CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks

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. Motivation. 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. Results. 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.Comment: 18 pages, 3 figure

Intelligent Mobile System for Improving Spatial Design Support and Security Inside Buildings

This paper concerns the an intelligent mobile application for spatial design support and security domain. Mobility has two aspects in our research: The first one is the usage of mobile robots for 3D mapping of urban areas and for performing some specific tasks. The second mobility aspect is related with a novel Software as a Service system that allows access to robotic functionalities and data over the Ethernet, thus we demonstrate the use of the novel NVIDIA GRID technology allowing to virtualize the graphic processing unit. We introduce Complex Shape Histogram, a core component of our artificial intelligence engine, used for classifying 3D point clouds with a Support Vector Machine. We use Complex Shape Histograms also for loop closing detection in the simultaneous localization and mapping algorithm. Our intelligent mobile system is built on top of the Qualitative Spatio-Temporal Representation and Reasoning framework. This framework defines an ontology and a semantic model, which are used for building the intelligent mobile user interfaces. We show experiments demonstrating advantages of our approach. In addition, we test our prototypes in the field after the end-user case studies demonstrating a relevant contribution for future intelligent mobile systems that merge mobile robots with novel data centers

Multiple peer effects in the diffusion of innovations on social networks: a simulation study

Abstract Peer effects in innovation adoption decisions have been extensively studied. However, the underlying mechanisms of peer effects are generally not explicitly accounted for. Gaps in this knowledge could lead to misestimation of peer effects and inefficient interventions. This study examined the role of two mechanisms—sharing experiences (namely, experience effect) and externalities—in the adoption of an agricultural innovation. By referring to the diffusion process of a new crop in Chinese villages, we developed a simulation model that incorporated experience effect and externality effect on a multiplex network. The model allowed us to estimate the influence of each specific effect and to investigate the interplay of the positive and negative directions of the effects. The main results of simulation experiments were the following: (1) a negative externality effect in the system caused the diffusion of innovation to vary around a middle-level rate, which resulted in a fluctuating diffusion curve rather than a commonly found S-shaped one; (2) in the case of full diffusion, experience effect significantly shaped the diffusion process at the early stage, while externality effect mattered more at the late stage; and (3) network properties (i.e. connectivity, transitivity, and network distance) imposed indirect influence on diffusion through specific peer effects. Overall, our study illustrated the need to understand specific causal mechanisms when studying peer effects. Simulation methods such as agent-based modelling provide an effective approach to facilitate such understanding