{"id":"https://openalex.org/W2128782793","doi":"https://doi.org/10.1093/bioinformatics/btl443","title":"SBML-PET: a Systems Biology Markup Language-based parameter estimation tool","display_name":"SBML-PET: a Systems Biology Markup Language-based parameter estimation tool","publication_year":2006,"publication_date":"2006-08-22","ids":{"openalex":"https://openalex.org/W2128782793","doi":"https://doi.org/10.1093/bioinformatics/btl443","mag":"2128782793","pmid":"https://pubmed.ncbi.nlm.nih.gov/16926221"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl443","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl443","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/21/2704/48838070/bioinformatics_22_21_2704.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/22/21/2704/48838070/bioinformatics_22_21_2704.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087731845","display_name":"Zhike Zi","orcid":"https://orcid.org/0000-0002-7601-915X"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Zhike Zi","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Ihnestr. 73 \u00a0 14195 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Ihnestr. 73 \u00a0 14195 Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003799374","display_name":"Edda Klipp","orcid":"https://orcid.org/0000-0002-0567-7075"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Edda Klipp","raw_affiliation_strings":["Max Planck Institute for Molecular Genetics, Ihnestr. 73 \u00a0 14195 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Ihnestr. 73 \u00a0 14195 Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5087731845"],"corresponding_institution_ids":["https://openalex.org/I4210142260"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.4952,"has_fulltext":true,"cited_by_count":87,"citation_normalized_percentile":{"value":0.9526323,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"21","first_page":"2704","last_page":"2705"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.991100013256073,"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":0.991100013256073,"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":0.9905999898910522,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9858999848365784,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.991635262966156},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.9458838105201721},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7061987519264221},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5690186023712158},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5384838581085205},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36265528202056885},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3319638967514038},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2534852921962738},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.18829482793807983},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.14517274498939514}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.991635262966156},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.9458838105201721},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7061987519264221},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5690186023712158},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5384838581085205},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36265528202056885},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3319638967514038},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2534852921962738},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.18829482793807983},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.14517274498939514}],"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":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":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":"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":"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":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":5,"locations":[{"id":"doi:10.1093/bioinformatics/btl443","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl443","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/21/2704/48838070/bioinformatics_22_21_2704.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:16926221","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16926221","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:pure.mpg.de:item_1585067","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0010-8361-8","pdf_url":"https://hdl.handle.net/11858/00-001M-0000-0010-8360-A","source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.127.9349","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.127.9349","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/22/21/2704.pdf","raw_type":"text"},{"id":"pmh:oai:edoc.mpg.de:313076","is_oa":false,"landing_page_url":"http://edoc.mpg.de/313076","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","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":"Bioinformatics, v.22, 2704-2705 (2006)","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl443","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl443","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/21/2704/48838070/bioinformatics_22_21_2704.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":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320327553","display_name":"International Max Planck Research School for Advanced Methods in Process and Systems Engineering","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128782793.pdf","grobid_xml":"https://content.openalex.org/works/W2128782793.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1798965550","https://openalex.org/W1963861745","https://openalex.org/W1980630205","https://openalex.org/W1982258483","https://openalex.org/W2031674568","https://openalex.org/W2033735656","https://openalex.org/W2043791622","https://openalex.org/W2108896820","https://openalex.org/W2121008927","https://openalex.org/W2128005489","https://openalex.org/W2128506325","https://openalex.org/W2132935366","https://openalex.org/W2139038899","https://openalex.org/W2143894094","https://openalex.org/W2151339633","https://openalex.org/W2156154713","https://openalex.org/W2165603655","https://openalex.org/W2171166218","https://openalex.org/W2894656633"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2981332207","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2100525485","https://openalex.org/W2890725831","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573"],"abstract_inverted_index":{"http://sysbio.molgen.mpg.de/SBML-PET/.":[0],"The":[1],"website":[2],"also":[3],"contains":[4],"detailed":[5],"documentation":[6],"for":[7],"SBML-PET.":[8]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"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":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}