Boolean network simulations for life scientists. Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an increasing role as they are eminently suited at mapping biological observations and hypotheses into a mathematical formalism. The conceptual underpinnings of Boolean modeling are very accessible even without a background in quantitative sciences, yet it allows life scientists to describe and explore a wide range of surprisingly complex phenomena. In this paper we provide a clear overview of the concepts used in Boolean simulations, present a software library that can perform these simulations based on simple text inputs and give three case studies. The large scale simulations in these case studies demonstrate the Boolean paradigms and their applicability as well as the advanced features and complex use cases that our software package allows. Our software is distributed via a liberal Open Source license and is freely accessible from

References in zbMATH (referenced in 8 articles )

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  1. Min, Byungjoon: Interplay between degree and Boolean rules in the stability of Boolean networks (2020)
  2. Rion Brattig Correia; Alexander J. Gates; Xuan Wang; Luis M. Rocha: CANA: A python package for quantifying control and canalization in Boolean Networks (2018) arXiv
  3. Wynn, Michelle L.; Egbert, Megan; Consul, Nikita; Chang, Jungsoo; Wu, Zhi-Fen; Meravjer, Sofia D.; Schnell, Santiago: Inferring intracellular signal transduction circuitry from molecular perturbation experiments (2018)
  4. Possieri, Corrado; Teel, Andrew R.: Asymptotic stability in probability for stochastic Boolean networks (2017)
  5. Price, Ian; Ermentrout, Bard; Zamora, Ruben; Wang, Bo; Azhar, Nabil; Mi, Qi; Constantine, Gregory; Faeder, James R.; Luckhart, Shirley; Vodovotz, Yoram: \textitInvivo, \textitinvitro, and \textitinsilico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes (2013)
  6. Ironi, Liliana; Panzeri, Luigi; Plahte, Erik; Simoncini, Valeria: Dynamics of actively regulated gene networks (2011)
  7. Larsson, Jan-Åke; Wadströmer, Niclas; Hermanson, Ola; Lendahl, Urban; Forchheimer, Robert: Modelling cell lineage using a meta-Boolean tree model with a relation to gene regulatory networks (2011)
  8. Saadatpour, Assieh; Albert, István; Albert, Réka: Attractor analysis of asynchronous Boolean models of signal transduction networks (2010)