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.
Most approaches to representing causality, such as the common causal graph, require a separate and static view, but in many cases it is useful to add the dimension of causality to the context of an existing visualization. Building on research from perceptual psychology that shows the perception of causality is a low-level visual event derived from certain types of motion, we are investigating how to add animated causal representations, called visual causal vectors, onto other visualizations. We refer to these as causal overlays. Our initial experimental results show this approach has great potential but that extra cues are needed to elicit the perception of causality when the motions are overlaid on other graphical objects. In this paper we describe the approach and report on a study that examined two issues of this technique: how to accurately convey the causal flow and how to represent the strength of the causal effect.  Michotte's theory of ampliation suggests that causal relationships are perceived by objects animated under appropriate spatiotemporal conditions. We extend the theory of ampliation and propose that the immediate perception of complex causal relations is also dependent on a set of structural and temporal rules. We designed animated representations, based on Michotte's rules, for showing complex causal relationships or causal semantics. In this paper we describe a set of animations for showing semantics such as causal amplification, causal strength, causal dampening, and causal multiplicity. In a two part study we compared the effectiveness of both the static and animated representations. The first study (N=44) asked participants to recall passages that were previously displayed using both types of representations. Participants were 8 more accurate in recalling causal semantics when they were presented using animations instead of static graphs. In the second study (N=112) we evaluated the intuitiveness of the representations. Our results showed that while users were as accurate with the static graphs as with the animations, they were 9 faster in matching the correct causal statements in the animated condition. Overall our results show that animated diagrams that are designed based on perceptual rules such as those proposed by Michotte have the potential to facilitate comprehension of complex causal relations.