CABEAN: A software for the control of asynchronous Boolean networks

Abstract

Summary: Direct cell reprogramming, also called transdifferentiation, has great potential for tissue engineering and regenerative medicine. Boolean networks, a popular modelling framework for gene regulatory networks, make it possible to identify intervention targets for direct cell reprogramming with computational methods. In this work, we present our software, CABEAN, for the control of asynchronous Boolean networks. CABEAN identifies efficacious nodes, whose perturbations can drive the dynamics of a network from a source attractor (the initial cell type) to a target attractor (the desired cell type). CABEAN provides several control methods integrating practical constraints. Thus, it has the ability to provide a rich set of control sets, such that biologists can select suitable ones for validation based on specific experimental settings.