BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks - Archive ouverte HAL
Article Dans Une Revue Bioinformatics Année : 2010

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

Stéphanie Rialle
  • Fonction : Auteur
Liza Felicori
  • Fonction : Auteur
Camila Dias-Lopes
  • Fonction : Auteur
Sanaâ El Atia
  • Fonction : Auteur
Alain Thierry
  • Fonction : Auteur
Patrick Amar
  • Fonction : Auteur
Franck Molina
  • Fonction : Auteur

Résumé

Abstract 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. 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. 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/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Dates et versions

hal-04814810 , version 1 (02-12-2024)

Identifiants

Citer

Stéphanie Rialle, Liza Felicori, Camila Dias-Lopes, Sabine Peres, Sanaâ El Atia, et al.. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. Bioinformatics, 2010, 26 (18), pp.2298-2304. ⟨10.1093/bioinformatics/btq409⟩. ⟨hal-04814810⟩

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