https://github.com/matthiaskoenig/canagliflozin-model
Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of canagliflozin
https://github.com/matthiaskoenig/canagliflozin-model
pkpd pkpd-modelling sbml sbml-model
Last synced: 3 months ago
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Physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of canagliflozin
- Host: GitHub
- URL: https://github.com/matthiaskoenig/canagliflozin-model
- Owner: matthiaskoenig
- Created: 2024-09-13T14:17:56.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-01-21T20:35:29.000Z (4 months ago)
- Last Synced: 2026-01-29T10:12:55.540Z (4 months ago)
- Topics: pkpd, pkpd-modelling, sbml, sbml-model
- Language: HTML
- Homepage:
- Size: 52.6 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Zenodo: .zenodo.json
Awesome Lists containing this project
README
[](https://doi.org/10.5281/zenodo.13759839)
[](https://github.com/matthiaskoenig/canagliflozin-model/actions/workflows/python.yml)
[](https://github.com/matthiaskoenig/sorafenib-model/actions/workflows/docker.yml)
# canagliflozin model
This repository provides the canagliflozin physiologically based pharmacokinetics/ pharmacodynamics (PBPK/PD) model.
The model is distributed as [SBML](http://sbml.org) format available from [`canagliflozin_body_flat.xml`](./models/canagliflozin_body_flat.xml) with
corresponding [SBML4humans model report](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/canagliflozin-model/main/models/canagliflozin_body_flat.xml) and [model equations](./models/canagliflozin_body_flat.md).
The COMBINE archive is available from [`canagliflozin_model.omex`](./canagliflozin_model.omex).
### Comp submodels
* **liver** submodel [`canagliflozin_liver.xml`](./models/canagliflozin_liver.xml) with [SBML4humans report](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/canagliflozin-model/main/models/canagliflozin_liver.xml) and [equations](./models/canagliflozin_liver.md).
* **kidney** submodel [`canagliflozin_kidney.xml`](./models/canagliflozin_kidney.xml) with [SBML4humans report](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/canagliflozin-model/main/models/canagliflozin_kidney.xml) and [equations](./models/canagliflozin_kidney.md).
* **intestine** submodel [`canagliflozin_intestine.xml`](./models/canagliflozin_intestine.xml) with [SBML4humans report](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/canagliflozin-model/main/models/canagliflozin_intestine.xml) and [equations](./models/canagliflozin_intestine.md).
* **whole-body** submodel [`canagliflozin_body.xml`](./models/canagliflozin_body.xml) with [SBML4humans report](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/matthiaskoenig/canagliflozin-model/main/models/canagliflozin_body.xml) and [equations](./models/canagliflozin_body.md).
## How to cite
[](https://doi.org/10.5281/zenodo.13758627)
> Tereshchuk, V., Elias, M. & König, M. (2026).
> *Physiologically based pharmacokinetic/pharmacodynamic (PBPK) model of canagliflozin.*
> Zenodo. [https://doi.org/10.5281/zenodo.13759839](https://doi.org/10.5281/zenodo.13759839)
## License
* Source Code: [MIT](https://opensource.org/license/MIT)
* Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
* Models: [CC BY-SA 4.0](https://creativecommons.org/licenses/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
```bash
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/):
```bash
uv run run_canagliflozin -a all -r results
```
#### pip
If you use pip install the package via
```bash
pip install -e .
```
Run the complete analysis in the environment via:
```bash
run_canagliflozin -a all -r results
```
### docker
Simulations can also be run within a docker container:
```bash
docker run -v "${PWD}/results:/results" -it matthiaskoenig/canagliflozin:latest /bin/bash
```
Run the complete analysis:
```bash
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:
```bash
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](https://livermetabolism.com)