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 [R16] section 3.1 for a complete description of the algorithm.

[R16]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.detect_energy_generating_cycles(model, metabolite_id)[source]

Detect erroneous energy-generating cycles for a a single metabolite.

The function will first build a dissipation reaction corresponding to the input metabolite. This reaction is then set as the objective for optimization, after closing all exchanges. If the reaction was able to carry flux, an erroneous energy-generating cycle must be present. In this case a list of reactions with a flux greater than zero is returned. Otherwise, the function returns False.

Parameters:

model : cobra.Model

The metabolic model under investigation.

metabolite_id : str

The identifier of an energy metabolite.

Notes

“[...] energy generating cycles (EGC) [...] charge energy metabolites without a source of energy. [...] To efficiently identify the existence of diverse EGCs, we first add a dissipation reaction to the metabolic network for each metabolite used to transmit cellular energy; e.g., for ATP, the irreversible reaction ATP + H2O → ADP + P + H+ is added. These dissipation reactions close any existing energy-generating cycles, thereby converting them to type-III pathways. Fluxes through any of the dissipation reactions at steady state indicate the generation of energy through the metabolic network. Second, all uptake reactions are constrained to zero. The sum of the fluxes through the energy dissipation reactions is now maximized using FBA. For a model without EGCs, these reactions cannot carry any flux without the uptake of nutrients. [R27].”

References

[R27](1, 2) Fritzemeier, C. J., Hartleb, D., Szappanos, B., Papp, B., & Lercher, M. J. (2017). Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal. PLoS Computational Biology, 13(4), 1–14. http://doi.org/10.1371/journal.pcbi.1005494
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_charge_imbalanced_reactions(model)[source]

Find metabolic reactions that are not charge balanced.

This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a charge defined.

Parameters:

model : cobra.Model

The metabolic model under investigation.
memote.support.consistency.find_deadends(model)[source]

Return metabolites that are only produced in reactions.

Parameters:

model : cobra.Model

The metabolic model under investigation.
memote.support.consistency.find_disconnected(model)[source]

Return metabolites that are not in any of the reactions.

Parameters:

model : cobra.Model

The metabolic model under investigation.
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 [R38] section 3.4 for a complete description of the algorithm.

References

[R38](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_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 [R49] section 3.3 for a complete description of the algorithm.

[R49]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_mass_imbalanced_reactions(model)[source]

Find metabolic reactions that are not mass balanced.

This will exclude biomass, exchange and demand reactions as they are unbalanced by definition. It will also fail all reactions where at least one metabolite does not have a formula defined.

Parameters:

model : cobra.Model

The metabolic model under investigation.
memote.support.consistency.find_orphans(model)[source]

Return metabolites that are only consumed in reactions.

Parameters:

model : cobra.Model

The metabolic model under investigation.
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) [R510].” They are defined by internal reactions that carry flux in spite of closed exchange reactions.

References

[R510](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 [R611] section 3.2 for a complete description of the algorithm.

[R611]Gevorgyan, A., M. G Poolman, and D. A Fell. “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245.