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sbmlutils: python utilities for SBML

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sbmlutils is a collection of python utilities for working with SBML <http://www.sbml.org>__ models implemented on top of libsbml <http://sbml.org/Software/libSBML>__ and other libraries with source code available from https://github.com/matthiaskoenig/sbmlutils <https://github.com/matthiaskoenig/sbmlutils>__.

Features include among others

• helper functions for model creation, manipulation, and annotation
• HTML reports of SBML models https://sbml4humans.de <https://sbml4humans.de>__.
• file converters (XPP)

The documentation is available on https://sbmlutils.readthedocs.io <https://sbmlutils.readthedocs.io>. If you have any questions or issues please open an issue <https://github.com/matthiaskoenig/sbmlutils/issues>.

.. image:: docs/presentations/reproducibility_center_2021/screenshot.png :target: https://youtu.be/SxIq8qeXxD0?t=1261 :alt: sbmlutils introduction :height: 200px

How to cite

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Contributing

Contributions are always welcome! Please read the contributing guidelines <https://github.com/matthiaskoenig/sbmlutils/blob/develop/.github/CONTRIBUTING.rst>__ to get started.

License

• Source Code: LGPLv3 <http://opensource.org/licenses/LGPL-3.0>__
• Documentation: CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>__

The sbmlutils source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding

Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 "QuaLiPerF <https://qualiperf.de>__ (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). SBML4Humans was funded as part of Google Summer of Code 2021 <https://summerofcode.withgoogle.com/>__. 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.

Installation

sbmlutils is available from pypi <https://pypi.python.org/pypi/sbmlutils>__ and can be installed via::

pip install sbmlutils

Requirements

tkinter is required which can be installed on linux via::

apt-get install python-tk
apt-get install python3-tk

Please see the respective installation instructions for your operating system.

Develop version

The latest develop version can be installed via::

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

Or via cloning the repository and installing via::

git clone https://github.com/matthiaskoenig/sbmlutils.git
cd sbmlutils
pip install -e .

To install for development use::

pip install -e .[development]

© 2017-2024 Matthias König