Elementary flux modes – state-of-the-art implementation and scope of application

Introduction Elementary flux modes discribe 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 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. 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.