Boolean networks: Beyond generalized asynchronicity

Abstract

Boolean networks are commonly used in systems biology to model dynamics of biochemical networks by abstracting away many (and often unknown) parameters related to speed and species activity thresholds. It is then expected that Boolean networks produce an over-approximation of behaviours (reachable configurations), and that subsequent refinements would only prune some impossible transitions. However, we show that even generalized asynchronous updating of Boolean networks, which subsumes the usual updating modes including synchronous and fully asynchronous, does not capture all transitions doable in a multi-valued or timed refinement. We define a structural model transformation which takes a Boolean network as input and outputs a new Boolean network whose asynchronous updating simulates both synchronous and asynchronous updating of the original network, and exhibits even more behaviours than the generalized asynchronous updating. We argue that these new behaviours should not be ignored when analyzing Boolean networks, unless some knowledge about the characteristics of the system explicitly allows one to restrict its behaviour.