1. A method for modeling cellular metabolism of an organism, comprising: constructing on a computer a flux balance analysis model utilizing stoichiometric mass balances of metabolic and cellular composition information of the organism to identify stoichiometric boundaries for available flux distributions of a metabolic network; applying logic constraints comprising a regulation matrix to the flux balance analysis model to produce an altered flux balance analysis model, wherein said logic constraints constrain one of said identified stoichiometric boundaries for one of said available flux distributions, wherein said altered flux balance analysis model has improved predictive capabilities of cellular metabolism of the organism over said flux balance analysis model and thereby provides a model of cellular metabolism of the organism; and providing an output to a user of said available flux distribution having said constrained stoichiometric boundary.