Computation of elementary modes: a unifying framework and the new binary approach

Background: Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. Results: We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of p...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Julien Gagneur, Steffen Klamt
• Keywords: Binary Approach, BMCBI 2004, Elementary Modes, Metabolic Pathway Analysis