Figure 1. (A) A simple geometric illustration of an FBA problem.

Constant constraints on the Vi limit the feasible solution to an n-dimensional cube (shown in gray). Further linear constraints from the S matrix create a cone of feasible solutions (blue). Linear programming algorithms find an optimal solution on a vertex (illustrated with orange circle). (B and C) Depiction of a simple metabolic network with compartmentalization and its associated stoichiometric matrix. The three compartments, denoted with subscripts b, e, and c represent the boundary, extracellular environment, and cytosol. The boundary is what separates the model from its environment, and mass balance is not assumed at the boundary; this allows for the implementation of source and sink reactions.