CABERNET is a Cytoscape app for Augmented Boolean modEls of gene Regulatory NETwork – is an App for Cytoscape, based on a dynamical model of cell differentiation originally described in “Villani M, Barbieri A, Serra R (2011). A Dynamical Model of Genetic Networks for Cell Differentiation. PLoS ONE 6(3): e17703. doi:10.1371/journal.pone.0017703“.
CABERNET introduces a series of innovative simulation and analysis features, which can be divided in six main stages:
The attractor landscape and the properties of the steady states (i.e., attractors) of the networks can be extensively investigated.
Given an input differentiation tree, the app allows to search for NRBNs whose emergent behaviour is in accordance with the input tree (in terms of the expected stability and dynamical trajectory).
The app is based on a generative approach, i.e., NRBNs are randomly created according to user-defined features such as statistical properties and topologies, and a batch process accepts/discard the GRNs matching the input lineage commitment tree.
Different kind of perturbations can be performed on the networks and the relative stability can be subsequently assessed via robustness analyses, for instance by analyzing measures such as avalanches and sensitivity.
A wide range of statical and dynamical properties of the simulated network can be analyzed with CABERNET.
The powerful visualization capabilities of Cytoscape can be used to analyze the topological and dynamical properties of the simulated networks.