17.1.1.3.1.2. cobra.flux_analysis.fastcc

Provide an implementation of FASTCC.

17.1.1.3.1.2.1. Module Contents

17.1.1.3.1.2.1.1. Functions

_find_sparse_mode(model: Model, rxns: List[‘Reaction’], flux_threshold: float, zero_cutoff: float) → List[‘Reaction’]

Perform the LP required for FASTCC.

_flip_coefficients(model: Model, rxns: List[‘Reaction’]) → None

Flip the coefficients for optimizing in reverse direction.

fastcc(model: Model, flux_threshold: float = 1.0, zero_cutoff: Optional[float] = None) → ‘Model’

Check consistency of a metabolic network using FASTCC 1.

cobra.flux_analysis.fastcc._find_sparse_mode(model: Model, rxns: List['Reaction'], flux_threshold: float, zero_cutoff: float) → List['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

list of cobra.Reaction

cobra.flux_analysis.fastcc._flip_coefficients(model: Model, rxns: List['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: Model, flux_threshold: float = 1.0, zero_cutoff: Optional[float] = None) → '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

cobra.Model

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

1(1,2,3)

Vlassis N, Pacheco MP, Sauter T (2014) Fast Reconstruction of Compact Context-Specific Metabolic Network Models. PLoS Comput Biol 10(1): e1003424. doi:10.1371/journal.pcbi.1003424