{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T17:53:18Z","timestamp":1770832398702,"version":"3.50.1"},"reference-count":20,"publisher":"World Scientific Pub Co Pte Lt","issue":"01","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,2]]},"abstract":"<jats:p> In the systems biology field, algorithms for structural identification of ordinary differential equations (ODEs) have mainly focused on fixed model spaces like S-systems and\/or on methods that require sufficiently good data so that derivatives can be accurately estimated. There is therefore a lack of methods and software that can handle more general models and realistic data. <\/jats:p><jats:p> We present ODEion, a software module for structural identification of ODEs. Main characteristic features of the software are: <\/jats:p><jats:p> \u2022 The model space is defined by arbitrary user-defined functions that can be nonlinear in both variables and parameters, such as for example chemical rate reactions. <\/jats:p><jats:p> \u2022 ODEion implements computationally efficient algorithms that have been shown to efficiently handle sparse and noisy data. It can run a range of realistic problems that previously required a supercomputer. <\/jats:p><jats:p> \u2022 ODEion is easy to use and provides SBML output. <\/jats:p><jats:p> We describe the mathematical problem, the ODEion system itself, and provide several examples of how the system can be used. <\/jats:p><jats:p> Available at: http:\/\/www.odeidentification.org . <\/jats:p>","DOI":"10.1142\/s0219720013500157","type":"journal-article","created":{"date-parts":[[2013,9,24]],"date-time":"2013-09-24T07:15:17Z","timestamp":1380006917000},"page":"1350015","source":"Crossref","is-referenced-by-count":5,"title":["ODEion \u2014 A SOFTWARE MODULE FOR STRUCTURAL IDENTIFICATION OF ORDINARY DIFFERENTIAL EQUATIONS"],"prefix":"10.1142","volume":"12","author":[{"given":"PETER","family":"GENNEMARK","sequence":"first","affiliation":[{"name":"Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden"},{"name":"Department of Mathematics, Uppsala University, Uppsala, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"DAG","family":"WEDELIN","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Chalmers University of Technology, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2014,1,28]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp050"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1049\/iet-syb:20050098"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0609476104"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1126\/science.1165893"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1088\/1478-3975\/8\/5\/055011"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2006-7-5-r36"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0014791"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-6-84"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg015"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(94)80516-8"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1021\/j100003a020"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti071"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1049\/iet-syb:20060064"},{"key":"rf17","volume-title":"Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology","author":"Savageau M. 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