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
- 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).
-
Fukuda, K. and Prodon, A., "Double description method revisited", 1995
in Combinatorics and Computer Science, pages 91-111.
-
Wagner, C., "Nullspace approach to determine the elementary modes of
chemical reaction systems", 2004,
J.Phys. Chem. B, 108, 2425-2431.
-
Gagneur, J. and Klamt, S., "Computation of elementary modes: A unifying
framework and the new binary approach", 2004,
BMC Bioinformatics, 5, 175.
-
Schuster, S. and Hilgetag, C., "On elementary flux modes in biochemical
reaction systems at steady state", 1994,
J.Biol. Syst., 2, 165-182.
- 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