{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:04:42Z","timestamp":1762898682007},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1992,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: CytoModeler is an open-source Java application based on the Cytoscape platform. It integrates large-scale network analysis and quantitative modeling by combining omics analysis on the Cytoscape platform, access to deterministic and stochastic simulators, and static and dynamic network context visualizations of simulation results.<\/jats:p>\n               <jats:p>Availability: Implemented in Java, CytoModeler runs with Cytoscape 2.6 and 2.7. Binaries, documentation and video walkthroughs are freely available at http:\/\/vrac.iastate.edu\/~jlv\/cytomodeler\/.<\/jats:p>\n               <jats:p>Contact: \u00a0julied@iastate.edu; netscape@iastate.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr150","type":"journal-article","created":{"date-parts":[[2011,4,22]],"date-time":"2011-04-22T00:25:05Z","timestamp":1303431905000},"page":"1578-1580","source":"Crossref","is-referenced-by-count":1,"title":["CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling"],"prefix":"10.1093","volume":"27","author":[{"given":"Tian","family":"Xia","sequence":"first","affiliation":[{"name":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Van Hemert","sequence":"additional","affiliation":[{"name":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie A.","family":"Dickerson","sequence":"additional","affiliation":[{"name":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"},{"name":"1 Program of Bioinformatics and Computational Biology and 2Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,4,20]]},"reference":[{"key":"2023012511153133300_B1","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1126\/science.292.5518.929","article-title":"Integrated genomic and proteomic analyses of a systematically perturbed metabolic network","volume":"292","author":"Ideker","year":"2001","journal-title":"Science"},{"key":"2023012511153133300_B2","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nrm2002","article-title":"SNAREs\u2013engines for membrane fusion","volume":"7","author":"Jahn","year":"2006","journal-title":"Nat. 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