":[42],"ANSI":[44],"C,":[45],"provides":[46],"bindings":[47],"variety":[50],"scripting":[52],"languages":[53],"distributed":[56],"under":[57],"LGPL":[58],"license.":[59],"package":[61],"uses":[62],"libSBML":[66],"parsing":[68],"models":[70],"systems,":[75],"CVODE":[77],"integration.":[80],"Optional":[81],"data":[82],"visualization":[83],"modules":[84],"based":[85],"on":[86],"XMGrace":[87],"Graphviz":[89],"allow":[90],"quick":[92],"inspection":[93],"model\u2019s":[96],"structure":[97],"dynamics,":[99],"providing":[100],"transparent":[102],"direct":[104],"interface":[105],"to":[106],"models,":[108],"which":[109],"especially":[111],"useful":[112],"educational":[114],"purposes.":[115],"Availability:":[116],"http://www.tbi.univie.ac.at/\ufffdraim/odeSolver/":[117],"Contact:":[118],"{raim,":[119],"xtof}@tbi.univie.ac.at":[120]},"counts_by_year":[],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
