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.
Efforts to effectively visualize graphs with nodes or edges that represent temporal data or that have a topology that evolves over time are cataloged by @cite_37 . They survey the landscape of dynamic graph visualization, categorizing projects primarily in terms of how they represent time, that is, whether or not they use animation or a static timeline to show the evolution of networks. These categories are then further parcellated according to which layout strategies they utilize and how they address particular problems inherent in dynamic datasets. Inspired by @cite_57 , who investigate animated network movies'' for a range of sociological datasets, our tool features an animated node-link diagram whose layout is determined by clusters of influence (measured by how likely rules are to fire at the same time), either on a per-frame basis or within a user-selected time window. An interactive timeline is used to navigate through time, and more detailed information about selected nodes is presented for the currently selected time period.
@cite_57 @cite_37
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Dynamic graph visualization focuses on the challenge of representing the evolution of relationships between entities in readable, scalable and effective diagrams. This work surveys the growing number of approaches in this discipline. We derive a hierarchical taxonomy of techniques by systematically categorizing and tagging publications. While static graph visualizations are often divided into node-link and matrix representations, we identify the representation of time as the major distinguishing feature for dynamic graph visualizations: either graphs are represented as animated diagrams or as static charts based on a timeline. Evaluations of animated approaches focus on dynamic stability for preserving the viewer's mental map or, in general, compare animated diagrams to timeline-based ones. A bibliographic analysis provides insights into the organization and development of the field and its community. Finally, we identify and discuss challenges for future research. We also provide feedback from experts, collected with a questionnaire, which gives a broad perspective of these challenges and the current state of the field. Dynamic graph visualization focuses on the challenge of representing the evolution of relationships between en- tities in readable, scalable, and effective diagrams. This work surveys the growing number of approaches in this discipline. We derive a hierarchical taxonomy of techniques by systematically categorizing and tagging publica- tions. While static graph visualizations are often divided into node-link and matrix representations, we identify the representation of time as the major distinguishing feature for dynamic graph visualizations: either graphs are represented as animated diagrams or as static charts based on a timeline. Evaluations of animated approaches focus on dynamic stability for preserving the viewer's mental map or, in general, compare animated diagrams to timeline-based ones. Finally, we identify and discuss challenges for future research. We present a novel dynamic graph visualization technique based on node-link diagrams. The graphs are drawn side-byside from left to right as a sequence of narrow stripes that are placed perpendicular to the horizontal time line. The hierarchically organized vertices of the graphs are arranged on vertical, parallel lines that bound the stripes; directed edges connect these vertices from left to right. To address massive overplotting of edges in huge graphs, we employ a splatting approach that transforms the edges to a pixel-based scalar field. This field represents the edge densities in a scalable way and is depicted by non-linear color mapping. The visualization method is complemented by interaction techniques that support data exploration by aggregation, filtering, brushing, and selective data zooming. Furthermore, we formalize graph patterns so that they can be interactively highlighted on demand. A case study on software releases explores the evolution of call graphs extracted from the JUnit open source software project. In a second application, we demonstrate the scalability of our approach by applying it to a bibliography dataset containing more than 1.5 million paper titles from 60 years of research history producing a vast amount of relations between title words. Graph drawing algorithms have classically addressed the layout of static graphs. However, the need to draw evolving or dynamic graphs has brought into question many of the assumptions, conventions and layout methods designed to date. For example, social scientists studying evolving social networks have created a demand for visual representations of graphs changing over time. Two common approaches to represent temporal information in graphs include animation of the network and use of static snapshots of the network at different points in time. Here, we report on two experiments, one in a laboratory environment and another using an asynchronous remote web-based platform, Mechanical Turk, to compare the efficiency of animated displays versus static displays. Four tasks are studied with each visual representation, where two characterise overview level information presentation, and two characterise micro level analytical tasks. For the tasks studied in these experiments and within the limits of the experimental system, the results of this study indicate that static representations are generally more effective particularly in terms of time performance, when compared to fully animated movie representations of dynamic networks.