efmtool

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.

Download

The current version is 4.7.1 (4-Dec-2009) (ZIP, 5.4 MB).
Source code: 4.7.1 (4-Dec-2009) (JAR, 2 MB) and on GitHub (TODO)

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: B/W, Color
  2. 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.
  3. 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.
  4. 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.

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)
 
 
Page URL: http://www.csb.ethz.ch/tools/software/efmtool.html
25.05.2015
© 2015 Eidgenössische Technische Hochschule Zürich