JaxKineticModel

Python package to simulate, build, and train kinetic models.

Installation

Install the package using

pip install jaxkineticmodel

Or the latest version using

git clone https://github.com/AbeelLab/jaxkineticmodel.git
python -m pip install .

Documentation package

Documentation on jaxkineticmodel can be found here

Running experiments as reported in paper

• Datasets generated from SBML models can be found in datasets
• Glucose pulse datasets can be found here
• Experiments as reported in [1] can be found in scripts. Results from these experiments can found in the 4tu-repository

Source code

All data, source code, scripts, and results can be found in the 4tu-repository

Reference

If you use this package in your work, please reference:

[1] van Lent, P., Bunkova, O., Magyar, B., Planken, L., Schmitz, J., & Abeel, T. (2025). Jaxkineticmodel: Neural ordinary differential equations inspired parameterization of kinetic models. PLOS Computational Biology, 21(7), e1012733.