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The goal of our iGEM project is to create a software with a graphical user interface that allow a biologist to build models of small biological circuits and to start the associate simulation through a tool originally dedicated to the description and simulation of electronic circuits.

Nowadays, the design approach used in synthetic biology is similar to the one used in microelectronics. At mid-term, the design of a synthetic biology function is expected to be a kind of LEGO™ game which consists in assembling a set of elementary BioBricks. Similarly, over the past twenty years, the designing of complex electronic circuits, such as microprocessors, also consist in the assembly of standards cells picked-up in a design kit provider by silicon factories.

By this way, it is possible to design functional microelectronic systems compounds with more than 2 billion transistor (eg: Intel Xeon “Nehalem-EX”). This performance is possible thanks to the existence of powerful designing tools which are mostly semi-automatic. Today, the designing a digital electronic system require only an initial behavioral description of the targeted system and the ability to click on some buttons (in practice, design skill are still required in order to well configure the EDA (Electronic Design Automation) tool and to manually optimize some aspects of the design).

The power of EDA tools is their ability to carry out virtual testing, simulation, prediction and verification during the design process. Thus, the models of the standard cells are the keystone of this method. These are generally encoded in VHDL or VHDL-AMS languages which are “Hardware Description Languages” that are adapted to the need for EDA tools: VHDL models are understandable and usable by both the designer and the software.

In synthetic biology, the creation of Genetic Design Automation tools would be undoubltly an important vehicle for development of the field.

Our team comes from a project carried out during our studies at the Ecole Nationale Superieure de Physique de Strasbourg (E.N.S.P.S.). The project was co-directed by Professor Jacques HAIECH (Faculty of Pharmacy of Strasbourg, France) and Professor Christophe LALLEMENT (Institute of Solid State Electronics and Systems, Strasbourg, France). In both, they have set up a joint research team that works on this topic. Their philosophy is that one of the most serious runways for the mid-term development of a Genetic Design Automation tool requires an adaptation of the tools of microelectronics. Among the projects they lead, we intervened in the modeling of biological structures with electronic-dedicated languages.

As you will quickly realize the following, models, language and the tool used to encode models in electronics is not biologist-friendly, leading to the need off an interface allowing the biologist to first describe the system to simulate and then gather the simulation results.