Check for futile energy cycles on taxa-specific reconstructions

[Robaina]

It seems this functionality is not present in CarveME's (AFAIK). Implement functionality and include it in reconstruction pipeline. Perhaps already implemented in memote.

UPDATE:

memote implements the energy cycle detection algorithm in this publication.

UPDATE:

However, remote only reports a list of metabolite IDs. This makes it difficult to remove and identify the cycles.

Another option could be running pFBA instead of regular FBA to avoid cycles in the solution space.

related tests:

• test_detect_energy_generating_cycles
• test_find_reactions_unbounded_flux_default_condition
• test_find_stoichiometrically_balanced_cycles

[Robaina]

CarveME uses these strategies according to their publication:

• "The model was tested for biomass and ATP production. Unlimited ATP generation was detected by flux variability analysis (34) and the reversibility of the reactions involved in energy-generating cycles was manually constrained in an iterative way until all reactions operated in the most thermodynamically favorable direction."

• "Since ΔGor
  could not be determined for all reactions, additional heuristic rules were applied: (i) ATP-consuming reactions were not allowed to proceed in the reverse direction; (ii) reactions present in thermodynamically curated models (29,33) assumed the reversibility constraints adopted in these models."