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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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[feature] make tests check on any objective function #230

Open ChristianLieven opened 6 years ago

ChristianLieven commented 6 years ago

Rather than specific only to the biomass reaction as the objective function extend tests to include any set objective.

Some models may not have a biomass objective function, but rather alternate cellular objectives. We should be able to detect and test those too.

steinng commented 6 years ago

Two relevant examples of metabolic models which do not have a biomass reacation are iAB-RBC-283 (red blood cells) and iAT-PLT-636 (platelets).

kcorreia commented 6 years ago

Maximizing ATP production is a good objective that can assess the quality of a model, especially if it is from the electron transport chain.

I have tested many models where the ATP yield on glucose is above theoretical limit of 38 mol/mol glucose. Usually, there is a free exchange of protons that increases the yield. In my experience focusing on getting this metric right fixes a lot of problems such as loops, proton exchanges in the electron transport chain, NADPH generation, etc.

One limitation of this test is that the yield depends on the organism. Scheffersoymces stipitis would have a yield of 36 mol ATP / mol glucose. Complex I in ETC has a P:O ratio of 2.5. Saccharoymces cerevisiae 22 mol ATP / mol glucose (aerobic). Type II NADH dehydrogenase has a P:O ratio of 1.5. Saccharoymces cerevisiae 2 mol ATP / mol glucose (anaerobic).

Even though the yield may differ it is essential for all metabolic models since you can't import ATP.