The polco.main package contains the {@link ch.javasoft.polco.main.Polco Polco} program with the {@link ch.javasoft.polco.main.Polco#main(String[]) main} method to start it from the command line.

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 current multi-core implementation is a variant of the double description method invented by Motzkin et al. [1]. Some selected references relating to the implementation are given below.

References

  1. Motzkin, T. S., Raiffa, H., Thompson, G., and Thrall, R. M., "The double description method", 1953
    in Contributions to the Theory of Games II, volume 8 of Annals of Math. Studies, pages51-73. Princeton University Press (Princeton/RI).
  2. Fukuda, K. and Prodon, A., "Double description method revisited", 1995
    in Combinatorics and Computer Science, pages 91-111.
  3. Wagner, C., "Nullspace approach to determine the elementary modes of chemical reaction systems", 2004,
    J.Phys. Chem. B, 108, 2425-2431.
  4. Gagneur, J. and Klamt, S., "Computation of elementary modes: A unifying framework and the new binary approach", 2004,
    BMC Bioinformatics, 5, 175.
  5. Schuster, S. and Hilgetag, C., "On elementary flux modes in biochemical reaction systems at steady state", 1994,
    J.Biol. Syst., 2, 165-182.
  6. Terzer, M. and Stelling, J., "Large scale computation of elementary flux modes with bit pattern trees",
    Bioinformatics, August 1, 2008, doi:10.1093/bioinformatics/btn401