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.

The predominant interaction paradigm of current audio spatialization tools, which are primarily geared towards expert users, imposes a design process in which users are characterized as stationary, limiting the application domain of these tools. Navigable 3D sonic virtual realities, on the other hand, can support many applications ranging from soundscape prototyping to spatial data representation. Although modern game engines provide a limited set of audio features to create such sonic environments, the interaction methods are inherited from the graphical design features of such systems, and are not specific to the auditory modality. To address such limitations, we introduce INVISO, a novel web-based user interface for designing and experiencing rich and dynamic sonic virtual realities. Our interface enables both novice and expert users to construct complex immersive sonic environments with 3D dynamic sound components. INVISO is platform-independent and facilitates a variety of mixed reality applications, such as those where users can simultaneously experience and manipulate a virtual sonic environment. In this paper, we detail the interface design considerations for our audio-specific VR tool. To evaluate the usability of INVISO, we conduct two user studies: The first demonstrates that our visual interface effectively facilitates the generation of creative audio environments; the second demonstrates that both expert and non-expert users are able to use our software to accurately recreate complex 3D audio scenes.