{"id":"https://openalex.org/W2126025430","doi":"https://doi.org/10.1093/bioinformatics/bth271","title":"MathSBML: a package for manipulating SBML-based biological models","display_name":"MathSBML: a package for manipulating SBML-based biological models","publication_year":2004,"publication_date":"2004-04-15","ids":{"openalex":"https://openalex.org/W2126025430","doi":"https://doi.org/10.1093/bioinformatics/bth271","mag":"2126025430","pmid":"https://pubmed.ncbi.nlm.nih.gov/15087311"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth271","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth271","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2829/48906411/bioinformatics_20_16_2829.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/20/16/2829/48906411/bioinformatics_20_16_2829.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034588960","display_name":"Bruce E. Shapiro","orcid":"https://orcid.org/0000-0003-3130-4659"},"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"]},{"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":true,"raw_author_name":"Bruce E. Shapiro","raw_affiliation_strings":["Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA. bshapiro@caltech.edu","Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA,#TAB#"],"affiliations":[{"raw_affiliation_string":"Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA. bshapiro@caltech.edu","institution_ids":["https://openalex.org/I1334627681"]},{"raw_affiliation_string":"Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA,#TAB#","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","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":["Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA and","Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA"],"affiliations":[{"raw_affiliation_string":"Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA and","institution_ids":["https://openalex.org/I122411786"]},{"raw_affiliation_string":"Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090126272","display_name":"Andrew Finney","orcid":null},"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":false,"raw_author_name":"Andrew Finney","raw_affiliation_strings":["Science and Technology Research Center, University of Hertfordshire, Hatfield, UK","Science and Technology Research Center, University of Hertfordshire, Hatfield, UK#TAB#"],"affiliations":[{"raw_affiliation_string":"Science and Technology Research Center, University of Hertfordshire, Hatfield, UK","institution_ids":["https://openalex.org/I141584323"]},{"raw_affiliation_string":"Science and Technology Research Center, University of Hertfordshire, Hatfield, UK#TAB#","institution_ids":["https://openalex.org/I141584323"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085737537","display_name":"John C. Doyle","orcid":"https://orcid.org/0000-0002-1828-2486"},"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":"John Doyle","raw_affiliation_strings":["Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA and","Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA"],"affiliations":[{"raw_affiliation_string":"Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA and","institution_ids":["https://openalex.org/I122411786"]},{"raw_affiliation_string":"Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5034588960"],"corresponding_institution_ids":["https://openalex.org/I122411786","https://openalex.org/I1334627681"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.1351,"has_fulltext":true,"cited_by_count":60,"citation_normalized_percentile":{"value":0.92039797,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"20","issue":"16","first_page":"2829","last_page":"2831"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9925000071525574,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9725000262260437,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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":0.9666266441345215},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.762447714805603},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6323943138122559},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5180326104164124},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.5092331171035767},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43352940678596497},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.3492697775363922},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34602493047714233},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15971964597702026}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9666266441345215},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.762447714805603},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6323943138122559},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5180326104164124},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5092331171035767},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43352940678596497},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.3492697775363922},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34602493047714233},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15971964597702026},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":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":"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":"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":"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},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bth271","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth271","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2829/48906411/bioinformatics_20_16_2829.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:15087311","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15087311","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:authors.library.caltech.edu:26314","is_oa":false,"landing_page_url":"https://resolver.caltech.edu/CaltechAUTHORS:20111004-150808819","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"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.829.2604","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.829.2604","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/content/20/16/2829.full.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1409765","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1409765","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth271","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth271","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/16/2829/48906411/bioinformatics_20_16_2829.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":[{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309398","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055"},{"id":"https://openalex.org/F4320338112","display_name":"Exploratory Research for Advanced Technology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126025430.pdf","grobid_xml":"https://content.openalex.org/works/W2126025430.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1576664335","https://openalex.org/W1645305843","https://openalex.org/W1988507461","https://openalex.org/W1996195324","https://openalex.org/W2066969405","https://openalex.org/W2082621456","https://openalex.org/W2109975391","https://openalex.org/W2150908245","https://openalex.org/W4232212213"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W3041939341"],"abstract_inverted_index":{"Open":[0],"Source":[1],"(LGPL)":[2],"at":[3],"http://www.sbml.org":[4],"and":[5],"http://www.sf.net/projects/sbml":[6]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
