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Bioinformatics. 2010 Sep 15;26(18):2298-304. doi: 10.1093/bioinformatics/btq409. Epub 2010 Jul 13.

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

Author information

1
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

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/.

PMID:
20628073
PMCID:
PMC2935418
DOI:
10.1093/bioinformatics/btq409
[Indexed for MEDLINE]
Free PMC Article
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