In the process of understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on the exploration of regions in proteins called loops. Analyzing various characteristics of these regions helps the experts to design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. As this process requires extensive manual treatment and currently there is no proper visual support for it, we designed LoopGrafter: a web-based tool that provides experts with visual support through all the loop grafting pipeline steps. The tool is logically divided into several phases, starting with the definition of two input proteins and ending with a set of grafted proteins. