mimeco 0.1.16

Multi-objective GEMs metabolic interaction inference

MIMEco is python package that explores communities metabolic interactions using multi-objective linear programming on GEnome-scale Metabolic models (GEMs). This tool automates the inference of interaction type, interaction score and exchanged metablites between two models in a given condition.

The concept of the methodology is described in Lambert, A., Budinich, M., Mahé, M., Chaffron, S., & Eveillard, D. (2024). Community metabolic modeling of host-microbiota interactions through multi-objective optimization. Iscience, 27(6). (http://doi.org/10.1016/j.isci.2024.110092)

Note : A technical note dedicated to this package will be published

Documentation

For detailed documentation, please go to readthedocs : mimeco

Dependancies

GLPK: MIMEco depends on benpy, which needs glpk to function. Its installation is clearly described in benpy’s pyPI page

Efficient solver To use MIMEco, you will need to download a solver, preferably CPLEX or gurobi. Both are free for academics, but require to get a license to be used at full capacity. A tutorial on how to make gurobi work with mimeco is written in the documentation

Installation

MIMEco is available on pyPI. You can install it with pip install mimeco