{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T13:15:08Z","timestamp":1770902108636,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2273,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks.<\/jats:p>\n               <jats:p>Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network.<\/jats:p>\n               <jats:p>Availability and implementation: BioNetCAD is freely available at http:\/\/www.sysdiag.cnrs.fr\/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http:\/\/compubiotic.sysdiag.cnrs.fr\/<\/jats:p>\n               <jats:p>Contact: \u00a0stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq409","type":"journal-article","created":{"date-parts":[[2010,7,14]],"date-time":"2010-07-14T02:24:06Z","timestamp":1279074246000},"page":"2298-2304","source":"Crossref","is-referenced-by-count":16,"title":["BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks"],"prefix":"10.1093","volume":"26","author":[{"given":"St\u00e9phanie","family":"Rialle","sequence":"first","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liza","family":"Felicori","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camila","family":"Dias-Lopes","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabine","family":"P\u00e9r\u00e8s","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sana\u00e2","family":"El Atia","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alain R.","family":"Thierry","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Amar","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Franck","family":"Molina","sequence":"additional","affiliation":[{"name":"1 SysDiag UMR 3145 CNRS\/Bio-Rad, Mod\u00e9lisation et ing\u00e9nierie de syst\u00e8mes complexes biologiques pour le diagnostic, Cap Delta\/Parc Eurom\u00e9decine, 1682 rue de la Valsi\u00e8re, CS 61003, 34184 Montpellier Cedex 4 and 2Laboratoire de Recherche en Informatique, CNRS, UMR 8623, Universit\u00e9 Paris-Sud 11, 91405 Orsay Cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,7,13]]},"reference":[{"key":"2023012508205549200_B1","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/1752-0509-2-27","article-title":"A stochastic automaton shows how enzyme assemblies may contribute to metabolic 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