Section: Overall Objectives

Overall Objectives

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 Beagle Team results from the merging of three researchers of the “Combining ” Team led by Jean-François Boulicaut in 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) (Computer Science), one researcher of the CARMEN institute(Laboratoire de Recherche en Cardiovasculaire, Métabolisme, Diabétologie et Nutrition: UMR U1060 INSERM, INSA-Lyon, INRA 1235, Univ. Claude Bernard Lyon 1.) (Biology) and two INRIA researchers (Computational Biology). It has been created as an “Équipe Centre” by INRIA Rhône-Alpes in June 2011(Beagle follows from the Combining team with a more focused topic: Combining is composed of 8 researchers and includes a data-mining research topic. To clarify the respective research areas of the INRIA Team and of the LIRIS Combining team, INRIA suggested to focus the Beagle research topic on computational biology. The members of Combining – including the data-mining part – collectively consented to this proposal.) and is on the way to be created as “Équipe-Projet”. The Beagle Team is led by Prof. Guillaume Beslon (INSA-Lyon, LIRIS, Computer Science Dept.).

Our research is based on an interdisciplinary scientific strategy: we are developing computer science formalisms and software for complex system modeling in synergy with multidisciplinary cooperations in the area of living sciences. Thanks to computational approaches we study abstractions of biological systems and processes in order to unravel the organizational principles of cellular systems. More precisely, the scientific activity of the Beagle group focuses on two different topics:

Computational Cell Biology

We are developing models of the spatio-temporal dynamic of cells and their molecular components. More precisely, we study the complex interplay between the reaction and the diffusion processes when the medium is not homogeneous or when the number of molecules is too low to account for a perfect mixing hypothesis. We particularly focus on the consequences on the signaling networks and on the stochasticity of transcription. In this domain, we always try to mix up modeling and “wet” experimental approaches by developing close collaborations with experimental biologists.

In silico Models of Evolution

To better understand the cellular structures (genome organization, transcription networks or signaling cascades) we propose to study their historical – evolutionary – origin. Individual-based evolutionary models (“in silico experimental evolution) allow to study how evolution leads to some specific structures shaped by the needs of robustness, variability or evolvability, depending on some specific conditions (e.g., large vs. small efficient population sizes, high vs. low mutation rates, stable vs. unstable environments...). The comparison with real data requires the reconstruction of the evolutionary events that have shaped the extant real genomes. To this aim, integrative models, including small substitutions as well as large reorganizations of a genome, are needed. The confrontation of what we can know of historical events and the laws we can infer from artificial experiments allow to explain some patterns of today's organisms and biodiversity.

Both topics are strongly complementary. Indeed, on the short time scales, biological systems are constrained by the physical nature of their substrate but, on long time scales, they are also constrained by their evolutionary history. Thus, studying both time scales and both constraints – including their interactions – gives us a global viewpoint on the roots of biological organization.

The scientific objectives of the Beagle team is to develop a consistent set of concepts and tools – mainly based on computational science – to in fine contribute to knowledge discovery in systems biology. Our strategy is to develop strong interactions with biologists and life science researchers to become active partners of the biological discovery process. Thus, our aim as a team is not to be a computer science team interacting with biologists, nor to be a team of biologists using computer science tools, but rather to stay in the middle and to become a trading zone [37] between biology and computer science. Our very scientific identity is thus fuzzy, melting components from both sciences. Indeed, one of the central claims of the team is that interdisciplinarity involves permanent exchanges between the disciplines. Such exchanges can hardly be maintained between distant teams. That's why the Beagle team tries to develop local collaborations with local scientists. That's also why Beagle also tries to organize itself as an intrinsically interdisciplinary group, gathering different sensibilities between biology and computer science inside the group. Our ultimate objective is to develop interdisciplinarity at the individual level, all members of the team being able to interact efficiently with specialists from both fields.