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pkpdsim: building blocks of PBPK/PD models

GitHub Actions CI/CD Status Documentation Version Python Versions MIT License

pkpdsim is a python package with the building blocks shared by physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models in SBML. The source code is available from https://github.com/matthiaskoenig/pkpdsim.

Background

The models of pkdb_models describe the pharmacokinetics and pharmacodynamics of a substance in the whole body: one SBML model per tissue, composed into a whole-body model, written in python with the factory of sbmlutils, simulated with sbmlsim against the studies curated in PK-DB. pkpdsim holds what these models share, so that the folder of a model imports nothing but itself and released packages and can live in a repository of its own.

Features

  • Templates and annotations - the creators and the terms of use of a model, the annotations of the compartments which recur in the models (liver, kidneys, gut, blood, urine, ...) with the terms of FMA, BTO, NCIT, UBERON and GO.
  • Study data - the study folders of PK-DB in a checkout of pkdb_data, found through the environment variable PKDB_DATA, and the data of a model collected from them into its own folder.
  • Initial values - the same initial concentration or amount of a substance in every tissue of a model, which removes the distribution kinetics.
  • Licenses - the texts of CC BY-SA 4.0 and MIT for the COMBINE archive of a model, written byte for byte the same on every platform.
  • Models and their commands - the model object and the commands of a model (run, fit, report, identifiability), the tests of a model as functions and the verification of a change, also across versions of sbmlsim (pkpdsim-verify).
  • Experiments and their metadata - the base class of the simulation experiments of a model (the SIds of its keys, the units of its data), the presets of the impaired organ function, the shared vocabulary of the metadata of a fit mapping and the filters which select the mappings of a fit by it.
  • Scans and sensitivity analyses - the timecourse of a point of a scan as sbmlsim 0.8 gave it and the table of the parameters and the distributions of a sensitivity analysis.

Quickstart

from pathlib import Path

from pkpdsim.annotations import compartments
from pkpdsim.licenses import License, write_license
from pkpdsim.templates import creators

print(creators[0].givenName, creators[0].familyName)
print([resource for _, resource in compartments["li"]])

results = Path("results")
results.mkdir()
print(write_license(results, License.MIT, copyright="2026 Matthias König").name)

Matthias König
['fma/FMA:7197', 'bto/BTO:0000759', 'ncit/C12392']
mit.txt

Continue with Installation and the Templates and annotations of a model.

How to cite

DOI

If you use pkpdsim please cite the archived software on Zenodo:

König, M. (2026). pkpdsim: building blocks of physiologically based pharmacokinetic and pharmacodynamic models in SBML (Version 0.5.1) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.23319918

License

Funding

Matthias König is supported by the German Research Foundation (DFG) within the Research Unit Programme 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).

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