memote.support.consistency module

Supporting functions for stoichiometric consistency checks.

memote.support.consistency.check_stoichiometric_consistency(model)[source]

Verify the consistency of the model stoichiometry.

Parameters:

model : cobra.Model

The metabolic model under investigation.

Notes

See [R15] section 3.1 for a complete description of the algorithm.

[R15]Gevorgyan, A., M. G Poolman, and D. A Fell. “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245.
memote.support.consistency.find_blocked_reactions(model)[source]

Find metabolic reactions that are blocked.

Parameters:

model : cobra.Model

The metabolic model under investigation.

Notes

Blocked reactions are those reactions that when optimized for cannot carry any flux while all exchanges are open.

memote.support.consistency.find_elementary_leakage_modes(model, atol=1e-13)[source]

Detect elementary leakage modes.

Parameters:

model : cobra.Model

The metabolic model under investigation.

atol : float, optional

Values below the absolute tolerance are treated as zero. Expected to be very small but larger than zero.

Notes

See [R26] section 3.4 for a complete description of the algorithm.

References

[R26](1, 2) Gevorgyan, A., M. G Poolman, and D. A Fell. “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245.
memote.support.consistency.find_imbalanced_reactions(model)[source]

Find metabolic reactions that not mass and/or charge balanced.

This will exclude biomass, exchange and demand reactions as they are unbalanced by definition.

Parameters:

model : cobra.Model

The metabolic model under investigation.
memote.support.consistency.find_inconsistent_min_stoichiometry(model, atol=1e-13)[source]

Detect inconsistent minimal net stoichiometries.

Parameters:

model : cobra.Model

The metabolic model under investigation.

atol : float, optional

Values below the absolute tolerance are treated as zero. Expected to be very small but larger than zero.

Notes

See [R37] section 3.3 for a complete description of the algorithm.

[R37]Gevorgyan, A., M. G Poolman, and D. A Fell. “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245.
memote.support.consistency.find_stoichiometrically_balanced_cycles(model)[source]

Find metabolic rxns in stoichiometrically balanced cycles (SBCs).

The flux distribution of nominal FVA is compared with loopless FVA (loopless=True) to determine reactions that participate in loops, as participation in loops would increase the flux through a given reactions to the maximal bounds. This function then returns reactions where the flux differs between the two FVA calculations.

Parameters:

model : cobra.Model

The metabolic model under investigation.

Notes

“SBCs are artifacts of metabolic reconstructions due to insufficient constraints (e.g., thermodynamic constraints and regulatory constraints) [R48].” They are defined by internal reactions that carry flux in spite of closed exchange reactions.

References

[R48](1, 2) Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature protocols. Nature Publishing Group. http://doi.org/10.1038/nprot.2009.203
memote.support.consistency.find_unconserved_metabolites(model)[source]

Detect unconserved metabolites.

Parameters:

model : cobra.Model

The metabolic model under investigation.

Notes

See [R59] section 3.2 for a complete description of the algorithm.

[R59]Gevorgyan, A., M. G Poolman, and D. A Fell. “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245.
memote.support.consistency.produce_atp_closed_exchanges(model)[source]

Close the model’s exchanges and tries to optimize the production of atp_c.

Parameters:

model : cobra.Model

The metabolic model under investigation.