{"id":"https://openalex.org/W2034463423","doi":"https://doi.org/10.1186/1752-0509-2-39","title":"SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks","display_name":"SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks","publication_year":2008,"publication_date":"2008-04-30","ids":{"openalex":"https://openalex.org/W2034463423","doi":"https://doi.org/10.1186/1752-0509-2-39","mag":"2034463423","pmid":"https://pubmed.ncbi.nlm.nih.gov/18447902"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-2-39","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-2-39","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-39","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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-39","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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 T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076 T\u00fcbingen, Germany. andreas.draeger@uni-tuebingen.de","Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076 T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076 T\u00fcbingen, Germany. andreas.draeger@uni-tuebingen.de","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084744080","display_name":"Nadine Hassis","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"]},{"id":"https://openalex.org/I4210133934","display_name":"Bernstein Center for Computational Neuroscience T\u00fcbingen","ror":"https://ror.org/03kfnwp54","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210092532","https://openalex.org/I4210133934"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nadine Hassis","raw_affiliation_strings":["Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210133934","https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110029974","display_name":"Jochen Supper","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133934","display_name":"Bernstein Center for Computational Neuroscience T\u00fcbingen","ror":"https://ror.org/03kfnwp54","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210092532","https://openalex.org/I4210133934"]},{"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":"Jochen Supper","raw_affiliation_strings":["Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210133934","https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102110109","display_name":"Adrian Schr\u00f6der","orcid":"https://orcid.org/0009-0009-1033-9351"},"institutions":[{"id":"https://openalex.org/I4210133934","display_name":"Bernstein Center for Computational Neuroscience T\u00fcbingen","ror":"https://ror.org/03kfnwp54","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210092532","https://openalex.org/I4210133934"]},{"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":"Adrian Schr\u00f6der","raw_affiliation_strings":["Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210133934","https://openalex.org/I8087733"]}]},{"author_position":"last","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"]},{"id":"https://openalex.org/I4210133934","display_name":"Bernstein Center for Computational Neuroscience T\u00fcbingen","ror":"https://ror.org/03kfnwp54","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210092532","https://openalex.org/I4210133934"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Zell","raw_affiliation_strings":["Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, Sand 1, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Center for Bioinformatics T\u00fcbingen (ZBIT), University of T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210133934","https://openalex.org/I8087733"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5065854572"],"corresponding_institution_ids":["https://openalex.org/I8087733"],"apc_list":null,"apc_paid":null,"fwci":2.6641,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.89909487,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"2","issue":"1","first_page":"39","last_page":"39"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5454000234603882,"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":0.5454000234603882,"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":0.3077000081539154,"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/T11445","display_name":"Origins and Evolution of Life","score":0.013100000098347664,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9946705102920532},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.664590060710907},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.6567298769950867},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.6411228775978088},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5200307369232178},{"id":"https://openalex.org/keywords/diagrammatic-reasoning","display_name":"Diagrammatic reasoning","score":0.4445967972278595},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32950088381767273},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3052405118942261},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2848920226097107},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13435396552085876},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.12018898129463196}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9946705102920532},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.664590060710907},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.6567298769950867},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.6411228775978088},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5200307369232178},{"id":"https://openalex.org/C106624574","wikidata":"https://www.wikidata.org/wiki/Q5270387","display_name":"Diagrammatic reasoning","level":2,"score":0.4445967972278595},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32950088381767273},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3052405118942261},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2848920226097107},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13435396552085876},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.12018898129463196},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002625","descriptor_name":"Chemistry, Organic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002625","descriptor_name":"Chemistry, Organic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002625","descriptor_name":"Chemistry, Organic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","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":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019146","descriptor_name":"Hypermedia","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1752-0509-2-39","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-2-39","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-39","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:18447902","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18447902","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:doaj.org/article:8dc20c8afdfa465eaf17908c5e50db0a","is_oa":false,"landing_page_url":"https://doaj.org/article/8dc20c8afdfa465eaf17908c5e50db0a","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 