This repository is dedicated to the genome-scale human metabolic reconstruction, Recon3D (Brunk et al, Nat Biotech, 2018).
The aim of this repository is to allow the user to post issues regarding current content, missing information, and (suggested) expansions.
We will review the issues and address them.
Please ensure to provide literature-evidence for suggested changes or expansions.
Please note that this is a project funded by research grants. Consequently, addressing issues may take time, depending on the complexity of the issue as well as the extent of supporting information provided by the user.
PLEASE NOTE THAT PULL-REQUESTS WILL BE AUTOMATICALLY CLOSED WITHOUT MERGING, as VMH.life already implements version control via a database implementation.
IMPORTANT:
Recon3D.mat and Recon3D.xml: refer to the genome-scale human metabolic reconstruction as it can be queried in http://VMH.life.
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. Please refer to Brunk et al, Nat Biotech, 2018 for more details.
Reference: Brunk, E., Sahoo, S., Zielinski, D., Altunkaya, A., Draeger, A., Mih, N., Gatto, F., Nilsson, A., Preciat, G., Aurich, M.K., Prlic, A., Sastry, A., Danielsdottir, A.D., Heinken, A., Noronha, A., Rose, P.W., Burley, S.K., Fleming, R.M.T., Nielsen, J., Thiele, I., Palsson, B.O., "Recon3D enables a three-dimensional view of gene variation in human metabolism, Nature Biotechnology (2018).