{"id":"https://openalex.org/W2146212356","doi":"https://doi.org/10.1093/bioinformatics/btg009","title":"Modeling biological systems using Dynetica\u2014a simulator of dynamic networks","display_name":"Modeling biological systems using Dynetica\u2014a simulator of dynamic networks","publication_year":2003,"publication_date":"2003-02-12","ids":{"openalex":"https://openalex.org/W2146212356","doi":"https://doi.org/10.1093/bioinformatics/btg009","mag":"2146212356","pmid":"https://pubmed.ncbi.nlm.nih.gov/12584138"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/435/718313/btg009.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/19/3/435/718313/btg009.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100401842","display_name":"Lingchong You","orcid":"https://orcid.org/0000-0003-3725-4007"},"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"]},{"id":"https://openalex.org/I4210110509","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210110509","https://openalex.org/I4210112577"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lingchong You","raw_affiliation_strings":["Division of Chemistry and Chemical Engineering, California Institute of Technology, USA","Division of Chemistry and Chemical Engineering, California Institute of Technology,,USA"],"affiliations":[{"raw_affiliation_string":"Division of Chemistry and Chemical Engineering, California Institute of Technology, USA","institution_ids":["https://openalex.org/I122411786","https://openalex.org/I4210110509"]},{"raw_affiliation_string":"Division of Chemistry and Chemical Engineering, California Institute of Technology,,USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014020830","display_name":"Apirak Hoonlor","orcid":"https://orcid.org/0000-0003-3133-652X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Apirak Hoonlor","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5048926506","display_name":"John Yin","orcid":"https://orcid.org/0000-0001-6146-0594"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"John Yin","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100401842"],"corresponding_institution_ids":["https://openalex.org/I122411786","https://openalex.org/I4210110509"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2582,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.78561531,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"3","first_page":"435","last_page":"436"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994999766349792,"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":0.9979000091552734,"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":0.7401363849639893},{"id":"https://openalex.org/keywords/user-friendly","display_name":"User Friendly","score":0.5029532313346863},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.45861437916755676},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.4519377648830414},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.40993204712867737},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.159559965133667},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14673203229904175},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07689669728279114},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07448622584342957}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7401363849639893},{"id":"https://openalex.org/C61437842","wikidata":"https://www.wikidata.org/wiki/Q281291","display_name":"User Friendly","level":2,"score":0.5029532313346863},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.45861437916755676},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.4519377648830414},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.40993204712867737},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.159559965133667},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14673203229904175},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07689669728279114},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07448622584342957},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btg009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/435/718313/btg009.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:12584138","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12584138","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:91758","is_oa":false,"landing_page_url":"https://authors.library.caltech.edu/91758/","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:10.1.1.542.1545","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.542.1545","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://yin.che.wisc.edu/images/publications/You1_2003a.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/3/435/718313/btg009.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":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146212356.pdf","grobid_xml":"https://content.openalex.org/works/W2146212356.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W101295507","https://openalex.org/W133158124","https://openalex.org/W1571919379","https://openalex.org/W1573602524","https://openalex.org/W1575619134","https://openalex.org/W1593308984","https://openalex.org/W1597762351","https://openalex.org/W1606784130","https://openalex.org/W1623155147","https://openalex.org/W1637936532","https://openalex.org/W1758395617","https://openalex.org/W1946177469","https://openalex.org/W1963861745","https://openalex.org/W1964287788","https://openalex.org/W1979565917","https://openalex.org/W1980570931","https://openalex.org/W1980717706","https://openalex.org/W1984886691","https://openalex.org/W1984902072","https://openalex.org/W1987129107","https://openalex.org/W1987220754","https://openalex.org/W1996791690","https://openalex.org/W1997766064","https://openalex.org/W1999866856","https://openalex.org/W1999908691","https://openalex.org/W2010245177","https://openalex.org/W2022907226","https://openalex.org/W2023574837","https://openalex.org/W2024797223","https://openalex.org/W2024963167","https://openalex.org/W2031369606","https://openalex.org/W2038883764","https://openalex.org/W2040155656","https://openalex.org/W2040280990","https://openalex.org/W2040890820","https://openalex.org/W2046538693","https://openalex.org/W2049445311","https://openalex.org/W2055122486","https://openalex.org/W2056313562","https://openalex.org/W2074743596","https://openalex.org/W2076659465","https://openalex.org/W2079445816","https://openalex.org/W2099269203","https://openalex.org/W2099798492","https://openalex.org/W2104855667","https://openalex.org/W2105640293","https://openalex.org/W2117056464","https://openalex.org/W2117857836","https://openalex.org/W2125345482","https://openalex.org/W2125820659","https://openalex.org/W2131067724","https://openalex.org/W2143435210","https://openalex.org/W2144091871","https://openalex.org/W2151235051","https://openalex.org/W2155418451","https://openalex.org/W2166633151","https://openalex.org/W2168518074","https://openalex.org/W2171445530","https://openalex.org/W2177381833","https://openalex.org/W2912848477"],"related_works":["https://openalex.org/W4245655816","https://openalex.org/W47675725","https://openalex.org/W2883882445","https://openalex.org/W2180210828","https://openalex.org/W2065381022","https://openalex.org/W1538500885","https://openalex.org/W2046207696","https://openalex.org/W2753099643","https://openalex.org/W2224473603","https://openalex.org/W2146212356"],"abstract_inverted_index":{"Dynetica":[0],"1.0,":[1],"example":[2],"models,":[3],"and":[4],"the":[5],"user's":[6],"guide":[7],"are":[8],"available":[9],"at":[10],"http://www.its.caltech.edu/~you/Dynetica/Dynetica_page.htm":[11]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
