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VirtualMetabolicHuman / Recon

The aim of this repository is to assist in further improving and expanding the genome-scale human metabolic reconstruction through the use of issues. Please note that pull requests will be automatically closed.
http://VMH.life
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Model version from here and the vmh.life homepage differ #5

Closed Porthmeus closed 2 years ago

Porthmeus commented 2 years ago

Hej ho,

I just realized that the models from here are different from the model which is provided on the vmh.life homepage (https://www.vmh.life/files/reconstructions/Recon/3D.01/Recon3D_301.zip). Both models carry the same version number but differ in the number of reactions and metabolites. The VMH version seems to be a superset of the GitHub version. Furthermore, the VMH version lacks the subsystem/groups annotation. My question would be now, which model do you recommend to work with and why?

Thanks in advance!

Jan

Porthmeus commented 2 years ago

If one is able to read the README.md one can figure out the answer to my question. "Recon3Model.mat and Recon3Model.xml:refer to a stoichiometrically and flux-consistent subset of Recon3D, which has been constrained such that the ATP yield from various carbon sources under oxic and anoxic conditions is comparable to the theoretical values" - that is what it is stated there.

However, I would recommend using different version numbers/names/anything to indicate that difference and make both models available on the vmh homepage with the respective disclaimer. I will have to run some analysis again now...