sbmlutils 0.1.5a2

SBML python utilities

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

Documentation with examples is available at

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

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© 2017 Matthias König.