Welcome to MIMEco

MIMEco is a 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 metabolites 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).

You can access the source code on github

Check out the Global usage and Enterocyte specific analysis sections for further information

Note

This project is under active development.

Contents

User Guide

• Home
• Installation
  • Dependencies
• Global usage
  • Models and medium definition
  • Metabolic interaction inference
  • Exchanged metabolites inference
• Extracting data to do further analysis
• Enterocyte specific analysis
  • Enterocyte model
  • Infering interaction score and type
  • Predicting cross-feeding between models

API modules

• Analysis module
  • crossfed_metabolites()
  • enterocyte_crossfed_metabolites()
  • enterocyte_interaction_score_and_type()
  • interaction_score_and_type()
• Utils Module
  • correlation()
  • create_ecosystem_metabolic_dict()
  • crossfed_mets()
  • extract_sampling_data()
  • find_namespace()
  • infer_interaction_score()
  • infer_interaction_type()
  • mo_fba()
  • mocba_to_cobra()
  • no_compartment_id()
  • oppositeSigns()
  • pareto_parsing()
  • pareto_plot()
  • pareto_sampling()
  • plot_exchange()
  • reac_to_met_id()
  • restrain_medium()
  • unrestrain_medium()