test_consistency

Stoichiometric consistency tests for an instance of cobra.Model.

Module Contents

Functions

test_stoichiometric_consistency(model)	Expect that the stoichiometry is consistent.
test_unconserved_metabolites(model)	Report number all unconserved metabolites.
test_inconsistent_min_stoichiometry(model)	Report inconsistent min stoichiometries.
test_detect_energy_generating_cycles(model, met)	Expect that no energy metabolite can be produced out of nothing.
test_reaction_charge_balance(model)	Expect all reactions to be charge balanced.
test_reaction_mass_balance(model)	Expect all reactions to be mass balanced.
test_blocked_reactions(model)	Expect all reactions to be able to carry flux in complete medium.
test_find_stoichiometrically_balanced_cycles(model)	Expect no stoichiometrically balanced loops to be present.
test_find_orphans(model)	Expect no orphans to be present.
test_find_deadends(model)	Expect no dead-ends to be present.
test_find_disconnected(model)	Expect no disconnected metabolites to be present.
test_find_metabolites_not_produced_with_open_bounds(model)	Expect metabolites to be producible in complete medium.
test_find_metabolites_not_consumed_with_open_bounds(model)	Expect metabolites to be consumable in complete medium.
test_find_reactions_unbounded_flux_default_condition(model)	Expect the fraction of unbounded reactions to be low.

test_consistency.test_stoichiometric_consistency(model)

Expect that the stoichiometry is consistent.

Stoichiometric inconsistency violates universal constraints: 1. Molecular masses are always positive, and 2. On each side of a reaction the mass is conserved. A single incorrectly defined reaction can lead to stoichiometric inconsistency in the model, and consequently to unconserved metabolites. Similar to insufficient constraints, this may give rise to cycles which either produce mass from nothing or consume mass from the model.

Implementation: This test uses an implementation of the algorithm presented in section 3.1 by Gevorgyan, A., M. G Poolman, and D. A Fell. “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245. doi: 10.1093/bioinformatics/btn425

test_consistency.test_unconserved_metabolites(model)

Report number all unconserved metabolites.

The list of unconserved metabolites is computed using the algorithm described in section 3.2 of “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245. doi: 10.1093/bioinformatics/btn425.

test_consistency.test_inconsistent_min_stoichiometry(model)

Report inconsistent min stoichiometries.

Only 10 unconserved metabolites are reported and considered to avoid computing for too long.

Implementation: Algorithm described in section 3.3 of “Detection of Stoichiometric Inconsistencies in Biomolecular Models.” Bioinformatics 24, no. 19 (2008): 2245. doi: 10.1093/bioinformatics/btn425.

test_consistency.test_detect_energy_generating_cycles(model, met)

Expect that no energy metabolite can be produced out of nothing.

When a model is not sufficiently constrained to account for the thermodynamics of reactions, flux cycles may form which provide reduced metabolites to the model without requiring nutrient uptake. These cycles are referred to as erroneous energy-generating cycles. Their effect on the predicted growth rate in FBA may account for an increase of up to 25%, which makes studies involving the growth rates predicted from such models unreliable.

Implementation: This test uses an implementation of the algorithm presented by: 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

First attempt to identify the main compartment (cytosol), then attempt to identify each metabolite of the referenced list of energy couples via an internal mapping table. Construct a dissipation reaction for each couple. Carry out FBA with each dissipation reaction as the objective and report those reactions that non-zero carry flux.

test_consistency.test_reaction_charge_balance(model)

Expect all reactions to be 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.

In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net charges of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a charge are not considered to be balanced, even though the remaining metabolites participating in the reaction might be.

Implementation: For each reaction that isn’t a boundary or biomass reaction check if each metabolite has a non-zero charge attribute and if so calculate if the overall sum of charges of reactants and products is equal to zero.

test_consistency.test_reaction_mass_balance(model)

Expect all reactions to be 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.

