Note : this training is subject to (minor changes).
Team and Contacts
Équipe Calcul Formel.
François Lemaire.
Francois.Lemaire@univ-lille1.fr
In collaboration with the Institut für Informatik II, Universität Bonn.
Keywords
Flux Balance Analysis. Fast/Slow Reactions
Context
Quoted from Wikipedia (see [3]) : Flux balance analysis (FBA) is a mathematical method for analyzing metabolism. It does not require knowledge of metabolite concentration or details of the enzyme kinetics of the system. The assumption is made that the system being studied is homeostatic and the technique then aims to answer the question: given some known available nutrients, which set of metabolic fluxes maximize the growth rate of an organism while preserving the internal concentration of metabolites?
Flux Balance Analysis is a "simple" and efficient technique based on linear algebra, taking care of extra assumptions such as the positiveness of the speed of a reaction (see [2]).
In practice, the FBA yields too many solutions, and one needs to take into account extra assumptions such as the gene regulation to obtain more relevant results (see [1]).
Subject
One wants to investigate the following question : is it relevant to take into account the slow/fast attribute of the reactions, in the FBA process.
Work to be done
- get used to the FBA, and experiment existent FBA software
- investigate the question and obtain an algorithm
- code the algorithm in an existing framework, or from scratch using the SBML library (C or Java)