GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics.
The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven their efficiency over the last 30 years. The complete framework is composed of a computation core directly adapted from an Electronic Design Automation tool, input and output interfaces, a library of elementary parts that can be achieved with gene regulatory networks, and an interface with an electrical circuit simulator. Each of these modules is an extension of microelectronics tools and concepts: ODIN II, ABC, the Verilog language, SPICE simulator, and SystemC-AMS. GeNeDA is first validated on a benchmark of several combinatorial circuits. The results highlight the importance of the part library. Then, this framework is used for the design of a sequential circuit including a biological state machine.
1 Laboratoire Icube, Université de Strasbourg/Centre National de Recherche Scientifique , Illkirch, France .
Morgan
M
Madec
2 Sorbonne Universités, Universite Pierre et Marie Curie , Paris, France .|3 CNRS , UMR, Paris, France .
François
F
Pecheux
1 Laboratoire Icube, Université de Strasbourg/Centre National de Recherche Scientifique , Illkirch, France .|4 ECAM Strasbourg-Europe , Schiltigheim, France .
Yves
Y
Gendrault
1 Laboratoire Icube, Université de Strasbourg/Centre National de Recherche Scientifique , Illkirch, France .
Elise
E
Rosati
1 Laboratoire Icube, Université de Strasbourg/Centre National de Recherche Scientifique , Illkirch, France .
Christophe
C
Lallement
5 Laboratoire d'Innovation Thérapeutique , Illkirch, France .
Jacques
J
Haiech
D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D017076:Computer-Aided Design; D004581:Electronics; D053263:Gene Regulatory Networks; D006801:Humans; D055616:Microtechnology; D012984:Software; D058615:Synthetic Biology
computer-aided design tools; design automation; gene regulatory networks; synthetic biology