{"id":"https://openalex.org/W2103563062","doi":"https://doi.org/10.1093/bioinformatics/bti018","title":"Simulation tools for biochemical networks: evaluation of performance and usability","display_name":"Simulation tools for biochemical networks: evaluation of performance and usability","publication_year":2004,"publication_date":"2004-09-10","ids":{"openalex":"https://openalex.org/W2103563062","doi":"https://doi.org/10.1093/bioinformatics/bti018","mag":"2103563062","pmid":"https://pubmed.ncbi.nlm.nih.gov/15358616"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/3/357/653749/bti018.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/21/3/357/653749/bti018.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048589959","display_name":"Antti Pettinen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Antti Pettinen","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046641062","display_name":"Tommi Aho","orcid":"https://orcid.org/0000-0003-3818-2623"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tommi Aho","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076316712","display_name":"Olli\u2010Pekka Smolander","orcid":"https://orcid.org/0000-0002-6795-7734"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Olli-Pekka Smolander","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037580924","display_name":"Tiina Manninen","orcid":"https://orcid.org/0000-0002-0456-1185"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tiina Manninen","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103818960","display_name":"Antti Saarinen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antti Saarinen","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004805771","display_name":"Kaisa-Leena Taattola","orcid":null},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Kaisa-Leena Taattola","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026230936","display_name":"Olli Yli\u2010Harja","orcid":"https://orcid.org/0000-0001-8581-4414"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Olli Yli-Harja","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008868538","display_name":"Marja\u2010Leena Linne","orcid":"https://orcid.org/0000-0003-2577-7329"},"institutions":[{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Marja-Leena Linne","raw_affiliation_strings":["Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland","institution_ids":["https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Institute of Signal Processing, Tampere University of Technology P.O. Box 553, 33101 Tampere, Finland#TAB#","institution_ids":["https://openalex.org/I4210133110"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048589959"],"corresponding_institution_ids":["https://openalex.org/I4210133110"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.625,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.8986858,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"3","first_page":"357","last_page":"363"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9240999817848206,"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":0.9240999817848206,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.010300000198185444,"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":0.008899999782443047,"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/usability","display_name":"Usability","score":0.8581176400184631},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7273461222648621},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.37888383865356445},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.3619169592857361}],"concepts":[{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.8581176400184631},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7273461222648621},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.37888383865356445},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3619169592857361}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012986","descriptor_name":"Software Validation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/3/357/653749/bti018.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:15358616","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15358616","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":"Comparative Study"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.108.6407","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.108.6407","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/bti018v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti018","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/3/357/653749/bti018.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/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103563062.pdf","grobid_xml":"https://content.openalex.org/works/W2103563062.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1502029496","https://openalex.org/W1507113656","https://openalex.org/W1797216850","https://openalex.org/W1963861745","https://openalex.org/W1964287788","https://openalex.org/W1982258483","https://openalex.org/W1999866856","https://openalex.org/W2044889656","https://openalex.org/W2049445311","https://openalex.org/W2049511526","https://openalex.org/W2071007053","https://openalex.org/W2072670807","https://openalex.org/W2117453669","https://openalex.org/W2131067724","https://openalex.org/W2133667940","https://openalex.org/W2145077980","https://openalex.org/W2150908245","https://openalex.org/W2152274602","https://openalex.org/W2158691076","https://openalex.org/W2164055371","https://openalex.org/W2171001939","https://openalex.org/W2496576080"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4389670110","https://openalex.org/W2187546663","https://openalex.org/W2429057255","https://openalex.org/W148745890","https://openalex.org/W2611942503","https://openalex.org/W2899790217","https://openalex.org/W1576092969","https://openalex.org/W4315621326","https://openalex.org/W2598865957"],"abstract_inverted_index":{"MOTIVATION:":[0],"Simulation":[1],"of":[2,14,17,30,33,48,52,57,83,89,107,111,152],"dynamic":[3],"biochemical":[4,84],"systems":[5],"is":[6],"receiving":[7],"considerable":[8],"attention":[9],"due":[10],"to":[11,139,160],"increasing":[12],"availability":[13],"experimental":[15,69],"data":[16,137],"complex":[18],"cellular":[19],"functions.":[20],"Numerous":[21],"simulation":[22,29,59,75,82,119,126],"tools":[23,60,76,130],"have":[24],"been":[25],"developed":[26],"for":[27,80,91,136,144],"numerical":[28],"the":[31,53,58,81,105,108,118,124,129,149,164],"behavior":[32],"a":[34,44,101],"system":[35],"described":[36],"in":[37,64,132,163],"mathematical":[38],"form.":[39],"However,":[40,128],"there":[41],"exist":[42],"only":[43],"few":[45],"evaluation":[46],"studies":[47],"these":[49,155],"tools.":[50,127],"Knowledge":[51],"properties":[54,157],"and":[55,95,142],"capabilities":[56],"would":[61],"help":[62],"bioscientists":[63],"building":[65],"models":[66],"based":[67],"on":[68],"data.":[70],"RESULTS:":[71],"We":[72,86,115],"examine":[73],"selected":[74],"that":[77,117,158],"are":[78,121,156],"intended":[79],"systems.":[85],"choose":[87],"four":[88],"them":[90],"more":[92],"detailed":[93],"study":[94],"perform":[96],"time":[97],"series":[98],"simulations":[99],"using":[100],"specific":[102],"pathway":[103],"describing":[104],"concentration":[106],"active":[109],"form":[110],"protein":[112],"kinase":[113],"C.":[114],"conclude":[116],"results":[120],"convergent":[122],"between":[123],"chosen":[125],"differ":[131],"their":[133],"usability,":[134],"support":[135,143],"transfer":[138],"other":[140],"programs":[141],"automatic":[145],"parameter":[146],"estimation.":[147],"From":[148],"experimentalists'":[150],"point":[151],"view,":[153],"all":[154],"need":[159],"be":[161],"emphasized":[162],"future.":[165]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}