{"id":"https://openalex.org/W2073061263","doi":"https://doi.org/10.1186/1752-0509-7-43","title":"Structure, function, and behaviour of computational models in systems biology","display_name":"Structure, function, and behaviour of computational models in systems biology","publication_year":2013,"publication_date":"2013-01-01","ids":{"openalex":"https://openalex.org/W2073061263","doi":"https://doi.org/10.1186/1752-0509-7-43","mag":"2073061263","pmid":"https://pubmed.ncbi.nlm.nih.gov/23721297"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-7-43","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-43","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-43","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-43","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107856156","display_name":"Christian Kn\u00fcpfer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210107832","display_name":"Ernst Abbe University of Applied Sciences Jena","ror":"https://ror.org/01rfnc002","country_code":"DE","type":"education","lineage":["https://openalex.org/I4210107832"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Christian Kn\u00fcpfer","raw_affiliation_strings":["Artificial Intelligence Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany. christian.knuepfer@uni-jena.de","Artificial Intelligence Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany. christian.knuepfer@uni-jena.de","institution_ids":["https://openalex.org/I4210107832"]},{"raw_affiliation_string":"Artificial Intelligence Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068049841","display_name":"Clemens Beckstein","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Clemens Beckstein","raw_affiliation_strings":["Artificial Intelligence Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Artificial Intelligence Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018987403","display_name":"Peter Dittrich","orcid":"https://orcid.org/0000-0002-2541-6745"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peter Dittrich","raw_affiliation_strings":["Bio Systems Analysis Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Bio Systems Analysis Group, University of Jena, Ernst-Abbe-Platz 2, Jena, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029796591","display_name":"Nicolas Gambardella Le Nov\u00e8re","orcid":"https://orcid.org/0000-0002-6309-7327"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicolas Nov\u00e8re","raw_affiliation_strings":["Le Nov\u00e8re lab, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK"],"affiliations":[{"raw_affiliation_string":"Le Nov\u00e8re lab, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5107856156"],"corresponding_institution_ids":["https://openalex.org/I4210107832"],"apc_list":null,"apc_paid":null,"fwci":1.0481,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.76581215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"7","issue":"1","first_page":"43","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9923999905586243,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9915000200271606,"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/computer-science","display_name":"Computer science","score":0.7036924362182617},{"id":"https://openalex.org/keywords/meaning","display_name":"Meaning (existential)","score":0.652752161026001},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.5995568037033081},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5940515995025635},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.5286626815795898},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5071127414703369},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.48111146688461304},{"id":"https://openalex.org/keywords/sketch","display_name":"Sketch","score":0.4658221900463104},{"id":"https://openalex.org/keywords/computational-semantics","display_name":"Computational semantics","score":0.43944051861763},{"id":"https://openalex.org/keywords/cognitive-science","display_name":"Cognitive science","score":0.3946845531463623},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3926295042037964},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39057186245918274},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.17393580079078674},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17391744256019592},{"id":"https://openalex.org/keywords/operational-semantics","display_name":"Operational semantics","score":0.166974276304245},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.1484072208404541},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10937952995300293}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7036924362182617},{"id":"https://openalex.org/C2780876879","wikidata":"https://www.wikidata.org/wiki/Q3054749","display_name":"Meaning (existential)","level":2,"score":0.652752161026001},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.5995568037033081},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5940515995025635},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.5286626815795898},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5071127414703369},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.48111146688461304},{"id":"https://openalex.org/C2779231336","wikidata":"https://www.wikidata.org/wiki/Q7534724","display_name":"Sketch","level":2,"score":0.4658221900463104},{"id":"https://openalex.org/C200065993","wikidata":"https://www.wikidata.org/wiki/Q3954981","display_name":"Computational