OpenRXN

A free, open-source tool for modeling chemical reaction networks in Python. Offers a single platform for pharmacokinetics, pharmacodynamics, and reaction-diffusion equations.

Features

• definition of compartments, reactions and species as Python objects
• capable of stochastic (e.g. Gillespie) or deterministic modeling (e.g. ODEs)
• uses Pint for units throughout
• easy definition of 1D, 2D or 3D compartment arrays
• can visualize compartment connectivity as graphs (NetworkX)

Dependencies

• NetworkX
• Numpy
• Scipy
• Pint
• pandas
• matplotlib

Installation with pip

First, clone the source from github:

git clone https://github.com/ADicksonLab/OpenRXN.git

Change into that directory and install using pip:

cd OpenRXN
pip install .

Check the install by running one of the examples. E.g.:

python examples/1D_diffusion.py