Patent ID: 8301393

Claim:
A computer-implemented method for developing data-driven dynamic models of biological networks comprising: providing, at a computer system, a data structure relating a plurality of biological network reactants to a plurality of biological network reactions, the plurality of biological network reactions comprising one or more flux distributions, wherein each of the biological network reactions comprises one or more biological network reactants identified as a substrate of the reaction, one or more biological network reactants identified as a product of the biological network reaction and a stoichiometric coefficient relating the substrate and the product; providing, at a computer system, a constraint set for the plurality of biological network reactions; providing, at a computer system, a constraint set for a plurality of concentrations associated with the plurality of biological network reactions; providing, at a computer system, a constraint set for a plurality of kinetic constants associated with the plurality of biological network reactions; providing, at a computer system, a constraint set for a plurality of equilibrium constants associated with the plurality of biological network reactions; integrating, at a computer system, the sets of constraints, thereby forming stoichiometric, gradient, and Jacobian matrices; providing, at a computer system, an objective function; and predicting, at a computer system, a physiological function related to at least one of the biological networks by determining using the computer system at least one flux distribution, from the one or more flux distributions, that minimizes or maximizes the objective function when at least one constraint set from the sets of constraints is applied to the data structure.