sbmlsim: SBML simulation made easy

sbmlsim is a collection of python utilities for the simulation of models in the Systems Biology Markup Language (SBML), built on libroadrunner.

Features include

• timecourse simulations - concatenated timecourses with changes of parameters and initial conditions, in the units of the model
• parameter scans - simulations over dimensions of values, simulations and models, serially or in a pool of processes, with results as labeled N-dimensional arrays with units (xarray)
• simulation experiments - models, datasets, simulations, tasks and figures of an experiment as one reproducible python object, with HTML and markdown reports
• parameter fitting - optimization problems from experimental data with local and global optimizers, and PEtab archives
• sensitivity analysis - local sensitivities and the global Morris, Sobol and FAST methods

The documentation is available at https://matthiaskoenig.github.io/sbmlsim.

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

How to cite

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

König, M. (2026). sbmlsim: SBML simulation made easy (Version 0.9.4) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.23324383

@software{konig_sbmlsim,
  author    = {König, Matthias},
  title     = {sbmlsim: SBML simulation made easy},
  year      = {2026},
  month     = oct,
  version   = {0.9.4},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.23324383},
  url       = {https://doi.org/10.5281/zenodo.23324383},
}

License

• Source Code: MIT
• Documentation: CC BY-SA 4.0
• Citation style: the bundled src/sbmlsim/resources/references.csl of the reports is the IEEE style of the Citation Style Language project under CC BY-SA 3.0, adapted to print the version note of a software.

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). Matthias König has received funding from the EOSCsecretariat.eu which has received funding from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.

© 2019-2026 Matthias König, https://livermetabolism.com