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

EFM computation is a special case of extreme ray enumeration of polyhedral cones. You might also want to considerpolco, a tool for general polyhedral computations.

Download

The current version isDownload4.7.1 (4-Dec-2009) (ZIP, 5.4 MB).
Source code:Download4.7.1 (4-Dec-2009) (JAR, 2 MB)
external pageGitLab

License

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

• DownloadLicense (TXT, 2 KB)
  
• Read aboutSimplified BSD Style Licenseatexternal pagehttp://www.opensource.org
  

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 (anefmtool directory will be created)
• Change current directory to the newly createdefmtool directory
  
• Start MATLAB fromefmtooldirectory, with Java Virtual Machine enabled (default)