The model package and subpackages defines interfaces and provides
default classes for the support of different algorithm variants. Different
variants typically require specified models to store intermediary data.
Currently, the {@link ch.javasoft.metabolic.efm.model.nullspace nullspace}
approach (see [1], [2]) and the {@link ch.javasoft.metabolic.efm.model.canonical canonical}
approach (see [3]) are supported. For implementation details, also see [4].
References
-
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