Biology Reference
In-Depth Information
Gap A missing reaction in the network needed to connect one or
more metabolic dead ends with the rest of the network.
Gene
e
protein
e
reaction (GPR) association A representation of the
flow from gene to protein to reaction including logical operators
(i.e., and/or) to describe protein complexes and isozymes.
Linear programming An optimization method where an objective
function is maximized or minimized subject to a set of linear
constraints.
Metabolic dead end Metabolites that can only be produced or only
consumed in the network, and are therefore only associated with
blocked reactions.
Metabolic model A computable form of a metabolic reconstruction
where bounds are set on each reaction.
Metabolic reconstruction An organism specific list of reactions and
their associated knowledge (e.g., associated genes, publications,
stoichiometry) comprising the metabolic pathways present within
the organism.
Objective function The reaction for which flux is maximized or
minimized in an optimization problem.
Shadow price Value associated with each metabolite following
optimization of the network via linear programming. The value
corresponds to the amount that the objective function value would
change with the incremental change of the exchange of that
metabolite.
Sink reaction Reactions added to the model to facilitate supply of
a metabolite when the relevant reaction is unknown or outside the
scope of the model.
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ACKNOWLEDGMENTS
This work was supported in part by a grant # R01GM057089 from the
National Institutes of Health.
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