Uploading a GEM to eQuilibrator 3 database

[Pınar Kocabaş]

Is there any way to upload full genome scale metabolic model to eQuilibrator 3 database and get all Keq values at once?

Thank you,

Kind Regards

Dr. Pınar Kocabaş

[Elad Noor]

Hello Pınar,

There is no option for doing this via the website (https://equilibrator.weizmann.ac.il/) but you can use the python package (equilibrator-api) for this:

https://equilibrator.readthedocs.io/en/latest/autoapi/equilibrator_api/compatibility/index.html#equilibrator_api.compatibility.map_cobra_reactions

Just note that when using large sets of Keq, one should take special care with the uncertainties (which are multivariate). We wrote a short tutorial about this here:

https://equilibrator.readthedocs.io/en/latest/covariance.html

If you don't find all the answers in the documentation, feel free to ask for more help.

Best,

Elad