In steady state, for each metabolite the sum of influx equals the sum of efflux. Hence the net masses of both sides of any model reaction have to be equal. Reactions where at least one metabolite does not have a formula are not considered to be balanced, even though the remaining metabolites participating in the reaction might be.

Implementation: For each reaction that isn’t a boundary or biomass reaction check if each metabolite has a non-zero elements attribute and if so calculate if the overall element balance of reactants and products is equal to zero.

test_consistency.test_blocked_reactions(model)

Expect all reactions to be able to carry flux in complete medium.

Universally blocked reactions are reactions that during Flux Variability Analysis cannot carry any flux while all model boundaries are open. Generally blocked reactions are caused by network gaps, which can be attributed to scope or knowledge gaps.

Implementation: Use flux variability analysis (FVA) implemented in cobra.flux_analysis.find_blocked_reactions with open_exchanges=True. Please refer to the cobrapy documentation for more information: https://cobrapy.readthedocs.io/en/stable/autoapi/cobra/flux_analysis/ variability/index.html#cobra.flux_analysis.variability. find_blocked_reactions

test_consistency.test_find_stoichiometrically_balanced_cycles(model)

Expect no stoichiometrically balanced loops to be present.

Stoichiometrically Balanced Cycles are artifacts of insufficiently constrained networks resulting in reactions that can carry flux when all the boundaries have been closed.

Implementation: Close all model boundary reactions and then use flux variability analysis (FVA) to identify reactions that carry flux.

test_consistency.test_find_orphans(model)

Expect no orphans to be present.

Orphans are metabolites that are only consumed but not produced by reactions in the model. They may indicate the presence of network and knowledge gaps.

Implementation: Find orphan metabolites structurally by considering only reaction equations and bounds. FBA is not carried out.

test_consistency.test_find_deadends(model)

Expect no dead-ends to be present.

Dead-ends are metabolites that can only be produced but not consumed by reactions in the model. They may indicate the presence of network and knowledge gaps.

Implementation: Find dead-end metabolites structurally by considering only reaction equations and bounds. FBA is not carried out.

test_consistency.test_find_disconnected(model)

Expect no disconnected metabolites to be present.

Disconnected metabolites are not part of any reaction in the model. They are most likely left-over from the reconstruction process, but may also point to network and knowledge gaps.

Implementation: Check for any metabolites of the cobra.Model object with emtpy reaction attribute.

test_consistency.test_find_metabolites_not_produced_with_open_bounds(model)

Expect metabolites to be producible in complete medium.

In complete medium, a model should be able to divert flux to every metabolite. This test opens all the boundary reactions i.e. simulates a complete medium and checks if any metabolite cannot be produced individually using flux balance analysis. Metabolites that cannot be produced this way are likely orphan metabolites, downstream of reactions with fixed constraints, or blocked by a cofactor imbalance. To pass this test all metabolites should be producible.

Implementation: Open all model boundary reactions, then for each metabolite in the model add a boundary reaction and maximize it with FBA.

test_consistency.test_find_metabolites_not_consumed_with_open_bounds(model)

Expect metabolites to be consumable in complete medium.

In complete medium, a model should be able to divert flux from every metabolite. This test opens all the boundary reactions i.e. simulates a complete medium and checks if any metabolite cannot be consumed individually using flux balance analysis. Metabolites that cannot be consumed this way are likely dead-end metabolites or upstream of reactions with fixed constraints. To pass this test all metabolites should be consumable.

Implementation: Open all model boundary reactions, then for each metabolite in the model add a boundary reaction and minimize it with FBA.

test_consistency.test_find_reactions_unbounded_flux_default_condition(model)

Expect the fraction of unbounded reactions to be low.

A large fraction of model reactions able to carry unlimited flux under default conditions indicates problems with reaction directionality, missing cofactors, incorrectly defined transport reactions and more.

Implementation: Without changing the default constraints run flux variability analysis. From the FVA results identify those reactions that carry flux equal to the model’s maximal or minimal flux.