A meta environment for biological network modelling
Ph.D. position, 3 years, Grenoble

re-posted from bioinfo.fr, 20.05.2010


A PhD student position is available in the TIMB team of the TIMC-IMAG lab , Grenoble. The position is funded through the Microsoft Research PhD Scholarship programme.
Building an integrated picture of the cell is one of today's Systems Biology big challenge. The concept of network is central in this endeavor. Biological networks, including genetic, metabolic, neural, immunological networks, are non-linear dynamical systems containing usually many feedback loops leading to complex behaviour. One of the benefits expected from such system-level models, besides a better understanding of the fundamentals of Life, is the design of combinatorial therapies taking into account the network structure (by targeting several nodes simultaneously). The building of network models from experimental data is a difficult task, and formal tools are needed to assist reasoning about models and hypotheses. A practical problem, in addition to the intrinsic complexity of biological systems, is that part of the information needed to build and execute a dynamical model is often not available. Consequently the models are under-determined and modellers are lead to make reasonable guesses (for example to assign values to parameters). We propose a more rational approach in which the structure of the network, the knowledge on system behaviour and additional hypotheses are all specified in terms of constraints (logical formulae).

The global goal is to develop software tools based on constraint technologies to assist biologists in the process of building models of complex interaction networks. High-level functionalities are needed, such as automatic model revision, inference of properties shared by a set of solutions, prioritization of experiments. At the meta level, the idea is to use the constraint formalism to reason on the queries, in particular in a collaborative environment where multiple overlapping sets of hypotheses are considered. This last part is a collaboration with the Constraint Reasoning Group in Microsoft Research Cambridge.

Our developments are rooted in real biological questions. The project involve the development of computational concepts and methods, and their implementation. The project also involve building specific models, and the formalization biological questions.

Qualifications and experience

Some knowledge about constraint programming and molecular biology would be a plus but is not mandatory. More importantly, the candidate should have the motivation to acquire that knowledge, and to have a strong taste for interdisciplinary work.

Keywords: Genetic/biochemical networks, Model building, Constraint programming, Boolean satisfiability.

Interested applicants should submit CV and statement of research interest to Eric Fanchon (Eric.FanchonRM@imagRM.fr) and Jacques Demongeot (Jacques.Demongeot@imag.fr) .