Finding MEMo: Minimum sets of elementary flux modes

Abstract

Metabolic network reconstructions are widely used in computational systems biology for in silico studies of cellular metabolism. A common approach to analyse these models are elementary flux modes (EFMs), which correspond to minimal functional units in the network. Already for medium-sized networks, it is often impossible to compute the set of all EFMs, due to their huge number. From a practical point of view, this might also not be necessary because a subset of EFMs may already be sufficient to answer relevant biological questions. In this article, we study MEMos or minimum sets of EFMs that can generate all possible steady-state behaviours of a metabolic network. The number of EFMs in a MEMo may be by several orders of magnitude smaller than the total number of EFMs. Using MEMos, we can compute generating sets of EFMs in metabolic networks where the whole set of EFMs is too large to be enumerated.

On the Geometry of Elementary Flux Modes

“…Larhlimi and Bockmayr [10] introduced metabolic behaviors and studied outer descriptions of the flux cone based on minimal metabolic behaviors , which are in a one-to-one correspondence with the minimal proper faces of the flux cone. Röhl and Bockmayr [12] introduced the concept of a minimal set of elementary flux modes (MEMo) and gave an algorithm to compute such a set. A MEMo consists of an EFM from each minimal proper face of the flux cone together with a vector space basis of the lineality space.…”

Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks

“…[11][12][13][14][15][16] The enumeration of all EFMs of large metabolic networks is not possible due to a severe combinatorial explosion in their number, 17 so that most research has focused on calculating only subsets of EFMs. [18][19][20][21][22][23][24][25][26][27][28][29][30] However, since many EFMs share the same overall substrates-to-products conversion and, therefore, indicate the same metabolic capability, their enumeration is not always required. Instead, for many applications it suffices to focus on all possible overall conversions that a cell can catalyze.…”