We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.
Designing visualizations of dynamic networks is challenging, both because the data sets tend to be complex and because the tasks associated with them are often cognitively demand- ing. We introduce the Matrix Cube, a novel visual representation and navigation model for dynamic networks, inspired by the way people comprehend and manipulate physical cubes. Users can change their perspective on the data by rotating or decomposing the 3D cube. These manipulations can produce a range of different 2D visualizations that emphasize specific aspects of the dynamic network suited to particular analysis tasks. We describe Matrix Cubes and the interactions that can be performed on them in the Cubix system. We then show how two domain experts, an astronomer and a neurologist, used Cubix to explore and report on their own network data.  Cascades appear in many applications, including biological graphs and social media analysis. In a cascade, a dynamic attribute propagates through a graph, following its edges. We present the results of a formal user study that tests the effectiveness of different types of cascade visualisations on node-link diagrams for the task of judging cascade spread. Overall, we found that a small multiples presentation was significantly faster than animation with no significant difference in terms of error rate. Participants generally preferred animation over small multiples and a hierarchical layout to a force-directed layout. Considering each presentation method separately, when comparing force-directed layouts to hierarchical layouts, hierarchical layouts were found to be significantly faster for both presentation methods and significantly more accurate for animation. Representing the history of the cascade had no significant effect. Thus, for our task, this experiment supports the use of a small multiples interf... The effective application of spatio-temporal network models to neuroimaging data is an emerging challenge in the field of neuroscience, and could help scientists to better understand the behavior of the brain across a range of different experiments. One of the main problems with deriving spatiotemporal networks is that it is difficulty to provide a clear view of computed results. In this paper, we introduce an interactive visualization tool for spatio-temporal networks computed from neuroimaging datasets. Our tool allows the user to change parameters interactively, at run-time, and to compare multiple versions of the results directly. Furthermore, we describe our approach to rapidly calculating spatio-temporal networks to support visual analytics tasks for neuroimaging data. This paper describes novel methods for constructing the intrinsic geometry of the human brain connectome using dimensionality-reduction techniques. We posit that the high-dimensional, complex geometry that represents this intrinsic topology can be mathematically embedded into lower dimensions using coupling patterns encoded in the corresponding brain connectivity graphs. We tested both linear and nonlinear dimensionality-reduction techniques using the diffusion-weighted structural connectome data acquired from a sample of healthy subjects. Results supported the nonlinearity of brain connectivity data, as linear reduction techniques such as the multidimensional scaling yielded inferior lower-dimensional embeddings. To further validate our results, we demonstrated that for tractography-derived structural connectome more influential regions such as rich-club members of the brain are more centrally mapped or embedded. Further, abnormal brain connectivity can be visually understood by inspecting the altered geometry of these three-dimensional (3D) embeddings that represent the topology of the human brain, as illustrated using simulated lesion studies of both targeted and random removal. Last, in order to visualize brain’s intrinsic topology we have developed software that is compatible with virtual reality technologies, thus allowing researchers to collaboratively and interactively explore and manipulate brain connectome data.  Identifying, tracking and understanding changes in dynamic networks are complex and cognitively demanding tasks. We present GraphDiaries, a visual interface designed to improve support for these tasks in any node-link based graph visualization system. GraphDiaries relies on animated transitions that highlight changes in the network between time steps, thus helping users identify and understand those changes. To better understand the tasks related to the exploration of dynamic networks, we first introduce a task taxonomy, that informs the design of GraphDiaries, presented afterwards. We then report on a user study, based on representative tasks identified through the taxonomy, and that compares GraphDiaries to existing techniques for temporal navigation in dynamic networks, showing that it outperforms them in terms of both task time and errors for several of these tasks. Maps offer a familiar way to present geographic data (continents, countries), and additional information (topography, geology), can be displayed with the help of contours and heat-map overlays. In this paper, we consider visualizing large-scale dynamic relational data by taking advantage of the geographic map metaphor. We describe a map-based visualization system which uses animation to convey dynamics in large data sets, and which aims to preserve the viewer's mental map while also offering readable views at all times. Our system is fully functional and has been used to visualize user traffic on the Internet radio station last.fm, as well as TV-viewing patterns from an IPTV service. All map images in this paper are available in high-resolution at [CHECK END OF SENTENCE] as are several movies illustrating the dynamic visualization.