Generating elementary flux modes in metabolic networks

Researchers: Anders Forsgren and Hildur Æsa Oddsdóttir, in cooperation with Véronique Chotteau and Erika Hagrot (KTH School of Biotechnology).

This project relates to cell metabolism. More specifically, optimization approaches for metabolic networks. This is a collaboration project with the School of Biotechnology at KTH, with one PhD student from each of the two participating research groups.
The aim of this project is to formulate and solve relevant optimization problems in order to gain information on the reactions
inside a cell. In particular we want to find the elementary flux modes of the network by using measurement data. This also gives
information about the dynamic equations governing the system. We have developed a method based on column generation that identifies elementary flux modes from measurement data. The current research is focused on a robust optimization approch to this problems, where measurement errors of the experimental data are taken more directly into account. From the robustness we plan to consider the model to include kinetics. The problem as it is now assumes steady state, and as future research we alswo want to examine if each macroscopic reaction can be assumed to have a dynamic equation and if that can predict the cell's behavior.