Date : 02/02/2011

Laboratory
LACL
Université Paris 12 - EA 4213
Bâtiment P2 - 240
Faculté des Sciences et technologies
61 rue du Général de Gaulle
94010 Créteil cedex
Director : Régine LALEAU

PhD Supervisor
Olivier MICHEL
email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
phone : +33 1 45 17 16 35

Subjects / Tools-Methodologies:
1 : A language for synthetic biology

Summary of lab's interests

- high-level programming language, synthetic biology, spatial computing, dynamical systems

Summary of project

This work is at the meeting point of amorphous computing [Abel01], autonomic computing [Hor01], spatial computing [Dag05] and synthetic biology. Our goal is to define a new high-level programming language defining the behaviour of a large number of entities that are unreliable, with local and dynamic interactions. Since we cannot specify the behaviour at the global level, it is necessary to articulate the description of the entities at the local level, the global state resulting from the interactions between the entities. One will obviously not address with this language the classical algorithmic problems but rather seek for applications where a stable condition or self-* (organisation, correction, optimisation...) properties are required.

The first step will require to carry out a bibliographical work in the fields of amorphous computing, autonomic computing, spatial computing and synthetic biology. Then, starting from the first results of the SYNBIOTIC project - L1 language based on an algebra of discrete differential operators and case studies - a set of operators, at the level of the entities (an "ideal" biological cell), must be defined and integrated into the language. This language will then be validated by its ability to describe basic morphogenetic processes (formation of static aggregates) and increasingly complex (self-organization on a moving substrate subject to noise, construction of patterns by aggregation and differentiation...).

The candidate must have a good knowledge of unconventional computing models and the framework in which this work takes place. A strong skill in the classical tools used for the development of programming languages (theoretical and practical) will be essential.


BIBLIOGRAPHIC REFERENCES

[Abel01] Amorphous Computing, Abelson et al., Communications off the ACM, Volume 43, Number 5, May 2001.
[Dag05] André DeHon, Jean-Louis Giavitto and Frédéric Gruau, Computing Media Languages for Space-Oriented Computation, Dagstuhl Seminar Proceedings, 2005.
[Hor01] Paul Horn. Autonomic computing: IBM\' S perspective one the state off information technology. Technical carryforward, IBM Research, October 2001