Medical Systems Biology

You are here:  Software > BoolNet


BoolNet is an R package for generation, reconstruction, simulation and analysis of synchronous, asynchronous and probabilistic Boolean networks. This page provides help on the installation and usage of the package. The most recent version of the package and its documentation is available from BoolNet's CRAN page.


Documentation is included in the R package. You can get help for a command by typing ?<command> (e.g. ?getAttractors) inside R when the package is loaded.

Additionally, a step-by-step tutorial is available here.

A description of methods and algorithms can be accessed here. Furthermore, this paper discusses the attractor search in BoolNet.


The most recent source and binary packages for BoolNet are available from CRAN. The Debian Med team also maintains a package r-cran-boolnet which can be obtained from the official repositories for Debian and Ubuntu.

CRAN (all systems)

In an R console, type install.packages("BoolNet"). The package is now installed and can be loaded via library(BoolNet). The packages igraph and XML are installed automatically, as BoolNet depends on them.

Debian package (Debian/Ubuntu)

To install BoolNet from the official Debian/Ubuntu repositories, open a terminal and type

sudo apt-get install r-cran-boolnet

Please note that the Debian package may not always be the most recent version of BoolNet.

Manual installation

To install BoolNet manually, the sources (BoolNet_<version>.tar.gz) must be downloaded from CRAN and compiled. As a prerequisite, the packages igraph and XML must be installed.

  • On Mac OS, ensure that XCode Tools are installed. On Windows, you must install R-Tools for the corresponding R version. Also, make sure that R is in the search path.
  • Open a root shell (Linux/Mac OS) or the Windows command prompt, and change to the folder where the package is located.
  • Type R CMD INSTALL BoolNet_<version>.tar.gz
  • You can now start R and load the package with the command

Citing BoolNet

To cite the package in publications, use:

Müssel C, Hopfensitz M, Kestler HA. BoolNet - an R package for generation, reconstruction, and analysis of Boolean networks. Bioinformatics 26(10): 1378-1380, 2010.

Job Openings

Wissenschaftlicher Mitarbeiter (m/w/d) 


Latest News


Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.


"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.


"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.

Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.


Our paper "Unsupervised domain adaptation for the detection of cardiomegaly in cross-domain chest X-ray images" has been published in Frontiers in Artificial Intelligence.


  1. "The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination" has been published online first in the British Journal of Cancer.


"Vaccine Side Effects in Health Care Workers after Vaccination against SARS-CoV-2: Data from TüSeRe:exact Study" has been published in Viruses-Basel.


"PREDICT-juvenile-stroke: PRospective evaluation of a prediction score determining individual clinical outcome three months after ischemic stroke in young adults – a study protocol" has been published in BMC Neurology.


Our paper "Federated Electronic Data Capture (fEDC): Architecture and Prototype" has been accepted for publiaction in the Journal of Biomedical Informatics.


Our paper "Efficient cross-valdation traversals in feature subset selection" has been published in Scientific Reports.


Our paper "CANTATA - prediction of missing links in Boolean networks using genetic programming" has been published in Bioinformatics.


Our paper "Interaction Empowerment in Mobile Health: Concepts, Challenges, and Perspectives" has been published in the Journal of Medical Internet Research mhealth and uhealth.


Our paper "Identification of dynamic driver sets controlling phenotypical landscapes" has been published in the Computational and Structural Biotechnology Journal.