Check for thermodynamically infeasible loops

opencobra / memote

memote – the genome-scale metabolic model test suite

https://memote.readthedocs.io/

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Check for thermodynamically infeasible loops #104

Closed ChristianLieven closed 6 years ago

ChristianLieven commented 7 years ago

Description

Memote currently lacks tests to identify reactions that are involved in Type III loops i.e. reactions that carry flux even though all boundary reactions are closed.

Implementation

FVA with blocked exchanges if the min/max fluxes == lb/ub => rxn is involved in a loop

ChristianLieven commented 6 years ago

I'm necroing this issue because @parizad may have had some ideas here that are worth implementing to get this tests back up and running in a reasonable amount of time.

Find Type-III cycles = Close boundary reactions and then run FVA identify reactions with min/max at system.lb/.ub
Flux coupling to identify looped reactions? Maybe? Outputs sets of looped reactions (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-57)

matthiaskoenig commented 6 years ago

Is there some way to check for thermodynamically infeasible loops with memote? How would be the format of the Delta G values and where would these be stored in the SBML?

Midnighter commented 6 years ago

We actually have a test in place to identify loops but are skipping it because it is too slow. It's not based on computing ΔG values.