SBML python utilities
Project description
.. raw:: html
<h1>
sbmlutils: python utilities for SBML
.. raw:: html
</h1>
|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 <http://www.sbml.org>`__ models implemented on top of
`libSBML <http://sbml.org/Software/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
|
How to cite
~~~~~~~~~~~
|DOI|
License
~~~~~~~
- Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__
- Documentation: `CC BY-SA
4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__
Installation
------------
``sbmlutils`` is available from
`pypi <https://pypi.python.org/pypi/sbmlutils>`__ 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
-------------
0.1.8
~~~~~
- 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 Matthias König
.. |PyPI version| image:: https://badge.fury.io/py/sbmlutils.svg
:target: https://badge.fury.io/py/sbmlutils
.. |GitHub version| image:: https://badge.fury.io/gh/matthiaskoenig%2Fsbmlutils.svg
:target: https://badge.fury.io/gh/matthiaskoenig%2Fsbmlutils
.. |Build Status| image:: https://travis-ci.org/matthiaskoenig/sbmlutils.svg?branch=develop
:target: https://travis-ci.org/matthiaskoenig/sbmlutils
.. |Documentation Status| image:: https://readthedocs.org/projects/sbmlutils/badge/?version=latest
:target: http://sbmlutils.readthedocs.io/en/latest/
.. |codecov| image:: https://codecov.io/gh/matthiaskoenig/sbmlutils/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/matthiaskoenig/sbmlutils
.. |License (LGPL version 3)| image:: https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=flat-square
:target: http://opensource.org/licenses/LGPL-3.0
.. |DOI| image:: https://zenodo.org/badge/55952847.svg
:target: https://zenodo.org/badge/latestdoi/55952847
<h1>
sbmlutils: python utilities for SBML
.. raw:: html
</h1>
|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 <http://www.sbml.org>`__ models implemented on top of
`libSBML <http://sbml.org/Software/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
|
How to cite
~~~~~~~~~~~
|DOI|
License
~~~~~~~
- Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__
- Documentation: `CC BY-SA
4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__
Installation
------------
``sbmlutils`` is available from
`pypi <https://pypi.python.org/pypi/sbmlutils>`__ 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
-------------
0.1.8
~~~~~
- 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 Matthias König
.. |PyPI version| image:: https://badge.fury.io/py/sbmlutils.svg
:target: https://badge.fury.io/py/sbmlutils
.. |GitHub version| image:: https://badge.fury.io/gh/matthiaskoenig%2Fsbmlutils.svg
:target: https://badge.fury.io/gh/matthiaskoenig%2Fsbmlutils
.. |Build Status| image:: https://travis-ci.org/matthiaskoenig/sbmlutils.svg?branch=develop
:target: https://travis-ci.org/matthiaskoenig/sbmlutils
.. |Documentation Status| image:: https://readthedocs.org/projects/sbmlutils/badge/?version=latest
:target: http://sbmlutils.readthedocs.io/en/latest/
.. |codecov| image:: https://codecov.io/gh/matthiaskoenig/sbmlutils/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/matthiaskoenig/sbmlutils
.. |License (LGPL version 3)| image:: https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=flat-square
:target: http://opensource.org/licenses/LGPL-3.0
.. |DOI| image:: https://zenodo.org/badge/55952847.svg
:target: https://zenodo.org/badge/latestdoi/55952847
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