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sbmlsim: SBML simulation made easy

GitHub Actions CI/CD Status Current PyPI Version Supported Python Versions GNU Lesser General Public License 3 Codecov Documentation Status Zenodo DOI Black

sbmlsim is a collection of python utilities to simplify simulations with SBML models implemented on top of roadrunner. Source code is available from https://github.com/matthiaskoenig/sbmlsim.

Features include among others

  • simulation experiments
  • simulation reports
  • parameter fitting

The documentation is available on https://sbmlsim.readthedocs.io. If you have any questions or issues please open an issue.

How to cite

Zenodo DOI

Contributing

Contributions are always welcome! Please read the contributing guidelines to get started.

License

The sbmlsim 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 (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 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

sbmlsim is available from pypi and can be installed via:

pip install sbmlsim

Requirements

HDF5 support is required which can be installed on linux via:

sudo apt-get install -y libhdf5-serial-dev

Develop version

The latest develop version can be installed via:

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

Or via cloning the repository and installing via:

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

To install for development use:

pip install -e .[development]

© 2019-2022 Matthias König