semantics","level":4,"score":0.43944051861763},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.3946845531463623},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3926295042037964},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39057186245918274},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.17393580079078674},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17391744256019592},{"id":"https://openalex.org/C156325763","wikidata":"https://www.wikidata.org/wiki/Q1930895","display_name":"Operational semantics","level":3,"score":0.166974276304245},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.1484072208404541},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10937952995300293},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-7-43","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-43","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-43","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:23721297","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23721297","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:europepmc.org:2713088","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3716781","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-7-43","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-7-43","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-7-43","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":[{"id":"https://openalex.org/G2258784989","display_name":null,"funder_award_id":"SPP 1395","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2773049710","display_name":null,"funder_award_id":"12038-514","funder_id":"https://openalex.org/F4320322621","funder_display_name":"Th\u00fcringer Ministerium f\u00fcr Bildung, Wissenschaft und Kultur"},{"id":"https://openalex.org/G3633743130","display_name":null,"funder_award_id":"SPP 1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5374402718","display_name":null,"funder_award_id":"DI 852/10-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5753548785","display_name":null,"funder_award_id":"BBS/E/B/000C0419","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G730969003","display_name":null,"funder_award_id":"BB/F010516/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320322145","display_name":"Ministerul Educa\u0163iei Na\u0163ionale","ror":"https://ror.org/00dh5gw98"},{"id":"https://openalex.org/F4320322621","display_name":"Th\u00fcringer Ministerium f\u00fcr Bildung, Wissenschaft und Kultur","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324438","display_name":"Rosa Luxemburg Stiftung","ror":"https://ror.org/0089t7988"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2073061263.pdf","grobid_xml":"https://content.openalex.org/works/W2073061263.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1566102697","https://openalex.org/W1570740602","https://openalex.org/W1589685702","https://openalex.org/W1597538863","https://openalex.org/W1606860353","https://openalex.org/W1608590154","https://openalex.org/W1733489975","https://openalex.org/W1757909678","https://openalex.org/W1788939232","https://openalex.org/W1970846593","https://openalex.org/W1980587508","https://openalex.org/W1986397618","https://openalex.org/W1989263028","https://openalex.org/W1991319904","https://openalex.org/W1996195324","https://openalex.org/W2001598892","https://openalex.org/W2003871372","https://openalex.org/W2045808901","https://openalex.org/W2049445311","https://openalex.org/W2090469206","https://openalex.org/W2091579301","https://openalex.org/W2096525273","https://openalex.org/W2097971625","https://openalex.org/W2107062718","https://openalex.org/W2122529434","https://openalex.org/W2128763542","https://openalex.org/W2137665890","https://openalex.org/W2139504329","https://openalex.org/W2143784594","https://openalex.org/W2145435867","https://openalex.org/W2150908245","https://openalex.org/W2154139219","https://openalex.org/W2156094678","https://openalex.org/W2157092888","https://openalex.org/W2167786318","https://openalex.org/W2170122529","https://openalex.org/W2757307321","https://openalex.org/W2913459036","https://openalex.org/W3215028400","https://openalex.org/W4246066782"],"related_works":["https://openalex.org/W2381894824","https://openalex.org/W2109668579","https://openalex.org/W2074638034","https://openalex.org/W2106631548","https://openalex.org/W2094744827","https://openalex.org/W2952204366","https://openalex.org/W4294365771","https://openalex.org/W2987318680","https://openalex.org/W4206266203","https://openalex.org/W4206931494"],"abstract_inverted_index":{"The":[0,61],"meaning":[1],"facets":[2],"framework":[3,48,64],"provides":[4],"a":[5,50,66,76],"systematic":[6],"in-depth":[7],"approach":[8],"to":[9,30],"the":[10,25,47],"semantics":[11],"of":[12,56],"bio-models.":[13],"It":[14],"can":[15,44],"serve":[16],"two":[17],"important":[18],"purposes:":[19],"First,":[20],"it":[21,43],"specifies":[22],"and":[23,38,74],"structures":[24],"information":[26],"which":[27],"biologists":[28],"have":[29],"take":[31],"into":[32],"account":[33],"if":[34],"they":[35],"build,":[36],"use":[37],"exchange":[39],"models.":[40],"Secondly,":[41],"because":[42],"be":[45],"formalised,":[46],"is":[49],"solid":[51],"foundation":[52],"for":[53,69,78],"any":[54],"sort":[55],"computer":[57],"support":[58],"in":[59,71],"bio-modelling.":[60],"proposed":[62],"conceptual":[63],"establishes":[65],"new":[67],"methodology":[68],"modelling":[70],"Systems":[72],"Biology":[73],"constitutes":[75],"basis":[77],"computer-aided":[79],"collaborative":[80],"research.":[81]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
