title: CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.
abstract: BACKGROUND
  Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and functional characterization of real GRNs is often still partial and an exhaustive picture of their functioning is missing.
  
  
  RESULTS
  We here introduce CABERNET, a Cytoscape app for the generation, simulation and analysis of Boolean models of GRNs, specifically focused on their augmentation when a only partial topological and functional characterization of the network is available. By generating large ensembles of networks in which user-defined entities and relations are added to the original core, CABERNET allows to formulate hypotheses on the missing portions of real networks, as well to investigate their generic properties, in the spirit of complexity science.
  
  
  CONCLUSIONS
  CABERNET offers a series of innovative simulation and modeling functions and tools, including (but not being limited to) the dynamical characterization of the gene activation patterns ruling cell types and differentiation fates, and sophisticated robustness assessments, as in the case of gene knockouts. The integration within the widely used Cytoscape framework for the visualization and analysis of biological networks, makes CABERNET a new essential instrument for both the bioinformatician and the computational biologist, as well as a computational support for the experimentalist. An example application concerning the analysis of an augmented T-helper cell GRN is provided.
authors: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, Milan, I-20126, Italy.
authors: Andrea
authors: A
authors: Paroni
authors: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, Milan, I-20126, Italy. alex.graudenzi@unimib.it.|Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Via F.lli Cervi, 93, Segrate, I-20090, (MI), Italy. alex.graudenzi@unimib.it.
authors: Alex
authors: A
authors: Graudenzi
authors: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, Milan, I-20126, Italy. giulio.caravagna@unimib.it.|School of Informatics, University of Edinburgh, 10 Crichton St, Edinburgh, EH8 9AB, UK. giulio.caravagna@unimib.it.
authors: Giulio
authors: G
authors: Caravagna
authors: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, Milan, I-20126, Italy. chiara.damiani@unimib.it.|SYSBIO Centre of Systems Biology, Piazza della Scienza 2, 20126 Milano, Italy, Viale Sarca 336, Milan, I-20126, Italy. chiara.damiani@unimib.it.
authors: Chiara
authors: C
authors: Damiani
authors: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, Milan, I-20126, Italy. giancarlo.mauri@unimib.it.|Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Via F.lli Cervi, 93, Segrate, I-20090, (MI), Italy. giancarlo.mauri@unimib.it.|SYSBIO Centre of Systems Biology, Piazza della Scienza 2, 20126 Milano, Italy, Viale Sarca 336, Milan, I-20126, Italy. giancarlo.mauri@unimib.it.
authors: Giancarlo
authors: G
authors: Mauri
authors: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, Milan, I-20126, Italy. marco.antoniotti@unimib.it.|Milan Center for Neuroscience, University of Milan-Bicocca, Milan, Italy. marco.antoniotti@unimib.it.
authors: Marco
authors: M
authors: Antoniotti
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D019070:Cell Lineage / Q000235:genetics*; D002477:Cells / Q000166:cytology* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D006801:Humans; D008957:Models, Genetic; D012984:Software