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biosustain / memote-meta-study

Test metabolic models in the wild and rank them according to popularity and how easily they can be improved.
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Memote Meta Study

DOI

We have collected a large number of genome-scale metabolic models (GEMs) and investigated the aggregated results of running the models through memote's test suite. The models can be found separately at https://github.com/biosustain/memote-meta-models.

The goals of this study were:

  1. Investigate the collective performance of those models.
  2. Use those insights to calibrate how memote calculates the final test score.

N.B.: We looked at distributions of test metrics because we are not interested in shaming individual model authors but we are interested in general trends and the current overall state of GEMs.

Installation

The easiest way to set up the dependencies for this project is to use the Makefile.

make requirements
make jupyter

This will install all Python requirements and configure the Jupyter notebook extensions. R dependencies are handled by a specialized Docker image midnighter/knit-memote:3.6.1. You can directly use that image in order to ensure reproducibility. If, for some reason, you wish to build the image yourself, you can do so with the command make build.

Usage

The main work can be performed via the make command make plot or for more fine grained control via the command line interface exposed by ./cli.py and the relevant R scripts.

Contact

For comments and questions get in touch via

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