https://github.com/matthiaskoenig/libsbgnpy
Python library for SBGN
https://github.com/matthiaskoenig/libsbgnpy
combine python sbgn
Last synced: about 2 months ago
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Python library for SBGN
- Host: GitHub
- URL: https://github.com/matthiaskoenig/libsbgnpy
- Owner: matthiaskoenig
- License: mit
- Created: 2015-04-20T22:13:20.000Z (about 10 years ago)
- Default Branch: develop
- Last Pushed: 2025-03-25T20:48:23.000Z (2 months ago)
- Last Synced: 2025-04-11T00:05:22.811Z (about 2 months ago)
- Topics: combine, python, sbgn
- Language: Python
- Homepage: http://matthiaskoenig.github.io/libsbgnpy/
- Size: 12 MB
- Stars: 9
- Watchers: 5
- Forks: 0
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Support: .github/SUPPORT.rst
Awesome Lists containing this project
README
# libsbgnpy: Python library for SBGN
[](https://github.com/matthiaskoenig/libsbgnpy/actions/workflows/main.yml)
[](https://pypi.org/project/libsbgnpy/)
[](https://pypi.org/project/libsbgnpy/)
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.5281/zenodo.597155)
Python library to work with the Systems Biology Graphical Notation ([SBGN](http://sbgn.github.io/sbgn/)). This library is based on the SBGN XML schema and supports reading,
writing and validation of SBGN files.
The initial library was generated using [generateDS](https://pypi.org/project/generateDS/). Additional utility functions for reading, writing, and rendering SBGN documents are provided.
Documentation with examples is available at https://matthiaskoenig.github.io/libsbgnpy/.
* `libsbgn.py` python library
* `libsbgnTypes.py` SBGN type definitions (GlyphClasses, ArcClasses, Languages)
* `utils.py` SBGN utility function like writing & reading of files
* `render.py` SBGN rendering
* `test/` unittests
* `examples/` python examples
* `validation/` validation of SBGN files
# How to cite
[](https://doi.org/10.5281/zenodo.597155)
# Installation
`libsbgnpy` is available from [pypi](https://pypi.python.org/pypi/libsbgnpy) and
can be installed via
```bash
pip install libsbgnpy
```
# License
- Source Code: [MIT](https://opensource.org/license/MIT)
- Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
# Funding
Matthias König (MK) 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). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program 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).
# Python Language Bindings
The python language bindings were created from the XML schema using generateDS and than adapted to include GlyphClasses and ArcClasses.
```bash
generateDS.py -o "libsbgn.py" -s "libsbgnSubs.py" SBGN.xsd
```
The necessary constraints for GlyphClasses, ArcClasses and Languages were added and some utility functions created.
© 2016-2025 Matthias König