15.1.1.2.1.3. cobra.flux_analysis.geometric

Provide an implementation of geometric FBA.

15.1.1.2.1.3.1. Module Contents

cobra.flux_analysis.geometric.geometric_fba(model, epsilon=1e-06, max_tries=200)[source]

Perform geometric FBA to obtain a unique, centered flux distribution.

Geometric FBA [1] formulates the problem as a polyhedron and then solves it by bounding the convex hull of the polyhedron. The bounding forms a box around the convex hull which reduces with every iteration and extracts a unique solution in this way.

Parameters:
  • model (cobra.Model) – The model to perform geometric FBA on.
  • epsilon (float, optional) – The convergence tolerance of the model (default 1E-06).
  • max_tries (int, optional) – Maximum number of iterations (default 200).
Returns:

The solution object containing all the constraints required for geometric FBA.
Return type:

cobra.Solution

References

[1]Smallbone, Kieran & Simeonidis, Vangelis. (2009). Flux balance analysis: A geometric perspective. Journal of theoretical biology.258. 311-5. 10.1016/j.jtbi.2009.01.027.