Section: Overall Objectives

Introduction

BIOCORE is a joint research team between Inria (Centre of Sophia-Antipolis Méditerranée), INRA (ISA - Institut Sophia Agrobiotech and LBE - Laboratory of Environmental Biotechnology in Narbonne) and UPMC-CNRS (Oceanographic Laboratory of Villefranche-sur-mer - LOV, UMR 7093/ Université P.M. Curie, Villefranche sur Mer, Team: Processes in Pelagic Ecosystems - PEPS).

Sustainable growth of living organisms is one of the major challenges of our time. In order to tackle it, the development of new technologies is necessary, and many of these new technologies will need to use modeling and computer tools. BIOCORE contributes to this theme, in the general field of design and control of artificial ecosystems (or biosystems). Its general goal is to design devices, systems and processes containing living cells or individuals and performing some tasks to decrease pollution, use of chemicals, or to produce bioenergy in a sustainable way. We build biological/ecological models in close collaborations with biologists and bioprocess engineers, and validate them with experimental platforms. Our activities are structured in three levels: mathematical and computational methods, a methodological approach to biology, and applications.

Research themes:

Mathematical and computational methods:

• Tools for modeling in biology: model design, validation, parameter identification.

• Mathematical properties of models in biology: mathematical studies of models and of their global behavior.

• Software sensors for biological systems: using the model and on-line measurements to estimate the variables that are not measured directly.

• Control, regulation, and optimization for biological systems; design of laws to maintain a variable at a given level, or to optimize the productivity of the system.

A methodological approach to biology: system study at different scales

• At the intra-individual level: theoretical and experimental study of simple metabolic-genetic networks, coarse grained models of the internal state.

• At the level of interactions between individuals in the population: individual behavior, resource allocation.

• At the scale of interaction between populations: interaction between prey and predator populations in a trophic network or competition between species in a chemostat.

• At the scale of interaction between ecosystems: coupling of two artificial ecosystems as a unique bioprocess or interactions between an artificial ecosystem and the surrounding natural ecosystem.

Fields of application:

• Bioenergy, in particular the production of lipids (which can be used as biofuel), methane and hydrogen by microorganisms (with LOV and LBE).

• CO2 fixation by micro-algae, with the aim of capturing industrial CO2 fluxes (with LOV). This theme can also include artificial ecosystems developed to improve the prediction of carbon fluxes between the ocean and the atmosphere.

• Design and optimization of ecologically friendly protection methods for plants and micro-plants artificial production systems (with ISA and LOV). This theme focuses in particular on biological control programs to control pathogens and pest invasions in crops and bioreactors.

• Biological waste treatment with microorganisms in bioreactors to reduce pollution emission levels (in collaboration with LBE).

Software for biological modeling and supervision of biological processes.

National, international and industrial relations

• National collaborations: IFREMER (Nantes), INRA (MISTEA Montpellier, BIOGER Grignon. IAM Nancy, Agrocampus Ouest, MaIAGE Jouy-en-en-Josas, BioEpAR Nantes), CIRAD Montpellier, Institut Méditerranéen d'Océanologie, LOCEAN (Paris), GIPSA Grenoble, IBIS, BANG, and ANGE Inria teams.

• Participation in French groups: ModStatSAP (Modélisation et Statistique en Santé des Animaux et des Plantes), GDR Invasions Biologiques.

• Participation to national programmes: ANR projects Phycover, FunFit, ICycle, and Maximic, ANR BioME projects Facteur 4 and Purple Sun, Projet d'Investissement d'Avenir RESET, UMT Fiorimed, and Labex SIGNALIFE.

• International collaborations: Université Catholique de Louvain (Belgium), Université de Mons (Belgium), University of Stuttgart (Germany), Rutgers University (USA), MacMaster University (Canada), University Ben Gurion (Israel), Imperial College (United-Kingdom), Massey University (New Zealand), Universidad Tecnica Federico Santa Maria and Universidad de Chile (Chile), Roslin Institute / University of Edinburgh (UK).