Pyboolnet

About pyboolnet

pyboolnet is a Python package for the generation, modification and analysis of Boolean networks. The accompanying paper was published with Bioinformatics and is available at

• https://doi.org/10.1093/bioinformatics/btw682

For report bugs, request features and give feedback at issues or contact

• hannes.klarner@fu-berlin.de (developer)
• heike.siebert@fu-berlin.de

Documentation

The documentation and tutorials are hosted here:

• https://pyboolnet.readthedocs.io/

Model repository

For examples of attractors, basins and phenotypes, browse the model repository here:

• pyboolnet/repository

Installation

To install the pyboolnet master branch use:

pip3 install pip --upgrade
pip3 install --force-reinstall git+https://github.com/hklarner/pyboolnet

To install a tagged version use the @:

pip3 install pip --upgrade
pip3 install git+https://github.com/hklarner/pyboolnet@3.0.16

To list PyBoolNet as a dependency add the following line to your requirements.txt:

git+https://github.com/hklarner/pyboolnet@3.0.16

For release notes, see

• pyboolnet/releasenotes.md

Requirements

clasp and gringo need to be on installed:

apt install clasp
apt install gringo

Command line tool

$ pyboolnet -h
$ pyboolnet --trap-spaces --type min grieco_mapk.bnet

Contributions

• send pull requests to the develop branch
• add tests to pyboolnet/tests/