efmtool

efmtool computes elementary flux modes (EFMs) of metabolic networks. It is implemented in Java and has been integrated into MATLAB (see documentation) and external pagepython

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.

License

Redistribution and use in source and binary forms, with or without
modification, are permitted provided agreeing to the Simplified BSD Style License.

References

  1. Terzer M (2009) Large scale methods to enumerate extreme rays and elementary modes. ETH PhD Thesis. ETH e-collection, Book at Lulu: external pageB/W, external pageColor
  2. Terzer M, Stelling J (2010) Parallel Extreme Ray and Pathway Computation. Parallel Processing and Applied Mathematics, Part Ii. pp. 300-309. external pagehttp://doi.org/10.1007/978-3-642-14403-5_32.
  3. Terzer M, Stelling J (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24: 2229-2235. external pagehttp://doi.org/10.1093/bioinformatics/btn401.
  4. Terzer M, Stelling J (2006) Accelerating the computation of elementary modes using pattern trees. Algorithms in Bioinformatics, Proceedings. pp. 333-343. external pagehttp://doi.org/10.1007/11851561_31.

Installation

  • 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)
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