Python utilities for SBML models
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README.md

sbmlutils logo sbmlutils: python utilities for SBML

PyPI version GitHub version Build Status Documentation Status codecov License (LGPL version 3) DOI

Matthias König

sbmlutils is a collection of python utilities for working with SBML models implemented on top of libSBML and other libraries available from https://github.com/matthiaskoenig/sbmlutils

Features include among others

  • HTML reports of SBML models
  • helper functions for model creation, manipulation, and annotation
  • interpolation functions to add experimental data to models
  • implementation of dynamic flux balance analysis (DFBA)
  • file converters (XPP)

For a more detailed description and examples see the documentation at
sbmlutils logo

How to cite

DOI

License

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).

Installation

sbmlutils is available from pypi and can be installed via

pip install sbmlutils

Requirements

tkinter is required which can be installed via

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

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

pip install -e .

Release notes

0.2.0

  • better comp support
  • hasOnlySubstanceUnits in sbmlreport added
  • initialAmounts and initialConcentrations supported in sbmlcreator
  • bug fixes

0.1.9

  • update dependencies
  • pip 10 fixes installer
  • fixed unit tests
  • bug fixes

0.1.8

  • DFBA release

0.1.7a0

  • xpp converter
  • updated SBML reports

0.1.6

  • update SBML reports (fbc & comp support)
  • modelcreator fixes
  • DFBA examples updated & annotated
  • annotation fixes

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

© 2017-2018 Matthias König