A free, open-source tool for modeling chemical reaction networks in Python. Offers a single platform for pharmacokinetics, pharmacodynamics, and reaction-diffusion equations.
- 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)
- NetworkX
- Numpy
- Scipy
- Pint
- pandas
- matplotlib
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