eXamine: a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

The State of the Art in Cartograms

Cartograms combine statistical and geographical information in thematic maps, where areas of geographical regions (e.g., countries, states) are scaled in proportion to some statistic (e.g., population, income). Cartograms make it possible to gain insight into patterns and trends in the world around us and have been very popular visualizations for geo-referenced data for over a century. This work surveys cartogram research in visualization, cartography and geometry, covering a broad spectrum of different cartogram types: from the traditional rectangular and table cartograms, to Dorling and diffusion cartograms. A particular focus is the study of the major cartogram dimensions: statistical accuracy, geographical accuracy, and topological accuracy. We review the history of cartograms, describe the algorithms for generating them, and consider task taxonomies. We also review quantitative and qualitative evaluations, and we use these to arrive at design guidelines and research challenges

Interactive Visual Analysis of Networked Systems: Workflows for Two Industrial Domains

We report on a first study of interactive visual analysis of networked systems. Working with ABB Corporate Research and Ericsson Research, we have created workflows which demonstrate the potential of visualization in the domains of industrial automation and telecommunications. By a workflow in this context, we mean a sequence of visualizations and the actions for generating them. Visualizations can be any images that represent properties of the data sets analyzed, and actions typically either change the selection of data visualized or change the visualization by choice of technique or change of parameters

Cyber situational awareness: from geographical alerts to high-level management

This paper focuses on cyber situational awareness and describes a visual analytics solution for monitoring and putting in tight relation data from network level with the organization business. The goal of the proposed solution is to make different security profiles (network security officer, network security manager, and financial security manager) aware of the actual network state (e.g., risk and attack progress) and the impact it actually has on the business tasks, making clear the relationships that exist between the network level and the business level. The proposed solution is instantiated on the ACEA infrastructure, the Italian company that provides power and water purification services to cities in central Italy (millions of end users

An Inquiry into the Practice of Proving in Low-Dimensional Topology

The aim of this article is to investigate specific aspects connected with visualization in the practice of a mathematical subfield: low-dimensional topology. Through a case study, it will be established that visualization can play an epistemic role. The background assumption is that the consideration of the actual practice of mathematics is relevant to address epistemological issues. It will be shown that in low-dimensional topology, justifications can be based on sequences of pictures. Three theses will be defended. First, the representations used in the practice are an integral part of the mathematical reasoning. As a matter of fact, they convey in a material form the relevant transitions and thus allow experts to draw inferential connections. Second, in low-dimensional topology experts exploit a particular type of manipulative imagination which is connected to intuition of two- and three-dimensional space and motor agency. This imagination allows recognizing the transformations which connect different pictures in an argument. Third, the epistemic—and inferential—actions performed are permissible only within a specific practice: this form of reasoning is subject-matter dependent. Local criteria of validity are established to assure the soundness of representationally heterogeneous arguments in low-dimensional topology