cobra.flux_analysis.geometric
¶
Provide an implementation of geometric FBA.
Module Contents¶
Functions¶
|
Perform geometric FBA to obtain a unique, centered flux distribution. |
Attributes¶
- cobra.flux_analysis.geometric.geometric_fba(model: cobra.Model, epsilon: float = 1e-06, max_tries: int = 200, processes: Optional[int] = None) cobra.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.