Compostions and methods for modeling Saccharomyces cerevisiae metabolism

A method for predicting a Saccharomyces cerevisiae physiological function, comprising:

• (a) providing a data structure relating a plurality of Saccharomyces cerevisiae reactants to a plurality of reactions, wherein each of said Saccharomyces cerevisiae reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a
• stoichiometric coefficient relating said substrate and said product, wherein at least one of said Saccharomyces cerevisiae reactions is annotated to indicate an associated gene;
• (b) providing a constraint set for said plurality of Saccharomyces cerevisiae reactions;
• (c) providing an objective function, and
• (d) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby predicting a Saccharomyces cerevisiae physiological function related to said gene.

A method for predicting Saccharomyces cerevisiae growth, comprising:

• (a) providing a data structure relating a plurality of Saccharomyces cerevisiae reactants to a plurality of Saccharomyces cerevisiae reactions, wherein each of said Saccharomyces cerevisiae reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
• (b) providing a constraint set for said plurality of Saccharomyces cerevisiae reactions;
• (c) providing an objective function, and
• (d) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby predicting Saccharomyces cerevisiae growth.

A method for making a data structure relating a plurality of Saccharomyces cerevisiae reactants to a plurality of Saccharomyces cerevisiae reactions in a computer readable medium or media, comprising:

• (a) identifying a plurality of Saccharomyces cerevisiae reactions and a plurality of Saccharomyces cerevisiae reactants that are substrates and products of said Saccharomyces cerevisiae reactions;
• (b) relating said plurality of Saccharomyces cerevisiae reactants to said plurality of Saccharomyces cerevisiae reactions in a data structure, wherein each of said Saccharomyces cerevisiae reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
• (c) determining a constraint set for said plurality of Saccharomyces cerevisiae reactions;
• (d) providing an objective function;
• (e) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, and
• (f) if said at least one flux distribution is not predictive of a Saccharomyces cerevisiae physiological function, then adding a reaction to or deleting a reaction from said data structure and repeating step (e), if said at least one flux distribution is predictive of a Saccharomyces cerevisiae physiological function, then storing said data structure in a computer readable medium or media.

A data structure relating a plurality of Saccharomyces cerevisiae reactants to a plurality of Saccharomyces cerevisiae reactions, wherein said data structure is produced by a process comprising:

• (a) identifying a plurality of Saccharomyces cerevisiae reactions and a plurality of Saccharomyces cerevisiae reactants that are substrates and products of said Saccharomyces cerevisiae reactions;
• (b) relating said plurality of Saccharomyces cerevisiae reactants to said plurality of Saccharomyces cerevisiae reactions in a data structure, wherein each of said Saccharomyces cerevisiae reactions comprises a reactant identified as a substrate of the reaction, a reactant identified as a product of the reaction and a stoichiometric coefficient relating said substrate and said product;
• (c) determining a constraint set for said plurality of Saccharomyces cerevisiae reactions;
• (d) providing an objective function;
• (e) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, and
• (f) if said at least one flux distribution is not predictive of Saccharomyces cerevisiae physiology, then adding a reaction to or deleting a reaction from said data structure and repeating step (e), if said at least one flux distribution is predictive of Saccharomyces cerevisiae physiology, then storing said data structure in a computer readable medium or media.