Installation

Basic requirements

• Python 3.x
• CPLEX along with its Python wrapper installed in your current distribution (please note that the Python version must be compatible with CPLEX)

Optional requirements

For easier model loading and analysis (using constraint-based methods), the following libraries can be used:

• cobrapy
• framed

Additionally, the escher library can be used to display elementary flux modes on metabolic maps and the networkx library can also be used to plot trees generated from EFM or MCS enumeration.

Via pip

The easiest method is to use pip to install the package from PyPI:

pip install cobamp

From source

• Download the latest source files from github

• Unpack the source files into a directory of your choosing

• Open the operating system’s command-line interface

• Change into the source file directory

• Run the following command

  python setup.py install
  

It is highly recommended that this package along with its requirements are installed in a separate Python environment. Tools such as virtualenv or conda can be used to create Python environments.