{"id":"https://openalex.org/W2166024359","doi":"https://doi.org/10.1093/bioinformatics/btr150","title":"CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling","display_name":"CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling","publication_year":2011,"publication_date":"2011-04-20","ids":{"openalex":"https://openalex.org/W2166024359","doi":"https://doi.org/10.1093/bioinformatics/btr150","mag":"2166024359","pmid":"https://pubmed.ncbi.nlm.nih.gov/21511714"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr150","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1578/48862558/bioinformatics_27_11_1578.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1578/48862558/bioinformatics_27_11_1578.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054677999","display_name":"Tian Xia","orcid":"https://orcid.org/0000-0002-0097-6949"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tian Xia","raw_affiliation_strings":["1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039760954","display_name":"John Van Hemert","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Van Hemert","raw_affiliation_strings":["1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077949687","display_name":"Julie Dickerson","orcid":"https://orcid.org/0000-0003-4973-5641"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julie A. Dickerson","raw_affiliation_strings":["1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054677999","https://openalex.org/A5077949687"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.13826632,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"27","issue":"11","first_page":"1578","last_page":"1580"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9962000250816345,"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":0.9962000250816345,"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":0.9954000115394592,"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":0.9538000226020813,"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/java","display_name":"Java","score":0.8419485092163086},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7964749336242676},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.6836870312690735},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6191706657409668},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5704447031021118},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.48911410570144653},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.44438958168029785},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4423847794532776},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4418324828147888},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4049069881439209},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3553500771522522},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32677412033081055},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.30064111948013306}],"concepts":[{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.8419485092163086},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7964749336242676},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.6836870312690735},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6191706657409668},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5704447031021118},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.48911410570144653},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.44438958168029785},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4423847794532776},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4418324828147888},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4049069881439209},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3553500771522522},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32677412033081055},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30064111948013306},{"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"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":"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":"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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr150","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1578/48862558/bioinformatics_27_11_1578.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21511714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21511714","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:open-archive.highwire.org:bioinfo:27/11/1578","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/11/1578","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3102219","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3102219","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr150","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr150","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1578/48862558/bioinformatics_27_11_1578.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5466941899","display_name":"(SEI+II (BIO)) Interactive Visualization and Analysis of Large-Scale Graphs for Biological Network Modeling","funder_award_id":"0612240","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6658813440","display_name":"NSF Engineering Reasearch Center for Biorenewable Chemicals (CBiRC)","funder_award_id":"0813570","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8774199850","display_name":null,"funder_award_id":"EEC-0813570","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166024359.pdf","grobid_xml":"https://content.openalex.org/works/W2166024359.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1495660511","https://openalex.org/W2000302106","https://openalex.org/W2018766909","https://openalex.org/W2100519678","https://openalex.org/W2101462174","https://openalex.org/W2115343689","https://openalex.org/W2159675211","https://openalex.org/W2168846334"],"related_works":["https://openalex.org/W4388870064","https://openalex.org/W4235186151","https://openalex.org/W2056057048","https://openalex.org/W2054685365","https://openalex.org/W2272354214","https://openalex.org/W2120383820","https://openalex.org/W2043010663","https://openalex.org/W2667588871","https://openalex.org/W4248308508","https://openalex.org/W1964405022"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"CytoModeler":[2,49],"is":[3],"an":[4],"open-source":[5],"Java":[6],"application":[7],"based":[8],"on":[9,25],"the":[10,26],"Cytoscape":[11,27,52],"platform.":[12],"It":[13],"integrates":[14],"large-scale":[15],"network":[16,39],"analysis":[17,24],"and":[18,32,35,37,54,58],"quantitative":[19],"modeling":[20],"by":[21],"combining":[22],"omics":[23],"platform,":[28],"access":[29],"to":[30],"deterministic":[31],"stochastic":[33],"simulators,":[34],"static":[36],"dynamic":[38],"context":[40],"visualizations":[41],"of":[42],"simulation":[43],"results.":[44],"Availability:":[45],"Implemented":[46],"in":[47],"Java,":[48],"runs":[50],"with":[51],"2.6":[53],"2.7.":[55],"Binaries,":[56],"documentation":[57],"video":[59],"walkthroughs":[60],"are":[61,73],"freely":[62],"available":[63,74],"at":[64,75],"http://vrac.iastate.edu/~jlv/cytomodeler/.":[65],"Contact:":[66],"julied@iastate.edu;":[67],"netscape@iastate.edu":[68],"Supplementary":[69,71],"Information:":[70],"data":[72],"Bioinformatics":[76],"online.":[77]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
