M Model Collection
To view the publications and organisms associated with each model, please see the key.
A collection of M models downloaded from published studies, along with notebooks which parse and solve them. The notebooks can be viewed at nbviewer.
To parse these reconstructions into a computing M-models, install
version 0.4.0b1 or later, along with the optional dependcies libsbml and scipy.
To load the reconstructions from the Microsoft Excel format, the
pandas library is also necessary. Then run
all_models.mat file can be used with both cobrapy and the
COBRA toolbox. This script also generates SBML files which use the SBML level 3
with the fbc package (version 2), which are placed in the "sbml3" directory.
Some of the models, however, could not be parsed correctly into solving models. Still, they give consistent results between floating point and exact solvers
Please note that these models are not the official versions. Many of the models in here have been updated at the original source. This is merely a snapshot of models which were used in the analysis for this study.
The models themselves, however, are provided only for reproducing the results in the included scripts. All other uses must be consistent with the initial license the model was released under.