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A free, open-source tool for modeling chemical reaction networks in Python

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ADicksonLab/OpenRXN

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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

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