A Cytoscape 3 app for augmented boolean models of gene regulatory networks

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:

1. Network generation

  • Random networks with specified structural properties. Given the key parameters, CABERNET can generate and simulate ensembles of random networks with shared features.
  • Import of characterized GRNs. GRNs that are characterized with respect to both the topology and the regulatory functions, either fetched from public datasets via Cytoscape or loaded via input textual file, can be processed with CABeRNET.
  • Augmentation of partial networks. Given partially defined networks as input, e.g., from publicly available dataset or known GRNs, CABERNET can augment the networks according to key structural and topological parameters.

2. Network simulation

The attractor landscape and the properties of the steady states (i.e., attractors) of the networks can be extensively investigated.

3. Network selection

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.

4. Robustness analysis

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.

5. Network analysis

A wide range of statical and dynamical properties of the simulated network can be analyzed with CABERNET.

6. Visualization

The powerful visualization capabilities of Cytoscape can be used to analyze the topological and dynamical properties of the simulated networks.

People involved

Andrea Paroni
Alex Graudenzi
Giulio Garavagna
Giancarlo Mauri

How to install

The plugin can be installed following the instructions in the manual.

IMPORTANT NOTE: CABERNET is compatible with Cytoscape 3.2.0, it has not been tested with other versions of the application.


The plugin is release under a BSD-like license which can be found here.