efmtool computes elementary flux modes (EFMs) of metabolic networks. It is implemented in Java and has been integrated into MATLAB (see documentation)
EFM computation is a special case of extreme ray enumeration of polyhedral cones. You might also want to consider polco, a tool for general polyhedral computations.
- Terzer M (2009) Large scale methods to enumerate extreme rays and elementary modes. ETH PhD Thesis. ETH e-collection, Book at Lulu: B/W, Color
- Terzer M, Stelling J (2010) Parallel Extreme Ray and Pathway Computation. Parallel Processing and Applied Mathematics, Part Ii. pp. 300-309. http://doi.org/10.1007/978-3-642-14403-5_32.
- Terzer M, Stelling J (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24: 2229-2235. http://doi.org/10.1093/bioinformatics/btn401.
- Terzer M, Stelling J (2006) Accelerating the computation of elementary modes using pattern trees. Algorithms in Bioinformatics, Proceedings. pp. 333-343. http://doi.org/10.1007/11851561_31.
- Download & unzip the current version from above (an efmtool directory will be created)
- Change current directory to the newly created efmtool directory
- Start MATLAB from efmtool directory, with Java Virtual Machine enabled (default)