EDA inspired Open-source Framework for Synthetic Biology

The topic of this paper is to develop an open-source framework to help bio-engineers through the different stages of a top-down design process for new artificial biosystems (synthetic biology). The presented tools address the upstream stages of the design, starting from a high-level behavioral description of the targeted biological function and ending with a working assembly of abstract BioBricks performing that very function. For that purpose, EDA (Electronic Design Automation) tools are indeed adapted to synthetic biology. The framework involves three main steps: the interpretation of the high-level description into a netlist of logical functions, the optimization of the netlist with respect to BioBricks capabilities and the automated generation of a SystemC-AMS abstracted simulatable netlist that can be used for further analysis (low-level simulation, optimization ... ). Throughout the paper, each stage of the framework is detailed and illustrated with a simple (from a logical point of view) but complex (from the biological viewpoint) example: an in-vivo chemical species regulation system.