Models and methods for determining systemic properties of regulated reaction networks
First Claim
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1. A computer readable medium or media, comprising:
- (a) a data structure relating a plurality of reactants to a plurality of reactions of a biochemical reaction network, wherein each of said 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, and wherein at least one of said reactions is a regulated reaction; and
(b) a constraint set for said plurality of reactions, wherein said constraint set comprises a variable constraint for said regulated reaction.
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Abstract
The invention provides a model of a reaction network integrated with regulatory controls related to the reactions. A method is provided for determining a systemic property of a reaction network using a model of the invention. Also provided is a method for modeling changes that occur in a reaction network at various time points due to regulatory events.
227 Citations
74 Claims
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1. A computer readable medium or media, comprising:
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(a) a data structure relating a plurality of reactants to a plurality of reactions of a biochemical reaction network, wherein each of said 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, and wherein at least one of said reactions is a regulated reaction; and
(b) a constraint set for said plurality of reactions, wherein said constraint set comprises a variable constraint for said regulated reaction. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33)
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34. A method for determining a systemic property of a biochemical reaction network, comprising:
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(a) providing a data structure relating a plurality of reactants to a plurality of reactions of a biochemical reaction network, wherein each of said 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, and wherein at least one of said reactions is a regulated reaction;
(b) providing a constraint set for said plurality of reactions, wherein said constraint set comprises a variable constraint for said regulated reaction;
(c) providing a condition-dependent value to said variable constraint;
(d) providing an objective function, and (e) determining at least one flux distribution that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby determining a systemic property of said biochemical reaction network. - View Dependent Claims (35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70)
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71. A method for determining a systemic property of a biochemical reaction network at a first and second time, comprising:
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(a) providing a data structure relating a plurality of reactants to a plurality of reactions of a biochemical reaction network, wherein each of said 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, and wherein at least one of said reactions is a regulated reaction;
(b) providing a constraint set for said plurality of reactions, wherein said constraint set comprises a variable constraint for said regulated reaction;
(c) providing a condition-dependent value to said variable constraint;
(d) providing an objective function;
(e) determining at least one flux distribution at a first time that minimizes or maximizes said objective function when said constraint set is applied to said data structure, thereby determining a systemic property of said biochemical reaction network at said first time;
(f) modifying said value provided to said variable constraint, and (g) repeating step (e), thereby determining a systemic property of said biochemical reaction network at a second time. - View Dependent Claims (72, 73, 74)
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Specification