2, Iss 1, p 39 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2412839","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2412839","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"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-2-39","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-2-39","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-2-39","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":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2034463423.pdf","grobid_xml":"https://content.openalex.org/works/W2034463423.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1484198052","https://openalex.org/W1495660511","https://openalex.org/W1525055187","https://openalex.org/W1576919957","https://openalex.org/W1577685668","https://openalex.org/W1592132377","https://openalex.org/W1976548998","https://openalex.org/W1981114175","https://openalex.org/W1987242421","https://openalex.org/W2002107667","https://openalex.org/W2006595428","https://openalex.org/W2045478141","https://openalex.org/W2063219876","https://openalex.org/W2087360343","https://openalex.org/W2095786703","https://openalex.org/W2102653059","https://openalex.org/W2106116918","https://openalex.org/W2108227345","https://openalex.org/W2109975391","https://openalex.org/W2115343689","https://openalex.org/W2117344541","https://openalex.org/W2117364474","https://openalex.org/W2121697173","https://openalex.org/W2133253518","https://openalex.org/W2137124525","https://openalex.org/W2144000913","https://openalex.org/W2150908245","https://openalex.org/W2171458571","https://openalex.org/W2319101143","https://openalex.org/W2324977356","https://openalex.org/W2479294836","https://openalex.org/W4298056715"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2981332207","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W1546010648","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,40,150],"development":[2,29],"of":[3,13,30,48,58,77,98,134,152,243,291],"complex":[4],"biochemical":[5],"models":[6],"has":[7],"been":[8],"facilitated":[9],"through":[10,303],"the":[11,27,31,56,92,106,112,114,126,135,203,211,226,241,274,286,300,304,310,317,323],"standardization":[12],"machine-readable":[14],"representations":[15],"like":[16],"SBML":[17,42],"(Systems":[18,36],"Biology":[19,37],"Markup":[20],"Language).":[21],"This":[22,266],"effort":[23],"is":[24,65,109],"accompanied":[25],"by":[26],"ongoing":[28],"human-readable":[32],"diagrammatic":[33,275],"representation":[34],"SBGN":[35,49,136],"Graphical":[38],"Notation).":[39],"graphical":[41],"editor":[43],"CellDesigner":[44,219],"allows":[45,140],"direct":[46],"translation":[47],"into":[50],"SBML,":[51,232],"and":[52,74,95,163,170,183,208,248,288,296,309,325],"vice":[53],"versa.":[54],"For":[55,103],"assignment":[57],"kinetic":[59,78,101,107,204,262],"rate":[60,252],"laws,":[61],"however,":[62],"this":[63,84],"process":[64,97,305],"not":[66],"straightforward,":[67],"as":[68,123,125],"it":[69],"often":[70],"requires":[71],"manual":[72],"assembly":[73],"specific":[75],"knowledge":[76],"equations.":[79,102],"RESULTS:":[80],"SBMLsqueezer":[81,175,239],"facilitates":[82],"exactly":[83],"modeling":[85,267],"step":[86],"via":[87],"automated":[88],"equation":[89,108],"generation,":[90],"overcoming":[91],"highly":[93],"error-prone":[94],"cumbersome":[96],"manually":[99],"assigning":[100],"each":[104,167,258],"reaction":[105],"derived":[110],"from":[111],"stoichiometry,":[113],"participating":[115,245],"species":[116],"(e.g.,":[117],"proteins,":[118],"mRNA":[119],"or":[120,131,147,220,234],"simple":[121],"molecules)":[122],"well":[124],"regulatory":[127],"relations":[128],"(activation,":[129],"inhibition":[130],"other":[132],"modulations)":[133],"diagram.":[137,306],"Such":[138],"information":[139,301],"distinctions":[141],"between,":[142],"for":[143,157,197,254,257],"example,":[144],"translation,":[145],"phosphorylation":[146],"state":[148],"transitions.":[149],"types":[151],"kinetics":[153,173,188,270],"considered":[154],"are":[155,189,206,264],"numerous,":[156],"instance":[158],"generalized":[159],"mass-action,":[160],"Hill,":[161],"convenience":[162],"several":[164],"Michaelis-Menten-based":[165],"kinetics,":[166],"including":[168],"activation":[169],"inhibition.":[171],"These":[172],"allow":[174,196],"to":[176,191,210,231],"cover":[177],"metabolic,":[178],"gene":[179],"regulatory,":[180],"signal":[181],"transduction":[182],"mixed":[184],"networks.":[185],"Whenever":[186],"multiple":[187],"applicable":[190,261],"one":[192],"reaction,":[193,259,293],"parameter":[194],"settings":[195],"user-defined":[198],"specifications.":[199],"After":[200],"invoking":[201],"SBMLsqueezer,":[202],"formulas":[205,263],"generated":[207],"assigned":[209],"model,":[212],"which":[213],"can":[214,228,313],"then":[215],"be":[216,229,314],"simulated":[217],"in":[218,271,322],"with":[221,273,299],"external":[222],"ODE":[223],"solvers.":[224],"Furthermore,":[225],"equations":[227],"exported":[230],"LaTeX":[233],"plain":[235],"text":[236],"format.":[237],"CONCLUSION:":[238],"considers":[240],"annotation":[242],"all":[244],"reactants,":[246],"products":[247],"regulators":[249],"when":[250],"generating":[251],"laws":[253],"reactions.":[255],"Thus,":[256],"only":[260],"considered.":[265],"scheme":[268],"creates":[269],"accordance":[272],"representation.":[276],"In":[277],"contrast":[278],"most":[279],"previously":[280],"published":[281],"tools":[282],"have":[283],"relied":[284],"on":[285],"stoichiometry":[287],"generic":[289],"modulators":[290],"a":[292],"thus":[294],"ignoring":[295],"potentially":[297],"conflicting":[298],"expressed":[302],"Additional":[307],"material":[308],"source":[311],"code":[312],"found":[315,321],"at":[316],"project":[318],"homepage":[319],"(URL":[320],"Availability":[324],"requirements":[326],"section).":[327]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}