The impl package and subpackages contain the actual implementation of
the algorithm to compute elementary modes (EFMs).
Different implementations might implement different algorithms, however, current
implementations are all versions of the double description method (see [1], [2]).
The default implementation class is {@link ch.javasoft.metabolic.efm.impl.SequentialDoubleDescriptionImpl
SequentialDoubleDescriptionImpl}. The algorithm supports {@link ch.javasoft.metabolic.efm.memory.incore in-core}
and {@link ch.javasoft.metabolic.efm.memory.outcore out-of-core} computation,
storing intermediary modes in memory (in-core) or on disk (out-of-core memory).
Different algorithm versions are reflected by different {@link ch.javasoft.metabolic.efm.model model}
versions, currently, the {@link ch.javasoft.metabolic.efm.model.nullspace nullspace}
approach (see [3], [4]) and the {@link ch.javasoft.metabolic.efm.model.canonical canonical}
approach (see [5]) are available. For implementation details, also see [6].
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