{"id":"https://openalex.org/W2117589890","doi":"https://doi.org/10.1093/bioinformatics/btp451","title":"Accessible methods for the dynamic time-scale decomposition of biochemical systems","display_name":"Accessible methods for the dynamic time-scale decomposition of biochemical systems","publication_year":2009,"publication_date":"2009-07-24","ids":{"openalex":"https://openalex.org/W2117589890","doi":"https://doi.org/10.1093/bioinformatics/btp451","mag":"2117589890","pmid":"https://pubmed.ncbi.nlm.nih.gov/19633098"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp451","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp451","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2816/48997194/bioinformatics_25_21_2816.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/25/21/2816/48997194/bioinformatics_25_21_2816.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048671973","display_name":"Irina Surovtsova","orcid":"https://orcid.org/0009-0003-4263-6250"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Irina Surovtsova","raw_affiliation_strings":["1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030791830","display_name":"Natalia Simus","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Natalia Simus","raw_affiliation_strings":["1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082301038","display_name":"Thomas Lorenz","orcid":"https://orcid.org/0000-0001-7000-8030"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Lorenz","raw_affiliation_strings":["1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048301373","display_name":"Artjom K\u00f6nig","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Artjom K\u00f6nig","raw_affiliation_strings":["1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111964760","display_name":"Sven Sahle","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sven Sahle","raw_affiliation_strings":["1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036398559","display_name":"Ursula Kummer","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ursula Kummer","raw_affiliation_strings":["1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Modeling of Biological Processes and 2 Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048671973"],"corresponding_institution_ids":["https://openalex.org/I223822909"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0048,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.74886622,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"21","first_page":"2816","last_page":"2823"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.4293000102043152,"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":0.4293000102043152,"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":0.3702999949455261,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.04910000041127205,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8407477140426636},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.7340772151947021},{"id":"https://openalex.org/keywords/clarity","display_name":"CLARITY","score":0.6959716081619263},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5825615525245667},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5600919127464294},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5470318794250488},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5329675674438477},{"id":"https://openalex.org/keywords/decomposition","display_name":"Decomposition","score":0.4444340765476227},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3716908097267151},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.370200514793396},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14193174242973328}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8407477140426636},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.7340772151947021},{"id":"https://openalex.org/C2777146004","wikidata":"https://www.wikidata.org/wiki/Q14949826","display_name":"CLARITY","level":2,"score":0.6959716081619263},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5825615525245667},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5600919127464294},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5470318794250488},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5329675674438477},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.4444340765476227},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3716908097267151},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.370200514793396},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14193174242973328},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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":"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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp451","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp451","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2816/48997194/bioinformatics_25_21_2816.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:19633098","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19633098","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp451","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp451","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/21/2816/48997194/bioinformatics_25_21_2816.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324316","display_name":"Klaus Tschira Stiftung","ror":"https://ror.org/052jep661"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117589890.pdf","grobid_xml":"https://content.openalex.org/works/W2117589890.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W240980843","https://openalex.org/W580923904","https://openalex.org/W1511267714","https://openalex.org/W1525349614","https://openalex.org/W1550716269","https://openalex.org/W1571781160","https://openalex.org/W1587845087","https://openalex.org/W1598576131","https://openalex.org/W1873506857","https://openalex.org/W1998995074","https://openalex.org/W2014807395","https://openalex.org/W2021918227","https://openalex.org/W2022440628","https://openalex.org/W2044431968","https://openalex.org/W2044484168","https://openalex.org/W2051755619","https://openalex.org/W2060925158","https://openalex.org/W2080009899","https://openalex.org/W2102653059","https://openalex.org/W2122407999","https://openalex.org/W2137818200","https://openalex.org/W2141906015","https://openalex.org/W2166927282","https://openalex.org/W2798909945","https://openalex.org/W3146102563","https://openalex.org/W6630484808","https://openalex.org/W6635733134","https://openalex.org/W7009171728"],"related_works":["https://openalex.org/W2086338133","https://openalex.org/W4367679314","https://openalex.org/W225526533","https://openalex.org/W2078361494","https://openalex.org/W2009234990","https://openalex.org/W4244083766","https://openalex.org/W2091016074","https://openalex.org/W2023583523","https://openalex.org/W2134615400","https://openalex.org/W26869551"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,98,112],"growing":[2],"complexity":[3],"of":[4,27,38,48,51,69,73,106],"biochemical":[5],"models":[6],"asks":[7],"for":[8,35,89,103,121],"means":[9],"to":[10,57],"rationally":[11],"dissect":[12],"the":[13,28,36,46,49,52,70,82,93,104,107],"networks":[14],"into":[15],"meaningful":[16],"and":[17,45,124],"rather":[18],"independent":[19],"subnetworks.":[20],"Such":[21],"foregoing":[22],"should":[23],"ensure":[24],"an":[25,40],"understanding":[26],"system":[29],"without":[30],"any":[31],"heuristics":[32],"employed.":[33],"Important":[34],"success":[37],"such":[39],"approach":[41,72,85],"is":[42,66,119],"its":[43],"accessibility":[44],"clarity":[47],"presentation":[50],"results.":[53],"RESULTS:":[54],"In":[55],"order":[56],"achieve":[58],"this":[59],"goal,":[60],"we":[61],"developed":[62],"a":[63,67],"method":[64,78],"which":[65,118],"modification":[68],"classical":[71,84],"time-scale":[74],"separation.":[75],"This":[76],"modified":[77],"as":[79,81],"well":[80],"more":[83],"have":[86],"been":[87],"implemented":[88],"time-dependent":[90],"application":[91],"within":[92],"widely":[94],"used":[95],"software":[96],"COPASI.":[97],"implementation":[99],"includes":[100],"different":[101],"possibilities":[102],"representation":[105],"results":[108],"including":[109],"3D-visualization.":[110],"AVAILABILITY:":[111],"methods":[113],"are":[114,134],"included":[115],"in":[116],"COPASI":[117],"free":[120],"academic":[122],"use":[123],"available":[125,135],"at":[126,136],"www.copasi.org.":[127],"CONTACT:":[128],"irina.surovtsova@bioquant.uni-heidelberg.de":[129],"SUPPLEMENTARY":[130],"INFORMATION:":[131],"Supplementary":[132],"data":[133],"Bioinformatics":[137],"online.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-08-19T15:00:24.278416","created_date":"2025-10-10T00:00:00"}