sbmlsim: SBML simulation made easy

sbmlsim is a collection of python utilities to simplify simulations with SBML models implemented on top of roadrunner. Source code is available from https://github.com/matthiaskoenig/sbmlsim.

Features include among others

simulation experiments
simulation reports
parameter fitting
sensitivity analysis

If you have any questions or issues please open an issue.

Installation

sbmlutils is available from pypi and can be installed via

pip install sbmlsim

Develop version

The latest develop version can be installed via

pip install git+https://github.com/matthiaskoenig/sbmlsim.git@develop

How to cite

License

Source Code: MIT
Documentation: CC BY-SA 4.0

Funding

Matthias König is supported and 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).

Development

Install dev dependencies:

To setup everything for the develop environment use

# install core dependencies
uv sync
# install dev dependencies
uv pip install -r pyproject.toml --extra dev
uv tool install tox --with tox-uv
uv pip install pre-commit
pre-commit install
pre-commit run

Testing

Testing is performed with tox Run single tox target

tox r -e py314

Run all tests in parallel

tox run-parallel

Documentation

If you haven’t already, you’ll need to install Quarto.