17.1.1.2.1.2. cobra.flux_analysis.fastcc
¶
Provide an implementation of FASTCC.
17.1.1.2.1.2.1. Module Contents¶
17.1.1.2.1.2.1.1. Functions¶
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Perform the LP required for FASTCC. |
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Flip the coefficients for optimizing in reverse direction. |
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Check consistency of a metabolic network using FASTCC 1. |
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cobra.flux_analysis.fastcc.
_find_sparse_mode
(model, rxns, flux_threshold, zero_cutoff)[source]¶ Perform the LP required for FASTCC.
- Parameters
model (cobra.core.Model) – The cobra model to perform FASTCC on.
rxns (list of cobra.core.Reactions) – The reactions to use for LP.
flux_threshold (float) – The upper threshold an auxiliary variable can have.
zero_cutoff (float) – The cutoff below which flux is considered zero.
- Returns
result – The list of reactions to consider as consistent.
- Return type
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cobra.flux_analysis.fastcc.
_flip_coefficients
(model, rxns)[source]¶ Flip the coefficients for optimizing in reverse direction.
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cobra.flux_analysis.fastcc.
fastcc
(model, flux_threshold=1.0, zero_cutoff=None)[source]¶ Check consistency of a metabolic network using FASTCC 1.
FASTCC (Fast Consistency Check) is an algorithm for rapid and efficient consistency check in metabolic networks. FASTCC is a pure LP implementation and is low on computation resource demand. FASTCC also circumvents the problem associated with reversible reactions for the purpose. Given a global model, it will generate a consistent global model i.e., remove blocked reactions. For more details on FASTCC, please check 1.
- Parameters
model (cobra.Model) – The constraint-based model to operate on.
flux_threshold (float, optional (default 1.0)) – The flux threshold to consider.
zero_cutoff (float, optional) – The cutoff to consider for zero flux (default model.tolerance).
- Returns
The consistent constraint-based model.
- Return type
Notes
The LP used for FASTCC is like so: maximize: sum_{i in J} z_i s.t. : z_i in [0, varepsilon] forall i in J, z_i in mathbb{R}_+
v_i ge z_i forall i in J Sv = 0 v in B
References