radiode: Python Module dedicated to water radiolysis simulation via ODE solver

Access to the code base

The codebase is hosted by the University of Namur. We are open to granting access upon receiving motivation sent via email to Pr. Dr. Anne-Catherine Heuskin (anne-catherine.heuskin@unamur.be).

Acknowledgments

The development of this code is made possible thanks to the EPT (Emerging protontherapies) project (Mecatech and BioWin poles), Convention n° 8341, 2020-2024.
Partners: IBA, Dekimo, V2i, UNamur, KUL, UCLouvain, UNantes.

This module was originally inspired by the R. Labarbe's validated MatLab code.

General description

This python3 module allows you to perform radiobiology-related simulations. The embedded science, which includes physics, chemistry, and biology, aims to solve systems of Ordinary Differential Equations (ODE) based on equations provided via an input file. The default solver used in this module is the LSODA solver from the scipy module.

Forewords

The following documentation assumes you already have or know how to install a new python3 environment on your local machine. If it is not yet the case, We suggest you to check this out.

Currently the main dependencies of this module are:

• scipy
• numpy
• pandas
• pandas-stubs
• lark
• more-itertools

For JupyterLab users, it is also suggested to install the following packages for a better experience:

• tqdm
• jupyterlab-widgets
• ipywidgets

Wiki Navigation

Getting Started
Configuration File
Usage
Tutorial

Remarks for developer

If you intend to join this dev. adventure, first of all, thank you for your time and support. Second, please be aware that this code base uses the fast RUFF linter and comply with the Mypy static type checker.

ps: Needless to say that Python2 is forbidden...
pps: There is currently no code coverage (tests)... a big problem to solve.