This repository (https://github.com/matthiaskoenig/glimepiride-model) provides the glimepiride physiologically based pharmacokinetics (PBPK) model.

The model is distributed as SBML available from glimepiride_body_flat.xml with corresponding SBML4humans model report at https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/glimepiride-model/main/models/glimepiride_body_flat.xml and equations from glimepiride_body_flat.md.

The COMBINE archive is available from glimepiride_model.omex.

The liver submodel is available from glimepiride_liver.xml with corresponding SBML4humans report at https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/glimepiride-model/main/models/glimepiride_liver.xml and equations from glimepiride_liver.md.

The kidney submodel is available from glimepiride_kidney.xml with corresponding SBML4humans report at https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/glimepiride-model/main/models/glimepiride_kidney.xml and equations from glimepiride_kidney.md.

The intestine submodel is available from glimepiride_intestine.xml with corresponding SBML4humans report at https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/glimepiride-model/main/models/glimepiride_intestine.xml and equations from glimepiride_intestine.md.

The whole-body submodel is available from glimepiride_body.xml with corresponding SBML4humans report at https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/glimepiride-model/main/models/glimepiride_body.xml and equations from glimepiride_body.md.

To cite the model repository

Elias, M., & König, M. (2025). Physiologically based pharmacokinetic (PBPK) model of glimepiride.
Zenodo. https://doi.org/10.5281/zenodo.14628700

To cite the main publication

Elias, M., & König, M. (2025). A Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment.
Front. Pharmacol. 16:1686415. doi:10.3389/fphar.2025.1686415

To cite the reproducibility publication

Elias, M., & König, M. (2025). Reproducibility of a Digital Twin of Glimepiride for Personalized and Stratified Diabetes Treatment
Physiome. 2025 October (accepted) doi:10.36903/physiome.28379193

• 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.

Clone the repository

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

Setup environment with uv (https://docs.astral.sh/uv/getting-started/installation/)

uv venv
uv sync

Run the complete analysis:

uv run run_glimepiride -a all -r results

If you use pip install the package via

pip install -e .

Run the complete analysis in the environment via:

run run_glimepiride -a all -r results

Simulations can also be run within a docker container:

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

Run the complete analysis:

uv run run_glimepiride -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"

Matthias König was supported by the Federal Ministry of Education and Research (BMBF, Germany) within LiSyM by grant number 031L0054 and 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).

© 2024-2025 Michelle Elias & Matthias König, Systems Medicine of the Liver