Computer Setup

This page describes how to install software when working with Boolean network modeling.

All commands are to be run in a terminal.

The installation process will work for Linux, Windows and MacOS.

On Windows use the Windows subsytem for Linux and follow the Linux instructions.
On MacOS install thecommand line tools by Apple by typing: xcode-select --install

Pixi environments

Currently, the best way to do scientific computing is via pixi software which is considered to be the next generation of conda environment management. With pixi you can create isolated software environments with a wide range of software packages.

All instructions here assume that you have pixi installed. Quick install for pixi:

# See the pixi website for the latest instructions
curl -fsSL https://pixi.sh/install.sh | sh

Open a new terminal to apply the changes.

Initialize the environment

We prepackaged the installation commands into a single file that you can inspect at

https://raw.githubusercontent.com/BooleanNet/booleannet.com/refs/heads/main/docs/code/setup.2026.txt

Run the code below to install all required software into an isolated environment:

# Create a new directory for the enviroment
mkdir -p boolean

# Change to this new directory
cd boolean

# Run the setup script
curl -fsSL https://raw.githubusercontent.com/BooleanNet/booleannet.com/refs/heads/main/docs/code/setup.2026.txt | sh

You now have a working enviroment for Boolean network modeling.

Active the enviroment and run the doctor command to check the installation:

# Activate the enviroment
pixi shell

# Run the doctor command
bnet doctor

It may take a little bit to run since I have to process all the Python libraries. Success looks like this:

#
# Checking python packages ...
#
# pyboolnet     ✓ installed
# pystablemotifs  ✓ installed
#
# Checking pyboolenet executables ...
#
nusmv           ✓ runs  /Users/ialbert/work/.pixi/envs/default/lib/python3.12/site-packages/pyboolnet/binaries/NuSMV-a/NuSMVa_mac64
gringo          ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/gringo
clasp           ✓ runs  /Users/ialbert/work/.pixi/envs/default/lib/python3.12/site-packages/pyboolnet/binaries/clasp-3.2.0/clasp-3.2.0_mac64
bnet2prime      ✓ runs  /Users/ialbert/work/.pixi/envs/default/lib/python3.12/site-packages/pyboolnet/binaries/BNetToPrime/BNetToPrime_mac64
espresso        ✓ runs  /Users/ialbert/work/.pixi/envs/default/lib/python3.12/site-packages/pyboolnet/binaries/espresso/espresso_mac64
eqntott         ✓ runs  /Users/ialbert/work/.pixi/envs/default/lib/python3.12/site-packages/pyboolnet/binaries/eqntott/eqntott_mac64
dot             ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/dot
neato           ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/neato
fdp             ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/fdp
sfdp            ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/sfdp
circo           ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/circo
twopi           ✓ runs  /Users/ialbert/work/.pixi/envs/default/bin/twopi
convert         ✓ runs  /usr/local/bin/convert
#
# settings file: /Users/ialbert/work/.pixi/envs/default/lib/python3.12/site-packages/pyboolnet/binaries/settings.cfg
#

Forked repositories

We maintain copies (forks) to existing software packages that have small fixes applied to allow them to operate on modern Python versions and/or to fix various problems arising from running them on different operating systems. All fixes are contributed back to the original repositories.

All credit for these tools go to the original authors.

Todo: other software

TODO: adding more instructions

cuda, and more advance software installation instructions go here