Chi

About

Chi is an open source Python package hosted on GitHub, which can be used to model dose response dynamics.

All features of the software are described in detail in the full API documentation.

Getting started

Installation

1. Install sundials

Chi uses the open source package Myokit to solve ordinary differential equations and compute their sensitivities efficiently. Myokit does this using sundials' CVODESS, which needs to be installed with:

• On Ubuntu:

apt-get install libsundials-dev

• On MacOS:

brew install sundials

• On Windows: No action required. Myokit will install sundial automatically.

2. Install chi

pip install chi-drm

You can now use chi's functionality by importing it

import chi

Tutorials

Tutorials and more detailed explanations on how to use chi can be found in the documentation's getting started section.

Citation

If you use this software in your work, please cite it using the following metadata:

Citation string

Augustin, D., (2024). Chi: A Python package for treatment response modelling. Journal of Open Source Software, 9(94), 5925, https://doi.org/10.21105/joss.05925

BibTeX

@article{
    Augustin2024, 
    doi = {10.21105/joss.05925}, 
    url = {https://doi.org/10.21105/joss.05925}, 
    year = {2024}, 
    publisher = {The Open Journal}, 
    volume = {9}, 
    number = {94}, 
    pages = {5925}, 
    author = {David Augustin}, 
    title = {Chi: A Python package for treatment response modelling}, 
    journal = {Journal of Open Source Software} 
}

Contributing

There are lots of ways how you can contribute to Chi's development, and you are welcome to join in! For example, you can report problems or make feature requests on the issues pages.

Similarly, if you would like to contribute documentation or code you can create and issue, and then provide a pull request for review. To facilitate contributions, we have written extensive contribution guidelines to help you navigate the code.

License

BSD-3-Clause