BioSysBio:abstracts/2007/Marco Terzer

Elementary Flux Modes – State-of-the-art Implementation and Scope of Application

Author(s): Marco Terzer¹, Jörg Stelling²

Affiliations: ^1,2Computational Systems Biology (csb) Research Group, Institute of Computational Science, ETH Zurich, Switzerland

Contact: email: {marco.terzer,joerg.stelling}@inf.ethz.ch

Homepage: http://csb.inf.ethz.ch

Keywords: 'elementary flux modes' 'extreme pathways' 'metabolic pathways'

Abstract

Elementary flux modes (EFMs) and extreme pathways (EPs) constitute two closely related concepts describing all possible flux distributions in a metabolic network under steady state conditions, acting as a minimal constructive basis of the solution space. The algorithms to compute EFMs/EPs originate from computational geometry, where the problem is known as enumeration of extreme rays of polyhedral cones. Due to combinatorial complexity, the algorithms scale poorly and various improvements have been proposed. Here, we present a selection of the most important contributions including a new dynamic adjacent ray enumeration approach. The new approach is based on candidate narrowing which has recently been proposed by the authors. However, the present variant is new and optimizes the method significantly, resulting to the best of our knowledge in the most efficient algorithm for elementary flux mode computation known today.

As a second aspect, we focus on the application of elementary modes, placing it into the context of constraint-based modeling approaches. Therefore, we compare pathway analysis (aggregating EFM/EP and related methods) with flux balance analysis (FBA) and minimization of metabolic adjustment (MoMA). A critical evaluation of the methods assesses properties such as computational costs, network size limitations, applicability and practical benefit.

Poster

A0 poster (pdf) or an A4 version (pdf)