{"id":"https://openalex.org/W2095786703","doi":"https://doi.org/10.1093/bioinformatics/btm105","title":"SBML export interface for the systems biology toolbox for MATLAB","display_name":"SBML export interface for the systems biology toolbox for MATLAB","publication_year":2007,"publication_date":"2007-03-23","ids":{"openalex":"https://openalex.org/W2095786703","doi":"https://doi.org/10.1093/bioinformatics/btm105","mag":"2095786703","pmid":"https://pubmed.ncbi.nlm.nih.gov/17384017"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm105","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1297/49812299/bioinformatics_23_10_1297.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/23/10/1297/49812299/bioinformatics_23_10_1297.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034232141","display_name":"Hening Schmidt","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139723","display_name":"Fraunhofer Chalmers Research Centre for Industrial Mathematics","ror":"https://ror.org/03tqh5n18","country_code":"SE","type":"nonprofit","lineage":["https://openalex.org/I4210139723","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE","SE"],"is_corresponding":false,"raw_author_name":"Hening Schmidt","raw_affiliation_strings":["1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4210139723","https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089113331","display_name":"Gunnar Drews","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139723","display_name":"Fraunhofer Chalmers Research Centre for Industrial Mathematics","ror":"https://ror.org/03tqh5n18","country_code":"SE","type":"nonprofit","lineage":["https://openalex.org/I4210139723","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE","SE"],"is_corresponding":false,"raw_author_name":"Gunnar Drews","raw_affiliation_strings":["1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4210139723","https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067743298","display_name":"Julio Vera","orcid":"https://orcid.org/0000-0002-3076-5122"},"institutions":[{"id":"https://openalex.org/I4210139723","display_name":"Fraunhofer Chalmers Research Centre for Industrial Mathematics","ror":"https://ror.org/03tqh5n18","country_code":"SE","type":"nonprofit","lineage":["https://openalex.org/I4210139723","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE","SE"],"is_corresponding":false,"raw_author_name":"Julio Vera","raw_affiliation_strings":["1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4210139723","https://openalex.org/I4665924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022724143","display_name":"Olaf Wolkenhauer","orcid":"https://orcid.org/0000-0001-6105-2937"},"institutions":[{"id":"https://openalex.org/I4210139723","display_name":"Fraunhofer Chalmers Research Centre for Industrial Mathematics","ror":"https://ror.org/03tqh5n18","country_code":"SE","type":"nonprofit","lineage":["https://openalex.org/I4210139723","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE","SE"],"is_corresponding":false,"raw_author_name":"Olaf Wolkenhauer","raw_affiliation_strings":["1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Fraunhofer-Chalmers Research Centre for Industrial Mathematics, Gothenburg, Sweden and 2Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4210139723","https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9422,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.7397273,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"10","first_page":"1297","last_page":"1298"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6960999965667725,"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":0.6960999965667725,"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":0.08510000258684158,"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":0.04270000010728836,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9909288883209229},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.8195655345916748},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7855528593063354},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.7800074815750122},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.777290940284729},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5862371921539307},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.569603681564331},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.46243417263031006},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.46020573377609253},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.4572434723377228},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2996615171432495},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.20063704252243042}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9909288883209229},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8195655345916748},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7855528593063354},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.7800074815750122},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.777290940284729},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5862371921539307},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.569603681564331},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.46243417263031006},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.46020573377609253},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.4572434723377228},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2996615171432495},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.20063704252243042},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"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}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"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":"D019451","descriptor_name":"Information Management","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019451","descriptor_name":"Information Management","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019451","descriptor_name":"Information Management","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"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/btm105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm105","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1297/49812299/bioinformatics_23_10_1297.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:17384017","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17384017","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},{"id":"pmh:oai:fraunhofer.de:N-62019","is_oa":false,"landing_page_url":"http://publica.fraunhofer.de/documents/N-62019.html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400801","display_name":"Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Fraunhofer ITWM","raw_type":"Journal Article"},{"id":"pmh:oai:publica.fraunhofer.de:publica/213396","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/213396","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm105","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm105","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/10/1297/49812299/bioinformatics_23_10_1297.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2095786703.pdf","grobid_xml":"https://content.openalex.org/works/W2095786703.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2115343689","https://openalex.org/W2137128504","https://openalex.org/W2150908245"],"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/W1546010648","https://openalex.org/W2890725831"],"abstract_inverted_index":{"UNLABELLED:":[0],"In":[1],"this":[2],"application":[3],"note,":[4],"we":[5],"present":[6],"an":[7,90],"Systems":[8,17,130],"biology":[9],"markup":[10],"language":[11],"(SBML)":[12],"export":[13,64,79,115,123],"interface":[14,23,111,124],"for":[15,20,133],"the":[16,32,47,55,78,81,101,105,116,129],"Biology":[18,131],"Toolbox":[19,132],"MATLAB.":[21],"This":[22],"allows":[24],"modelers":[25],"to":[26,37,52,76,89,97,113,118],"automatically":[27],"convert":[28],"models,":[29],"represented":[30],"in":[31,68],"toolbox's":[33],"own":[34],"format":[35],"(SBmodels)":[36],"SBML":[38,91,122],"files.":[39],"Since":[40],"SBmodels":[41],"do":[42],"not":[43],"explicitly":[44],"contain":[45],"all":[46],"information":[48,57],"that":[49],"is":[50,58,74,96,136],"required":[51],"generate":[53],"SBML,":[54],"necessary":[56],"gathered":[59],"by":[60],"parsing":[61],"SBmodels.":[62],"The":[63,93,121,144],"can":[65],"be":[66],"done":[67],"two":[69],"different":[70],"ways.":[71],"First,":[72],"it":[73],"possible":[75],"call":[77],"from":[80,142],"command":[82],"line,":[83],"thereby":[84],"directly":[85],"converting":[86],"a":[87,108,148],"model":[88,117],"file.":[92],"second":[94],"option":[95],"inspect":[98],"and":[99,112,139,152],"edit":[100],"conversion":[102],"results":[103],"with":[104],"help":[106],"of":[107],"graphical":[109],"user":[110],"subsequently":[114],"SBML.":[119],"AVAILABILITY:":[120],"has":[125],"been":[126],"integrated":[127],"into":[128],"MATLAB,":[134],"which":[135],"open":[137],"source":[138],"freely":[140],"available":[141],"http://www.sbtoolbox.org.":[143],"website":[145],"also":[146],"contains":[147],"tutorial,":[149],"extensive":[150],"documentation":[151],"examples.":[153]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}