Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1109/BioCAS.2013.6679717 | Biomedical Circuits and Systems Conference |
Keywords | Field | DocType |
biomedical electronics,biomedical engineering,biomimetics,electronic design automation,optimisation,public domain software,eda inspired open-source framework,abstract biobricks database,artificial biosystems,bioengineers,electronic design automation tools,in-vivo chemical species regulation system,logical functions,low-level simulation,netlist optimization,synthetic biology,targeted biological function,top-down design process | Netlist,Software engineering,Computer science,Biomimetics,Electronic engineering,Electronic design automation,Design process,Electrical engineering,Synthetic biology,Public domain software | Conference |
ISSN | Citations | PageRank |
2163-4025 | 1 | 0.39 |
References | Authors | |
4 | 6 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Morgan Madec | 1 | 23 | 12.13 |
| François Pêcheux | 2 | 121 | 16.70 |
| Yves Gendrault | 3 | 15 | 4.95 |
| loic bauer | 4 | 1 | 0.39 |
| Jacques Haiech | 5 | 20 | 7.51 |
| Christophe Lallement | 6 | 69 | 17.84 |