fbc-curation 0.1.3

FBC reference files for SBML model curation.

fbc_curation

fbc_curation: Reproducibility of constraint-based models available from https://github.com/matthiaskoenig/fbc_curation.

This repository creates standardized reference files for a given FBC model based on cobrapy and glpk. These files can be used in the model curation process for validating the model behavior. The format of the standardized reference files is described below. Currently two separate implementations of the reference files are included in the package:

• cobrapy based on COBRApy (Constraint-Based Reconstruction and Analysis in Python) available from https://github.com/opencobra/cobrapy

• cameo based on Cameo (Cameo—Computer Aided Metabolic Engineering and Optimization) available from https://github.com/biosustain/cameo

fbc_curation is a python package which can be included in python applications. In addition a command line tool is provided which allows easy usage outside of python.

The documentation is available on https://fbc-curation.readthedocs.io. If you have any questions or issues please open an issue.

Documentation

The documentation is available on https://fbc-curation.readthedocs.io.

How to cite

Installation

fbc_curation is available from pypi and can be installed via:

pip install fbc-curation

Develop version

The latest develop version can be installed via:

pip install git+https://github.com/matthiaskoenig/fbc-curation.git@develop

Or via cloning the repository and installing via:

git clone https://github.com/matthiaskoenig/fbc_curation.git
cd fbc_curation
pip install -e .

To install for development use:

pip install -e .[development]

Testing

To run the tests clone the repository:

git clone https://github.com/matthiaskoenig/fbc_curation.git
cd fbc_curation
pip install -e .
pytest

License

• Source Code: LGPLv3

• Documentation: CC BY-SA 4.0

The fbc_curation 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).

© 2020 Matthias König