title: BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  METHODS
  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/.
authors.affiliation: SysDiag UMR 3145 CNRS/Bio-Rad, Modélisation et ingénierie de systèmes complexes biologiques pour le diagnostic, Cap Delta/Parc Euromédecine, Montpellier, France. stephanie.rialle@sysdiag.cnrs.fr
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Rialle
authors.forename: Liza
authors.initials: L
authors.lastname: Felicori
authors.forename: Camila
authors.initials: C
authors.lastname: Dias-Lopes
authors.forename: Sabine
authors.initials: S
authors.lastname: Pérès
authors.forename: Sanaâ
authors.initials: S
authors.lastname: El Atia
authors.forename: Alain R
authors.initials: AR
authors.lastname: Thierry
authors.forename: Patrick
authors.initials: P
authors.lastname: Amar
authors.forename: Franck
authors.initials: F
authors.lastname: Molina
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D017076:Computer-Aided Design; D016208:Databases, Factual; D008954:Models, Biological; D011381:Programming Languages; D014176:Protein Biosynthesis; D011506:Proteins; D012984:Software; D049490:Systems Biology / Q000379:methods*
chemical_list: D011506:Proteins