cobra.flux_analysis.fastcc
¶
Provide an implementation of FASTCC.
Module Contents¶
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. |
- cobra.flux_analysis.fastcc._find_sparse_mode(model: cobra.core.Model, rxns: List[cobra.core.Reaction], flux_threshold: float, zero_cutoff: float) List[cobra.core.Reaction] [source]¶
Perform the LP required for FASTCC.
- Parameters
model (cobra.Model) – The model to perform FASTCC on.
rxns (list of cobra.Reaction) – 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
The list of reactions to consider as consistent.
- Return type
- cobra.flux_analysis.fastcc._flip_coefficients(model: cobra.core.Model, rxns: List[cobra.core.Reaction]) None [source]¶
Flip the coefficients for optimizing in reverse direction.
- Parameters
model (cobra.Model) – The model to operate on.
rxns (list of cobra.Reaction) – The list of reactions whose coefficients will be flipped.
- cobra.flux_analysis.fastcc.fastcc(model: cobra.core.Model, flux_threshold: float = 1.0, zero_cutoff: Optional[float] = None) cobra.core.Model [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 model to operate on.
flux_threshold (float, optional) – The flux threshold to consider (default 1.0).
zero_cutoff (float, optional) – The cutoff to consider for zero flux (default model.tolerance).
- Returns
The consistent 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