# 17.1.1.2.1.4. cobra.flux_analysis.geometric¶

Provide an implementation of geometric FBA.

## 17.1.1.2.1.4.1. Module Contents¶

### 17.1.1.2.1.4.1.1. Functions¶

 geometric_fba(model: Model, epsilon: float = 1e-06, max_tries: int = 200, processes: Optional[int] = None) → ‘Solution’ Perform geometric FBA to obtain a unique, centered flux distribution.
cobra.flux_analysis.geometric.logger[source]
cobra.flux_analysis.geometric.geometric_fba(model: Model, epsilon: float = 1e-06, max_tries: int = 200, processes: Optional[int] = None) → 'Solution'[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).

• processes (int, optional) – The number of parallel processes to run. If not explicitly passed, will be set from the global configuration singleton (default None).

Returns

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

Return type

cobra.Solution

Raises

RuntimeError – If iteration count becomes equal to max_tries.

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.