polco
The polco tool enumerates extreme rays of polyhedral cones. It can also be used to enumerate vertices of polytopes, and for the dual problem, the enumeration of facets given the extreme points (aka convex hull). The Java tool currently supports two multi-core implementations of the double description method: standard and born/die (for details, see [1], [2] and background section).
For the computation of elementary flux modes (EFMs) – basic biochemical operation modes in metabolic networks – you might also want to consider the specialized efmtool instead.
Download
The current version is Download 4.7.1 (4-Dec-2009) (JAR, 2.8 MB).
Source code: Download 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.
- 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 the Download polco.jar (JAR, 2.8 MB) Java archive. It also contains all necessary library classes.
- A external page Java VM (version 5 or newer) is required on your system.
- For HDF5 support, also download the appropriate external page hdf-java binary (.dll or .so file)
Documentation & Sources
See documentation