Biocore (

The overall goal of BIOCORE is to contribute to environment preservation by developing new energy sources, minimizing water pollution or the use of chemicals for crops. In this context, we design, model, analyse, control and optimize artificial ecosystems (i.e. designed by man, built by man, or deeply modified by man).

We have been working since 20 years in close partnership with the LOV on microalgae. Their ability to fix CO2 (atmospheric or industrial), their response to a nitrogenous mineral deficiency, particularly to stimulate the production of carbon storage (lipids and sugars) . BIOCORE has also worked extensively in collaboration with the LBE on energy recovery from organic waste through anaerobic digestion, and on the coupling between anaerobic digestion and microalgae cultures. O. Bernard from BIOCORE led the Shamash project, a pioneer in Europe, to use lipid productive species and stimulate triglyceride production (ANR 2006-2010 Shamash project). BIOCORE participated to the Symbiosis ANR project (ANR 2008-2012 coupling anaerobic digestion / microalgae) and Salinalgue (FUI 2011-20114 project covering both lanes of energy recovery). More recently BIOCORE launched the Purple Sun project, for coupling microalgae photosynthesis and photovoltaic panels. Moreover BIOCORE coordinated the Nautilus ARC (2011-2012) on the coupling between hydrodynamics and photosynthetic activity.

BIOCORE is a common Inria project team including some members of Villefranche Laboratory Oceanography (CNRS / UPMC) and the Environmental Biotechnology Laboratory of Narbonne (Narbonne INRA).

Key contacts: Olivier Bernard


ANGE (Numerical Analysis, Geophysics and Ecology) is a joint team between INRIA, CEREMA (Ministry of Ecology, Sustainable Development and Energy) and UPMC (J.-L. Lions Laboratory, UMR CNRS 7598). It is interested in geophysical flows mainly with free surface.

The research program of the team is focused on modelling, mathematical analysis and numerical simulation of models involving reduced complexity compared to the Navier-Stokes equations. The core of the approach consists in releasing conventional assumptions found in shallow water modelling.

The multilayer Saint-Venant discretisation provides efficient and relatively generic digital tools that can address difficult and varied problems. While geophysical flows are at the heart of many issues, ANGE team chose to focus its efforts on three complex, emerging and high potential impact themes:

– Natural risks and gravitational flows,

– Marine energy

– Ecology-biodiversity.

During the Nautilus ARC, ANGE has developed a 3D Navier-Stokes discretisation code, which must be enriched (see “Axes of the major action”).

Key contacts: Jacques Sainte-Marie, Marie-Odile Bristeau,

Dyliss (

Dyliss is a research team in bioinformatics. The team focuses on sequence analysis and systems biology. We use qualitative formal systems to characterize genetic actors from non model species, such as algae or mining bacteria, that control phenotypic answers when triggered by their environment. The main computational challenge is to face lacks and incompleteness in both expert knowledge and experimental observations. To that goal, we use formal systems to build discrete abstractions of available information at both genomic and physiological scales. The goal of these knowledge-based approaches is to increase sensitivity and expressivity of data, especially for those non-model organisms for which genetic perturbation are uneasy and make probabilistic-based integrative methods less efficient. Our methods combine data integration with constraint programming (to identify genomic and physiological characteristics of studied species), the analysis of biological sequences with expressive languages and grammatical inference (detailed characterisation of actors in genomes), and dynamical systems using symbolic approaches (to quantify the impact of the environment on the system). Approaches are already applied on non-model organisms under various national project (ANR Investment Future IDEALG, ANR, BIOTEMPO ANR SYSTERRA ECS team OMICS Centre Inria Chile).

Key contacts: Anne Siegel



IBIS is a project-team involving INRIA Grenoble – Rhône-Alpes and the Laboratory of Microbial Pathogenesis and Adaptation (University Joseph Fourier, CNRS UMR 5163). The objective of IBIS is to analyse bacterial regulatory networks using approaches that combine mathematical models, computational methods and experiments in microbiology and molecular biology. Specifically, researchers in IBIS are working on IBIS the modelling of complex regulatory networks in bacteria, the simulation of the dynamics of these networks using these models, the development of tools to measure accurately and in real-time gene expression, the use of these data for validation and identification of models and the development of tools for engineering and control of bacterial regulatory networks. The work in IBIS is carried out within several national and international projects, such as GeMCo (ANR, 2010-2014) and RESET (IAP, 2012-2016). Both of these projects involve Biocore as well.

Key contacts: Hidde de Jong


The aim of this COMMANDS is the design of numerical methods for optimizing dynamical systems, coming either from physical systems, of from economical ones. The dynamics can be deterministic or stochastic, in discrete or continuous time. The applications deal with aerospace trajectories, the management of energy storage, bioproduction processes.

The optimization of systems governed by differential equations, by direct discretization methods combined with interior-point algorithms, as well as by shooting algorithms.

  • The resolution of deterministic optimal control problems through the numerical integratio of the HJB (Hamilton-Jacobi-Bellman) equation
  • Stochastic control and specific schemes for the associated second-order HJB equation
  • Stochastic programming and associated questions on risk measure

Key contact: Pierre Martinon




The core endeavor of McTAO is to develop methods in control theory for finite-dimensional nonlinear systems, as well as in optimal transport, and to be involved in real applications of these techniques. Some mathematical fields like dynamical systems and optimal transport may benefit from control theory techniques. Our primary domain of industrial applications will be space engineering, namely designing trajectories in space mechanics using optimal control and stabilization techniques: Transfer of a satellite between two Keplerian orbits, rendez-vous problem, transfer of a satellite from the Earth to the Moon or more complicated space missions. A second field of applications is quantum control with applications to Nuclear Magnetic Resonance and medical image processing. A third and more recent one is the control of micro-swimmers, i.e. swimming robots where the fluid-structure coupling has a very low Reynolds number.

