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 page python
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 Download 4.7.1 (4-Dec-2009) (ZIP, 5.4 MB).
Source code: Download 4.7.1 (4-Dec-2009) (JAR, 2 MB)
external page GitLab
License
Redistribution and use in source and binary forms, with or without
modification, are permitted provided agreeing to the Simplified BSD Style License.
- Download License (TXT, 2 KB)
- Read about Simplified BSD Style License at external page http://www.opensource.org
References
- Terzer M (2009) Large scale methods to enumerate extreme rays and elementary modes. ETH PhD Thesis. ETH e-collection, Book at Lulu: external page B/W, external page Color
- Terzer M, Stelling J (2010) Parallel Extreme Ray and Pathway Computation. Parallel Processing and Applied Mathematics, Part Ii. pp. 300-309. external page 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. external page 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. external page 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)