Section: Overall Objectives

An interface between biology and computer science

The expanded name for the Beagle research group is “Artificial Evolution and Computational Biology”. Our aim is to position our research at the interface between biology and computer science and to contribute new results in biology by modeling biological systems. In other words we are making artifacts – from the Latin artis factum (an entity made by human art rather than by Nature) – and we explore them in order to understand Nature. The team is an Inria Project-Team since January, 2014. It gathers researchers from Inria, INSA, UCBL, who are members of three different labs, the LIRIS (Laboratoire d'Informatique en Image et Systèmes d'Information: UMR 5205 CNRS, INSA-Lyon, Univ. Claude Bernard Lyon 1, Univ. Louis Lumière Lyon 2, École Centrale de Lyon), the LBBE (Laboratoire de Biometrie et Biologie Evolutive: UMR CNRS 5558, Univ. Claude Bernard Lyon 1.), and CARMEN (Laboratoire de Recherche en Cardiovasculaire, Métabolisme, Diabétologie et Nutrition: UMR U1060 INSERM, INSA-Lyon, INRA 1235, Univ. Claude Bernard Lyon 1.). It is led by Prof. Guillaume Beslon (INSA-Lyon, LIRIS, Computer Science Dept.).

Our research program requires the team members to have skills in computer science but also in life sciences: they must have or develop a strong knowledge in biosciences to interact efficiently with biologists or, ideally, to directly interpret the results given by the models they develop. A direct consequence of this claim is that it is mandatory to restrict the domain of expertise in life sciences. This is why we focus on a specific scale, central in biology: the cellular scale. Indeed, we restrict our investigations on the cell, viewed as a dynamical system made of molecular elements. This specific scale is rich in open questions that deserve modeling and simulation approaches. We also focus on two different kinds of constraints that structure the cellular level: biophysical constraints and historical constraints. The cell is a system composed of molecules that physically interact and the spatio-temporal nature of these interactions is likely to strongly influence its dynamics. But the cell is also the result of an evolutionary process that imposes its own limits on what can evolve (or is the most likely to evolve) and what cannot (or is the less likely to evolve). A better understanding of what kind of systems evolution is the most likely to lead to in a given context could give us important clues for the analysis of extant biological systems.