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libsbgnpy

libsbgnpy is a Python library to work with 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 xsdata. Additional utility functions for reading, writing, and rendering SBGN documents are provided.

libsbgnpy screenshot

The source code is available from the https://github.com/matthiaskoenig/libsbgnpy. To report bugs, request features, or ask questions, please file an issue. Documentation with examples is available at https://matthiaskoenig.github.io/libsbgnpy/.

A presentation introducing libsbgnpy can be found here: HARMONY2025 libsbgnpy.

How to cite

To cite libsbgnpy, use the following DOI: 10.5281/zenodo.597155.

License

Source Code: MIT
Documentation: CC 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).