Section: Scientific Foundations

A methodological approach to biology: from genes to ecosystems

One of the objectives of BIOCORE is to develop a methodology that leads to the integration of the different biological levels in our modeling approach: from the biochemical reactions to ecosystems. The regulatory pathways at the cellular level are at the basis of the behavior of the individual organism but, conversely, the external stresses perceived by the individual or population will also influence the intracellular pathways. In a modern “systems biology” view, the dynamics of the whole biosystem/ecosystem emerge from the interconnections among its components, cellular pathways/individual organisms/population. The different scales of size and time that exist at each level will also play an important role in the behavior of the biosystem/ecosystem. The interplay and information transfer between the different levels and scales within a biosystem/ecosystem introduces many new dynamical aspects. We intend to develop methods to understand the mechanisms at play at each level, from cellular pathways to individual organisms and populations; we assess and model the interconnections and influence between two scale levels (eg., metabolic and genetic; individual organism and population); we explore the possible regulatory and control pathways between two levels; we aim at reducing the size of these large models, in order to isolate subsystems of the main players involved in specific dynamical behaviors.

We develop a theoretical approach of biology by simultaneously considering different levels of description and by linking them, either bottom up (scale transfer) or top down (model reduction). These approaches are used on modeling and analysis of the dynamics of populations of organisms; modeling and analysis of small artificial biological systems using methods of systems biology; control and design of artificial and synthetic biological systems, especially through the coupling of systems.

The goal of this multi level approach is to be able to design or control the cell or individuals to optimize some production or behavior at higher level: for example, control the growth of microalgae via their genetic or metabolic networks, to optimize the production of lipids for bioenergy at the photobioreactor level.