{"id":"https://openalex.org/W2137128504","doi":"https://doi.org/10.1093/bioinformatics/btl111","title":"SBMLToolbox: an SBML toolbox for MATLAB users","display_name":"SBMLToolbox: an SBML toolbox for MATLAB users","publication_year":2006,"publication_date":"2006-03-30","ids":{"openalex":"https://openalex.org/W2137128504","doi":"https://doi.org/10.1093/bioinformatics/btl111","mag":"2137128504","pmid":"https://pubmed.ncbi.nlm.nih.gov/16574696"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl111","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl111","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/10/1275/48838861/bioinformatics_22_10_1275.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/22/10/1275/48838861/bioinformatics_22_10_1275.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049649026","display_name":"Sarah Keating","orcid":"https://orcid.org/0000-0002-3356-3542"},"institutions":[{"id":"https://openalex.org/I141584323","display_name":"University of Hertfordshire","ror":"https://ror.org/0267vjk41","country_code":"GB","type":"education","lineage":["https://openalex.org/I141584323"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sarah M. Keating","raw_affiliation_strings":["Science and Technology Research Institute, University of Hertfordshire 1 \u00a0 1 \u00a0 \u00a0 Hatfield, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Science and Technology Research Institute, University of Hertfordshire 1 \u00a0 1 \u00a0 \u00a0 Hatfield, UK","institution_ids":["https://openalex.org/I141584323"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114254681","display_name":"Benjamin Bornstein","orcid":null},"institutions":[{"id":"https://openalex.org/I1334627681","display_name":"Jet Propulsion Laboratory","ror":"https://ror.org/027k65916","country_code":"US","type":"facility","lineage":["https://openalex.org/I122411786","https://openalex.org/I1334627681","https://openalex.org/I4210124779"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin J. Bornstein","raw_affiliation_strings":["NASA Jet Propulsion Laboratory 2 \u00a0 2 \u00a0 \u00a0 Pasadena, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NASA Jet Propulsion Laboratory 2 \u00a0 2 \u00a0 \u00a0 Pasadena, CA, USA","institution_ids":["https://openalex.org/I1334627681"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090126272","display_name":"Andrew Finney","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Andrew Finney","raw_affiliation_strings":["Physiomics PLC 3 \u00a0 3 \u00a0 \u00a0 Oxford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Physiomics PLC 3 \u00a0 3 \u00a0 \u00a0 Oxford, UK","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016716446","display_name":"Michael Hucka","orcid":"https://orcid.org/0000-0001-9105-5960"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Hucka","raw_affiliation_strings":["Biological Network Modeling Centre, Beckman Institute 139-74, California Institute of Technology 4 \u00a0 4 \u00a0 \u00a0 Pasadena, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Network Modeling Centre, Beckman Institute 139-74, California Institute of Technology 4 \u00a0 4 \u00a0 \u00a0 Pasadena, CA, USA","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049649026"],"corresponding_institution_ids":["https://openalex.org/I141584323"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.3077,"has_fulltext":true,"cited_by_count":145,"citation_normalized_percentile":{"value":0.8789613,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"22","issue":"10","first_page":"1275","last_page":"1277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9941999912261963,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9941999912261963,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9934999942779541,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"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/sbml","display_name":"SBML","score":0.994053840637207},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7947031855583191},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.7510244846343994},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7295709252357483},{"id":"https://openalex.org/keywords/software-portability","display_name":"Software portability","score":0.7252005338668823},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.7222018837928772},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.649373471736908},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.36618703603744507},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3248029947280884},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23858538269996643},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.1442546248435974}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.994053840637207},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7947031855583191},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7510244846343994},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7295709252357483},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.7252005338668823},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.7222018837928772},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.649373471736908},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.36618703603744507},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3248029947280884},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23858538269996643},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.1442546248435974}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"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":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btl111","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl111","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/10/1275/48838861/bioinformatics_22_10_1275.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:16574696","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16574696","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":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.103.1198","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.1198","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btl111v1.pdf","raw_type":"text"},{"id":"pmh:oai:authors.library.caltech.edu:4243","is_oa":false,"landing_page_url":"https://resolver.caltech.edu/CaltechAUTHORS:KEAbioinf06","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl111","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl111","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/10/1275/48838861/bioinformatics_22_10_1275.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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G8794720479","display_name":null,"funder_award_id":"R01 GM70923","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137128504.pdf","grobid_xml":"https://content.openalex.org/works/W2137128504.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1965014786","https://openalex.org/W2100525485","https://openalex.org/W2115343689"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2890725831","https://openalex.org/W3041939341"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"present":[2],"SBMLToolbox,":[3],"a":[4],"toolbox":[5],"that":[6,30],"facilitates":[7],"importing":[8],"and":[9,21,27,50,60],"exporting":[10],"models":[11],"represented":[12],"in":[13,20],"the":[14,24,42,48],"Systems":[15],"Biology":[16],"Markup":[17],"Language":[18],"(SBML)":[19],"out":[22],"of":[23,35,45,52,62],"MATLAB":[25,39,46],"environment":[26],"provides":[28],"functionality":[29],"enables":[31],"an":[32,53],"experienced":[33],"user":[34],"either":[36],"SBML":[37,54],"or":[38],"to":[40],"combine":[41],"computing":[43],"power":[44],"with":[47],"portability":[49],"exchangeability":[51],"model.":[55],"SBMLToolbox":[56,65],"supports":[57],"all":[58],"levels":[59],"versions":[61],"SBML.":[63],"AVAILABILITY:":[64],"is":[66],"freely":[67],"available":[68],"from":[69],"http://sbml.org/software/sbmltoolbox":[70]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":12},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":13}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}