geometricFBA¶

geometricFBA(model, varargin)[source]¶

Finds a unique optimal FBA solution that is (in some sense) central to the range of possible fluxes; as described in K Smallbone, E Simeonidis (2009). Flux balance analysis: A geometric perspective. J Theor Biol 258: 311-315 http://dx.doi.org/10.1016/j.jtbi.2009.01.027

Usage

flux = geometricFBA(model, varargin)

Input

model – COBRA model structure

Optional inputs

printLevel – [default: 1] printing level, = 0 - silent = 1 - show algorithm progress and times

epsilon – [default: 1e-6] convergence tolerance of algorithm, defined in more detail in paper above

flexRel – [default: 0] flexibility to flux bounds try e.g. 1e-3 if the algorithm has convergence problems

Output

flux – unique centered flux

Optional parameters can be entered as parameter name followed by parameter value: i.e. ...,’epsilon’, 1e-9)