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