1. Installation and Requirements

Prerequisites

CBMPy

The dynamic-community-fba package utilizes the CBMPy library [1] for managing constraint-based metabolic models. Similar to COBRApy [2], CBMPy is a Python package designed for loading, creating, and manipulating constraint-based models. Furthermore, it streamlines the interaction with linear program solvers, such as CPLEX [3].

To install CBMPy, you can use the following command:

pip install cbmpy

For more information and detailed documentation on using CBMPy, please refer to the CBMPy GitHub repository and the CBMPy documentation.

Please make sure CBMPy is up and running correctly before preceding with the analyses provided by dcFBA. See also: 2.1. Loading a model using CBMPy section

CPLEX

CBMPy currently provides an interface to CPLEX and GLPK. However, to fully utilize dcFBA, we strongly recommend using the CPLEX linear solver.

You can download the CPLEX Python interface from IBM . Please follow the installation instructions from the installer. Don’t forget to execute the following command in your designated Python environment after the installation is completed to link CPLEX in the environment:

python PATH_TO_CPLEX/setup.py install

Dynamic Community FBA

After the installation of CBMPy and CPLEX you can install dynamic community FBA using the following command

pip install dcFBA