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

  1. Wagner, C., "Nullspace approach to determine the elementary modes of chemical reaction systems", 2004,
    J.Phys. Chem. B, 108, 2425-2431.
  2. Gagneur, J. and Klamt, S., "Computation of elementary modes: A unifying framework and the new binary approach", 2004,
    BMC Bioinformatics, 5, 175.
  3. Schuster, S. and Hilgetag, C., "On elementary flux modes in biochemical reaction systems at steady state", 1994,
    J.Biol. Syst., 2, 165-182.
  4. 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