Integration of SBML models for the description of biological system in a lab-on-chip

Abstract

Lab-on-chips (LOCs) are small systems, which integrate, in the same device, several functions involving chemical analysis with bio-processing functionalities typically performed in a laboratory. As a consequence, it is a multi-domain system that can be described and designed with VHDL-AMS, a hardware description language that natively supports electronics, thermics and fluidics. On the other hand, the biological part of the LOC is often modeled and simulated with languages suitable to the field of biology. One of the most commonly used ones is SBML (System Biology Markup Language). To promote the integration of biological parts of the LOCs in the VHDL-AMS environment, we have developed software that automatically generates the VHDL-AMS models from SBML descriptions. The potential of this tool is illustrated in the context of the design of the lab-on-chip suitable for the detection of micro-pollutants in drinking water.

Application à la biologie synthétique des méthodes et outils de CAO de la microélectronique

“…Un outil de traduction de modèle, développé dans le langage Java, assure le passage d'un langage à l'autre [44]. La description SBML pouvant elle-même être générée à partir d'un outil graphique (comme Virtual Cell), nous obtenons donc une suite logicielle complète, allant de la saisie du schéma biologique à sa simulation.…”