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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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Memote doesn’t account for thermodynamics constraints to calculate directionality of reactions #673

Open ChristianLieven opened 4 years ago

ChristianLieven commented 4 years ago

Opening this issue on behalf of Anush @anushchp:

Problem description

It complains that O2 consuming reactions don’t have fixed bounds. Thermodynamics (using pyTFA: https://github.com/EPFL-LCSB/pytfa/ or matTFA: https://github.com/EPFL-LCSB/mattfa) can define the directionality of those reactions. Maybe it is worth considering linking those repositories to memote to perform thermodynamically consistent analyses

My additional thoughts: Perhaps we could somehow allow users to optionally include thermodynamic databases and to run pyTFA. Which would improve the accuracy for many of our tests for a given condition/ medium? We could implement this similarly to how we implemented our experimental tests: the user provides data (thermoDB) and config file.

Midnighter commented 4 years ago

This also relates to the debate about reconstructions vs models...

anushchp commented 4 years ago

Thank you! I was not aware of that debate. I think the tests for networks are anyways a subset of those for models (although the assessment of the results is different). Since memote is a genome-scale metabolic model test suite, it might be worth including both network and model-related tests as long as they are labeled as "network" and "model". Users will decide what to focus on for quality assessment based on the usage they want to give to the network/model. Just a suggestion. I envision memote setting the quality standards for both and some SOPs on how to differentiate the quality assessment between them. That would be super cool.