https://github.com/adicksonlab/openrxn
A free, open-source tool for modeling chemical reaction networks in Python
https://github.com/adicksonlab/openrxn
compartmental-models gillespie gillespie-algorithm pharmacokinetics reaction-diffusion reactions
Last synced: 28 days ago
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A free, open-source tool for modeling chemical reaction networks in Python
- Host: GitHub
- URL: https://github.com/adicksonlab/openrxn
- Owner: ADicksonLab
- License: mit
- Created: 2019-07-17T20:03:38.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-01-16T15:07:00.000Z (about 2 years ago)
- Last Synced: 2025-09-08T23:58:15.887Z (5 months ago)
- Topics: compartmental-models, gillespie, gillespie-algorithm, pharmacokinetics, reaction-diffusion, reactions
- Language: Python
- Size: 46.9 KB
- Stars: 13
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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
```