Welcome to MMODES’s documentation!

MMODES is a package built on top of COBRApy and SciPy to allow fast set up of dynamic simulations with GEM models (dFBA), isolated or in a consortium.

Contents:

• Installing MMODES
  • PIP Install
  • Build from SOURCE
  • DOCKER Install
  • Uninstall
• Getting started
  • First steps: the Consortium object
  • Instantiating the medium
  • Run the simulation!
• The Consortium Object
  • Most common parameters
  • Setting models
  • Setting media
  • Running the Community simulation
  • Adding perturbations
• The dModel Object
  • Adding models to the Consortium
  • Limiting growth of the model
  • Death rate
• The Experiment Object
  • Instantiating the Experiment
  • Running an Experiment
  • Filtering the output

Indices and tables

• Index
• Module Index
• Search Page