The efm package and subpackages contain classes for the computation of elementary modes (EFMs) for {@link ch.javasoft.metabolic metabolic} networks; {@link ch.javasoft.metabolic.efm.ElementaryFluxModes ElementaryFluxModes} provides different methods to invoke computation from a java program, classes for command line invocation are contained in the {@link ch.javasoft.metabolic.efm.main main} subpackage.

Elementary flux modes (EFMs) are non-decomposable minimal pathways of metabolic networks under steady state conditions. Valid states of the network are linear superpositions of elementary modes. Geometrically, the solution space shapes a polyhedral cone (the flux cone), which is a well studied convex set in computational geometry. Computing EFMs is thus basically equivalent to extreme ray enumeration of polyhedral cones.

Most implementations to compute elementary modes are variants of the double description method invented by Motzkin et al. [1]. Some selected references relating to EFMs 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