Thermodynamic elementary flux mode analysis - tEFMA
Elementary flux modes (EFMs) are important structural tools for the analysis of metabolic networks. Many of these are only mathematically feasible, but biologically irrelevant. tEFMA is a (command-line) software tool, which uses an (experimentally measured) cellular metabolome to identify only the set of thermodynamically feasible EFMs. Specifically, given a metabolic network and a not necessarily complete metabolome, tEFMA efficiently returns the full set of thermodynamically feasible EFMs consistent with the metabolome. tEFMA strongly reduces the memory consumption and the overall runtime.
tEFMA as an extension of the open source software efmtool (originally developed by Marco Terzer and Jörg Stelling). Both tEFMA and efmtool are implemented as Java packages and can be used on virtually all computer platforms. tEFMA requires CPLEX, a powerful commercial linear programming solver by IBM (for which academic licenses are available on request).
- Matthias P. Gerstl, David E. Ruckerbauer, Diethard Mattanovich, Christian Jungreuthmayer, and Jürgen Zanghellini. Metabolomics integrated elementary flux mode analysis in large metabolic networks. Scientific Reports 5:8930 (2015). DOI:10.1038/srep08930
- Matthias P. Gerstl, Christian Jungreuthmayer, and Jürgen Zanghellini. tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks. Bioinformatics 31:2232 (2015). DOI:10.1093/bioinformatics/btv111