This repository contains the source code of a PFAS PBK model implementation based on the PFOA and PFOS PBK model by Loccisano et al. and the subsequently modified version thereof by Westerhout et al.. The model is implemented in Antimony and available as a FAIR PBK annotated SBML.
The model implementation files can be found in the model folder. The file PBK_PFAS.ant contains the Antimony implementation. The file PBK_PFAS.csv contains the unit specifications and the model element annotations according the FAIR PBK standard, using the harmonized terminology of the PBPKO ontology.
The Jupyter notebook test_dosing.ipynb demonstrates how this model can be used in simulations. To run this notebook, you need Python with Jupyter Notebook and the python packages listed in the requirements file.
Install the required python packages using the command:
pip install -r requirements.txt