Ondřej Strnad

Deng Luo, Alexandre Kouyoumdjian, Ondřej Strnad et al.

We propose a new abstraction set (SynopSet) that has a continuum of visual representations for the explanatory analysis of molecular dynamics simulations (MDS) in the DNA nanotechnology domain. By re-purposing the commonly used progress bar and designing novel visuals, as well as transforming the data from the domain format to a format that better fits the newly designed visuals, we compose this new set of representations. This set is also designed to be capable of showing all spatial and temporal details, and all structural complexity, or abstracting these to various degrees, enabling both the slow playback of the simulation for detailed examinations or very fast playback for an overview that helps to efficiently identify events of interest, as well as several intermediate levels between these two extremes. For any pair of successive representations, we demonstrate smooth, continuous transitions, enabling users to keep track of relevant information from one representation to the next. By providing multiple representations suited to different temporal resolutions and connected by smooth transitions, we enable time-efficient simulation analysis, giving users the opportunity to examine and present important phases in great detail, or leverage abstract representations to go over uneventful phases much faster. Domain experts can thus gain actionable insight about their simulations and communicate it in a much shorter time. Further, the novel representations are more intuitive and also enable researchers unfamiliar with MDS analysis graphs to better understand the simulation results. We assessed the effectiveness of SynopSet on 12 DNA nanostructure simulations together with a domain expert. We have also shown that our set of representations can be systematically located in a visualization space, dubbed SynopSpace.

David Kouřil, Ondřej Strnad, Peter Mindek et al.

We present a method for producing documentary-style content using real-time scientific visualization. We produce molecumentaries, i.e., molecular documentaries featuring structural models from molecular biology. We employ scalable methods instead of the rigid traditional production pipeline. Our method is motivated by the rapid evolution of interactive scientific visualization, which shows great potential in science dissemination. Without some form of explanation or guidance, however, novices and lay-persons often find it difficult to gain insights from the visualization itself. We integrate such knowledge using the verbal channel and provide it along an engaging visual presentation. To realize the synthesis of a molecumentary, we provide technical solutions along two major production steps: 1) preparing a story structure and 2) turning the story into a concrete narrative. In the first step, information about the model from heterogeneous sources is compiled into a story graph. Local knowledge is combined with remote sources to complete the story graph and enrich the final result. In the second step, a narrative, i.e., story elements presented in sequence, is synthesized using the story graph. We present a method for traversing the story graph and generating a virtual tour, using automated camera and visualization transitions. Texts written by domain experts are turned into verbal representations using text-to-speech functionality and provided as a commentary. Using the described framework we synthesize automatic fly-throughs with descriptions that mimic a manually authored documentary. Furthermore, we demonstrate a second scenario: guiding the documentary narrative by a textual input.