sbmlsim

sbmlsim: SBML simulation made easy

https://github.com/matthiaskoenig/sbmlsim

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sbmlsim: SBML simulation made easy

README.rst

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sbmlsim: SBML simulation made easy
==================================

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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
===========

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   :alt: Zenodo DOI

Contributing
============

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

License
=======

* Source Code: `LGPLv3 `__
* Documentation: `CC BY-SA 4.0 `__

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

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