# pkpdsim

> The building blocks of physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models in SBML

The links below point to the markdown source of the documentation. [llms-full.txt](https://matthiaskoenig.github.io/pkpdsim/llms-full.txt) contains all of it in a single file.

## Documentation

- [Home](https://matthiaskoenig.github.io/pkpdsim/index.md): `pkpdsim` is a python package with the building blocks shared by physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models in SBML.
- [Installation](https://matthiaskoenig.github.io/pkpdsim/installation.md): `pkpdsim` requires python >= 3.13 and is available from pypi.
- [Contributing](https://matthiaskoenig.github.io/pkpdsim/development.md): Contributions are welcome.

## User guide

- [Models and their commands](https://matthiaskoenig.github.io/pkpdsim/models.md): A model package describes itself once, in its `__init__.py`, as a `PKPDModel`. The commands, the verification and the tests of pkpdsim work with this object; what stays in the package is what is the model's own: its factory, the registry of its experiments, its fit definitions and parameters, the filters of its mapping collections and its tolerances.
- [Experiments and their metadata](https://matthiaskoenig.github.io/pkpdsim/experiments.md): An experiment of a model is a published study as code: it loads the digitized data of the study, encodes its dosing protocol as simulations and pairs the data with the observables of the model (the fit mappings).
- [Scans and sensitivity analyses](https://matthiaskoenig.github.io/pkpdsim/scans.md): Two modules hold what the scripts of the models around scans and sensitivity analyses share.
- [Templates and annotations](https://matthiaskoenig.github.io/pkpdsim/templates.md): Every model of pkdb_models names its creators, carries the terms of use under which it is published and annotates its compartments with the terms of ontologies, so that a reader of the SBML, a person or a program, knows who made it, how it may be used and what a compartment is.
- [Study data](https://matthiaskoenig.github.io/pkpdsim/data.md): The studies against which the models are fitted and validated are curated in PK-DB, in a checkout of pkdb_data: its folder `studies` holds a folder per substance and in it a folder per study, with the publication, its figures and tables and the digitized data as hidden `.tsv` files (`.Boulton1996a_Fig1.tsv`).
- [Initial values](https://matthiaskoenig.github.io/pkpdsim/initial_values.md): A substance which is given before a study starts, or which the body produces itself, is present in every tissue at the start of a simulation.
- [Licenses](https://matthiaskoenig.github.io/pkpdsim/licenses.md): A model is published under two licenses: the model and its documentation under CC BY-SA 4.0, the source code which creates and simulates it under MIT.

## API reference

- [Overview](https://matthiaskoenig.github.io/pkpdsim/api/index.md): The API reference is generated from the docstrings of the package.
- [pkpdsim](https://matthiaskoenig.github.io/pkpdsim/api/pkpdsim.md): pkpdsim: the building blocks of physiologically based PK/PD models in SBML.
- [templates](https://matthiaskoenig.github.io/pkpdsim/api/templates.md): The creators and the terms of use of a model.
- [annotations](https://matthiaskoenig.github.io/pkpdsim/api/annotations.md): The annotations of the recurring compartments of the models.
- [data](https://matthiaskoenig.github.io/pkpdsim/api/data.md): The study data of a model, collected from the study folders of PK-DB.
- [initial_values](https://matthiaskoenig.github.io/pkpdsim/api/initial_values.md): The initial values of a substance in every tissue of a model.
- [licenses](https://matthiaskoenig.github.io/pkpdsim/api/licenses.md): The license texts of a model, e.g.
- [model](https://matthiaskoenig.github.io/pkpdsim/api/model.md): The description of a PBPK/PD model, which the commands of pkpdsim work with.
- [run](https://matthiaskoenig.github.io/pkpdsim/api/run.md): Running the simulation experiments of a model and collecting their figures.
- [cli](https://matthiaskoenig.github.io/pkpdsim/api/cli.md): The commands of a model.
- [fit](https://matthiaskoenig.github.io/pkpdsim/api/fit.md): The fit settings, the metadata filters and the selection of the mappings.
- [metadata](https://matthiaskoenig.github.io/pkpdsim/api/metadata.md): The vocabulary with which the fit mappings of the models are described.
- [experiment](https://matthiaskoenig.github.io/pkpdsim/api/experiment.md): The base class of the simulation experiments of a model.
- [impairment](https://matthiaskoenig.github.io/pkpdsim/api/impairment.md): The classes of impaired organ function: the factors of their parameters and colors.
- [pk](https://matthiaskoenig.github.io/pkpdsim/api/pk.md): The labels and units of the pharmacokinetic parameters in the figures.
- [scan](https://matthiaskoenig.github.io/pkpdsim/api/scan.md): The results of the scans of a model: the dimension and the timecourse of a point.
- [sensitivity](https://matthiaskoenig.github.io/pkpdsim/api/sensitivity.md): The parameters of the sensitivity analyses of a model.
- [testing](https://matthiaskoenig.github.io/pkpdsim/api/testing.md): The tests of a model as functions: the registry, the experiments, the fits.
- [verify](https://matthiaskoenig.github.io/pkpdsim/api/verify.md): Verify that a change of a model changes only what it is meant to change.

## Optional

- [Repository](https://github.com/matthiaskoenig/pkpdsim): source code, issues and releases.
- [Sitemap](https://matthiaskoenig.github.io/pkpdsim/sitemap.xml): all pages of the rendered site.
- [objects.inv](https://matthiaskoenig.github.io/pkpdsim/objects.inv): the API objects of the reference as a sphinx inventory.