Motivation The problem of model inference is of fundamental importance to systems biology.
Logical models (eg Boolean networks; BNs) represent a computationally attractive approach …

AEON. py is a Python library for the analysis of the long-term behaviour in very large
asynchronous Boolean networks. It provides significant computational improvements over …

Boolean Networks (BNs) play a crucial role in modeling, analyzing, and controlling
biological systems. One of the most important problems on BNs is to compute all the …

Boolean networks (BNs) are a well-accepted modelling formalism in computational systems
biology. Nevertheless, modellers often cannot identify only a single BN that matches the …

Recent developments in both computational analysis and data-driven synthesis enable a
new era of automated reasoning with logical models (Boolean networks in particular) in …

BoNesis is a Python library which offers a declarative framework for the synthesis of Boolean
networks from advanced dynamical properties, such as reachability, bifurcation, minimal trap …

Detection of bottom strongly connected components (BSCC) in state-transition graphs is an
important problem with many applications, such as detecting recurrent states in Markov …

Abstract Partially specified Boolean networks (PSBNs) represent a promising framework for
the qualitative modelling of biological systems in which the logic of interactions is not …

Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of
biological systems. Nonetheless, it might be difficult to gather enough data to precisely …

Minimal trap spaces (MTSs) capture subspaces in which the Boolean dynamics is trapped,
whatever the update mode. They correspond to the attractors of the most permissive mode …