FluxModeCalculator: an efficient tool for large-scale flux mode computation | Zendy

Jan B. van Klinken | Zendy; Ko Willems van Dijk | Zendy

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FluxModeCalculator: an efficient tool for large-scale flux mode computation

Author(s) -

Jan B. van Klinken,

Ko Willems van Dijk

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv742

Subject(s) - computer science , computation , matlab , mit license , workstation , robustness (evolution) , limiting , scale (ratio) , algorithm , computational science , theoretical computer science , software , computer engineering , data mining , operating system , mechanical engineering , biochemistry , chemistry , physics , quantum mechanics , engineering , gene

Elementary flux mode (EFM) analysis is a powerful technique for determining the metabolic capacities and robustness of stoichiometric networks. Recently, several improvements have been made to the algorithm for enumerating the EFMs, making the study of large models possible. However, currently these tools require high performance workstations to perform large-scale EFM computations, thus limiting their applicability. We developed a more time and memory efficient implementation of the algorithm for EFM enumeration in MATLAB, called FluxModeCalculator, which enables large-scale EFM computation on ordinary desktop computers.

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