Date : 01/02/2010

Laboratory
IBISC
CNRS FRE 3901
523 place des terrasses de l'AGORA
91025 EVRY
Director :Jean Louis Giavitto

PhD Supervisor :
Franck Delaplace
email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
phone : +33 160873825

Subjects / Tools-Methodologies:
1 : Complex systems / Formal methods
2 : synthetic biology / Compiler Design
3 : Unconventional languages / Biological Network Analysis

Web site : www.ibisc.univ-evry.fr

Summary of lab's interests

IBISC lab (UNIVERSITY- CNRS - GENOPOLE) is involved in complex systems, biology and computer sciences. The research topics cover different aspects of theses fields with a special emphasis on systems biology. See Web site http://www.ibisc.univ-evry.fr/ for complementary information.

Summary of project

Synthetic biology is an emergent scientific discipline that combines sciences and engineering in order to design novel biological functions. The current trend is to establish principles to facilitate the design of reliable large synthetic systems. Synthetic biology envisions the redesign of natural biological systems for greater efficiency, as well as the construction of functional "genetic circuits" and metabolic pathways for practical purposes. This issuer be envisioned as the discovery of programming principles accounting a new medium, a living organism. These principles are seemingly assimilated to those governing the computer design based on a hierarchical organization of components; ranging from elementary bricks to more complex and integrated systems. Each layer corresponds to a level of integration of more complex biological functions. The fundamental component corresponds to biobricks that address elementary function as well as DNA sequence. Functional units (Devices) result from the assemblage of biobricks and constitute the parts of a system. The assessment of the risks involved in synthetic biology enforce the development of methods and models leading to reliable, safe and secure design of synthetic biological systems. A compilation based approach complies with these requirements. Ultimately, the objective is to conceive a "compiler" translating a specification of a global behavior at the scale of a population (of bacteria) into a genetic program controlling cellular processes. The approach is based on programming languages layouts where the most abstract language defines a computational model for a cellular population and the most fundamental corresponds to DNA sequence assembly. The subject is first focused on the fundamental layer: from a specification described in a computer language, the objective consists in generating a DNA sequence from a program. The issue is to examine methods to automatically perform the translation. The research covers the compilation aspects by adapting compiler method to an unconventional medium and the biological aspects by exhibiting processes that supply the basic language constructs. The subject will evolve to the identification of more abstract lawyers.