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sbmlutils: python utilities for SBML

sbmlutils is a collection of python utilities for working with models in the Systems Biology Markup Language (SBML), built on libsbml.

Features include

model creation - a model is a python object, create_model writes it as validated SBML, with support for the comp, fbc, distrib and layout packages
units written as strings (mmole/min/l) and checked for consistency
annotations - MIRIAM annotations and SBO terms, in the model definition or from an annotation spreadsheet
notes written as markdown
model composition - hierarchical models, merging and flattening
converters - SBML to an ODE system (python, R, julia, markdown, latex), XPP to SBML, antimony in both directions

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

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

How to cite

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

König, M. (2026). sbmlutils: Python utilities for SBML (Version 0.12.0) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.22853867

@software{konig_sbmlutils,
  author    = {König, Matthias},
  title     = {sbmlutils: Python utilities for SBML},
  year      = {2026},
  month     = sep,
  version   = {0.12.0},
  publisher = {Zenodo},
  doi       = {10.5281/zenodo.22853867},
  url       = {https://doi.org/10.5281/zenodo.22853867},
}

License

Source Code: MIT
Documentation: CC BY-SA 4.0

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.

Metadata

Release files for sbmlutils 0.12.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for sbmlutils 0.12.2
File	Size	Uploaded
sbmlutils-0.12.2.tar.gz	23.7 MB	Sep 23, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for sbmlutils 0.12.2
File	Interpreter	ABI	Platform	Reset
sbmlutils-0.12.2-py3-none-any.whl 3.6 MB Sep 23, 2026	Python 3	none	any	Details

Total release size: 27.3 MB

Release files / sbmlutils-0.12.2.tar.gz

Download URL	sbmlutils-0.12.2.tar.gz
Size	23.7 MB
Tags	Source
SHA-256 checksum How to use checksums	`2e9dc2195ae72d6c740ca6cf73b85c3f531f20d44b724945a166254949db1bdc`
BLAKE2b-256 checksum How to use checksums	`931c2c0cac5088f8e84abcdcfe21ad2b070995e7c14149a10d1778991ee12dad`
Upload date	Sep 23, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/matthiaskoenig/sbmlutils
Publishing commit: github.com/matthiaskoenig/sbmlutils/tree/b0f55b9bdf7906d92093eeed056efd62e802c8f5

Workflow

Publishing configuration: github.com/matthiaskoenig/sbmlutils/blob/b0f55b9bdf7906d92093eeed056efd62e802c8f5/.github/workflows/ci-cd.yml
Publishing logs: github.com/matthiaskoenig/sbmlutils/actions/runs/35895441324/attempts/1

Artifact

Subject: sbmlutils-0.12.2.tar.gz
SHA-256 checksum: 2e9dc2195ae72d6c740ca6cf73b85c3f531f20d44b724945a166254949db1bdc Verifying attestations

Release files / sbmlutils-0.12.2-py3-none-any.whl

Download URL	sbmlutils-0.12.2-py3-none-any.whl
Size	3.6 MB
Tags	Python 3
SHA-256 checksum How to use checksums	`6029c4c1331c5571b0d407354afa61bc6c40793dc43f59a68e2c9ff3221256cb`
BLAKE2b-256 checksum How to use checksums	`837ef208d9aeb2126a676a3a35ba1a1576d72f5c2117f02a2de31710cdeb0a38`
Upload date	Sep 23, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/matthiaskoenig/sbmlutils
Publishing commit: github.com/matthiaskoenig/sbmlutils/tree/b0f55b9bdf7906d92093eeed056efd62e802c8f5

Workflow

Publishing configuration: github.com/matthiaskoenig/sbmlutils/blob/b0f55b9bdf7906d92093eeed056efd62e802c8f5/.github/workflows/ci-cd.yml
Publishing logs: github.com/matthiaskoenig/sbmlutils/actions/runs/35895441324/attempts/1

Artifact

Subject: sbmlutils-0.12.2-py3-none-any.whl
SHA-256 checksum: 6029c4c1331c5571b0d407354afa61bc6c40793dc43f59a68e2c9ff3221256cb Verifying attestations