SBML python utilities
Project description
sbmlutils: Python utilities for SBML
The sbmlutils package provides a collection of python utilities for working with SBML. sbmlutils are implemented on top of the `libSBML <http://sbml.org/Software/libSBML>`__ python bindings.
Features are among others * HTML reports of SBML models * helper functions for model creation and manipulation * interpolation functions to add experimental data to models * implementation of dynamic flux balance analysis (DFBA).
For a more detailed description and examples see the documentation.
@MISC{sbmlutils,
author = {Matthias König},
title = {sbmlutils: python utilities for SBML},
month = {Mar.},
year = {2017},
doi = "{10.5281/zenodo.439006}",
url = "{http://dx.doi.org/10.5281/zenodo.439006}"
}
License
Source Code: LGPLv3
Documentation: CC BY-SA 4.0
Documentation
Installation
Requirements
For plotting tkinter is required which can be installed via
apt-get install python-tk
or for python 3 via
apt-get install python3-tk
Stable version
sbmlutils is available from pypi and be installed via
pip install sbmlutils
To update an existing version use
pip install sbmlutils --upgrade
Develop version
The latest develop version is available via
pip install git+https://github.com/matthiaskoenig/sbmlutils.git@develop
Or via cloning the repository and installing via
pip install -e .
Release notes
0.1.4
documentation update
DFBA update & bug fixes
DFBA examples (toy and diauxic growth)
bug fixes
0.1.3
python 3 support
clean travis build with pip
DFBA implementation
bugfixes & improvements
0.1.2
fixed unittests and bug fixes
0.1.1
bug fixes, refactoring, unit tests
model creator examples
0.1.0
initial release
© 2017 Matthias König.
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