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

DOI: 10.1186/1471-2105-5-175

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Abstract:

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 participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date.The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks.The background section presents the importance of computing elementary modes for metabolic system analysis, its computational difficulties and the existence of various known algorithms. A theoretical section brings these algorithms into a unified framework. In a following section we introduce a new approach, called the binary approach. Although relying on concepts introduced in the theoretical section, this section gives enough practical details to be stand-alone for the implementer. Results obtained from example networks and a conclusion section close the article.We consider a metabolic network with m metabolites and q reactions. Reactions may involve further metabolites that are not considered as proper members of the system of study. The latter metabolites, considered to be buffered, are cal

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