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Damien Eveillard : Constraint programming to improve the bacterial metabolic network

Seminar, Thursday, January 9, 2014, 11 AM, Salle F107, INRIA Grenoble - Rhône-Alpes, Montbonnot


Optimization-based analysis of metabolic networks has proved valuable in designing metabolic engineering strategies aiming at enhancing the production of a target of interest. Several approaches have been proposed, most of them are based on the seminal approach flux balance analysis (FBA), which investigates reaction fluxes in a metabolic network at steady state. Recently,we proposed a novel method which identifies a suitable chemically feasible transformation, called stoichiometric capacitance, allowing for a significant increase in the metabolic network capabilities. This later will be presented and illustrated on several standard bacteria metabolic network. In extension to this, I will practically present our tool MeDUSA (MEtabolic Design Using SAge) which, given a metabolic network and an objective function, (i) computes a stoichiometric capacitance (SC) and (ii) investigates the effect of including in the model the calculated SC. MeDUSA has been implemented using Sage, a free open-source python-based software that smoothly handles the use of advanced optimization packages.


INRIA Grenoble - Rhône-Alpes, Montbonnot