{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T02:20:20Z","timestamp":1779330020905,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Modelers naturally build large models from smaller components that each represent subsets of reactions within the larger network. To assist modelers in this process, we present model aggregation, which defines models in terms of components that are designed for the purpose of being combined.<\/jats:p>\n               <jats:p>Results: We have implemented a model editor that incorporates model aggregation, and we suggest supporting extensions to the Systems Biology Markup Language (SBML) Level 3. We illustrate aggregation with a model of the eukaryotic cell cycle \u2018engine\u2019 created from smaller pieces.<\/jats:p>\n               <jats:p>Availability: Java implementations are available in the JigCell Aggregation Connector. See http:\/\/jigcell.biol.vt.edu.<\/jats:p>\n               <jats:p>Contact: \u00a0shaffer@vt.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp581","type":"journal-article","created":{"date-parts":[[2009,10,31]],"date-time":"2009-10-31T00:13:10Z","timestamp":1256947990000},"page":"3289-3295","source":"Crossref","is-referenced-by-count":12,"title":["Model aggregation: a building-block approach to creating large macromolecular regulatory networks"],"prefix":"10.1093","volume":"25","author":[{"given":"Ranjit","family":"Randhawa","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and 2Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clifford A.","family":"Shaffer","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and 2Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John J.","family":"Tyson","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and 2Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,10,29]]},"reference":[{"key":"2023013112143653200_B1","first-page":"183","article-title":"The potential coupling interface: Metadata for model coupling","volume-title":"Proceedings of the 2004 Winter Simulation Conference","author":"Bulatewicz","year":"2004"},{"key":"2023013112143653200_B2","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1063\/1.1778376","article-title":"Efficient formulation of the stochastic simulation algorithm for chemically reacting systems","volume":"121","author":"Cao","year":"2004","journal-title":"J. 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