canagliflozin model

This repository provides the canagliflozin physiologically based pharmacokinetics/ pharmacodynamics (PBPK/PD) model.

The model is distributed as SBML format available from canagliflozin_body_flat.xml with corresponding SBML4humans model report and model equations.

The COMBINE archive is available from canagliflozin_model.omex. The FAIR assessment is available from canagliflozin_model_fair.xlsx.

Comp submodels

• liver submodel canagliflozin_liver.xml with SBML4humans report and equations.
• kidney submodel canagliflozin_kidney.xml with SBML4humans report and equations.
• intestine submodel canagliflozin_intestine.xml with SBML4humans report and equations.
• whole-body submodel canagliflozin_body.xml with SBML4humans report and equations.

How to cite

To cite the model repository

Tereshchuk, V., Elias, M. & König, M. (2026). Physiologically based pharmacokinetic/pharmacodynamic (PBPK) model of canagliflozin.
Zenodo. https://doi.org/10.5281/zenodo.13759839

To cite the preprint

Vera Tereshchuk, Michelle Elias, Matthias König A Digital Twin of Canagliflozin Pharmacokinetics and Pharmacodynamics in Type 2 Diabetes Mellitus Preprints 2026, 10.20944/preprints202601.2095.v1 (preprint). doi:10.20944/preprints202601.2095.v1

License

• Source Code: MIT
• Documentation: CC BY-SA 4.0
• Models: CC BY-SA 4.0

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Run simulations

python

Clone the repository

git clone https://github.com/matthiaskoenig/canagliflozin-model.git
cd canagliflozin-model

uv

Run the complete analysis with uv (https://docs.astral.sh/uv/getting-started/installation/):

uv sync
uv run run_canagliflozin -a all -r results

pip

If you use pip install the package via

pip install -e .

Run the complete analysis in the environment via:

run_canagliflozin -a all -r results

docker

Simulations can also be run within a docker container:

docker run -v "${PWD}/results:/results" -it matthiaskoenig/canagliflozin:latest /bin/bash

Run the complete analysis:

uv run run_canagliflozin -a all -r /results

The results are written into the mounted /results folder on the host.

In case of permission issues with the mounted folder, adjust ownership and access rights with:

sudo chown $(id -u):$(id -g) -R "${PWD}/results"
sudo chmod 775 "${PWD}/results"

Funding

Matthias König was supported by the Federal Ministry of Research, Technology and Space (BMFTR, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA). This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B).

© 2023-2026 Vera Tereshchuk, Michelle Elias, and Matthias König, Systems Medicine of the Liver