Key contact: Laetitia Giraldi



The study of biology associates pattern recognition of diversity with modeling of functional and evolutionary processes. Pleiade addresses the double challenge 
of measuring dissimilarity between biological objects quickly and precisely, and exploring the relations between diversity in traits and diversity in function at multiple scales. We develop algorithms, models, and software frameworks for applications in ecology, evolution, and biotechnology.


  • Distances and pattern recognition
  • Hierarchical hybrid modeling
  • E-science


  • Genome and transcriptome annotation
  • Molecular-based systematics and taxonomy
  • Community ecology and population genetics

Key contacts: David Sherman and Pascal Durrens


IFREMER – Physiology and Biotechnology of Algae (

Physiology of microalgae is little known, and understanding the mechanisms specific to this very diverse group is crucial for their industrial use. Indeed, the knowledge of the major metabolic pathways and its changes induced by modifications in the environment, both at the level of the cell and of the population, provides a way to trigger, control and optimize culture development.

PBA laboratory consists of two teams:

  • The “Ecophysiology” team explores the relationship between microalgae and their environment, in terms of growth and biochemical composition. Original experimental tools have been internally developed to study the influence of abiotic factors (light, nutrients, temperature, pH) for each species. Relationships between microalgae and the microbiological environment constitute a second field of investigation.
  • Using molecular approaches, the team “Algae and Genomes” studies metabolism which are characteristics of specific physiological conditions. Tools for functional genomics are used to identify and characterize genes and metabolic pathways that have a biotechnological potential. Furthermore, genetic engineering approaches have been developed to carry out functional studies by reverse genetics, and to use the potential of microalgae as cell factories.

Key contacts: Gael Bougaran and Francis Mairet

Laboratory of Environmental Biotechnology – INRA (

LBE-INRA is specialized in the field of biological treatment of solid waste and liquid domestic, agricultural and agro-industrial effluents. LBE consists of five thematic research teams: microbial ecology, process engineering / anaerobic pathways, microbial biofilms, predictive biodegradability and industrial transfer and has extensive expertise in anaerobic digestion. Some researchers of the LBE are associated to the MODEMIC and BIOCORE Inria project teams. Since 2003, researchers at the LBE published 142 articles on the subject in 63 journals ranked A and with colleagues from 26 different countries. This team has developed since 1993 a great experience on instrumentation, modelling and control of biological decontamination processes and bioenergy production, especially for microalgae cultures coupled with anaerobic digestion.

One of the research areas of the team ‘Microbial Ecology and Biodiversity’ is dealing with survival and spread of undesirable microorganisms in biological waste treatment. The use of molecular techniques to address these issues (analysis of microbial diversity by SSCP and molecular inventories qPCR) has led to an internationally acknowledgement on this topic.

A highly instrumented pilot raceway (60 m2) was developed during the ANR Symbiosis (coupling between microalgae production and water treatment by anaerobic digestion). This unique experimental device can lead to innovative experiments. The link between operating conditions (dilution rate, mixing rate, depth, …), and productivity can be studied at high sampling frequency. Experiments on this pilot since 2010 led to a database with original and rich information.

Key contacts:  Jean-Philippe Steyer

Oceanography Laboratory of Villefranche (CNRS/University Paris VI).(

The LOV is a multidisciplinary laboratory that studies the role of marine plankton in the functioning of marine ecosystems, the response of biodiversity and biogeochemical cycles to global changes (global warming and acidification).

Team 1 of the LOV has long studied the radiative transfer in the oceans, and is therefore interested in determining the inherent and apparent properties of the microalgae medium, in a highly diffusive medium. They also assess biodiversity by remote sensing calibrated by analytic determination of pigments, which are seen as tracer for phytoplanktonic groups.

Team 3 of the LOV, which is associated to BIOCORE has long been specialized in the cultivation (Malara & Sciandra 1991 Sciandra & Ramani, 1994, Bernard et al., 1996, Le Floc’h et al. 2002) and ecophysiological study of phytoplankton ( Sciandra 1991, 1993, & Sciandra Amara 1994 Sciandra 1996 Sciandra et al. 1997 Leboulanger et al., 1998, Stramski et al., 2002, Sciandra et al., 2003, MacIntyre et al. 2009). This team has developed, within the Biocore team, a Computer Driven Marine Environment Simulator (SEMPO) which allows real time control of the growth conditions, and measuring at high frequency the response of organisms to changes in their environment, which is particularly useful for experiments in day-night cycles, or to study the effects of a disturbance on microalgae growth. The team is also specialized on nitrogen fixing cyanobacteria.


Key contact: Antoine Sciandra


Process Engineering and Materials Laboratory (CentraleSupelec).(

The LGPM laboratory is involved in two inextricably linked fields of investigation: Process Engineering and Materials. Modelling, simulation and experimentation are the key words in common between these different research subjects.

This complementarity allows an understanding of microscopic phenomena to be used in the simulation, optimization, and intensification of transformation and development processes. Our expertise is, in particular, applied to sustainable aspects of processes (e.g., material and energy savings) and bio-processes (use of renewable resources).

In particular, the LGPM has a long history in using microalgae for bioenergy production, bioremediation, or high added products.

Key contact: Filipa Lopes


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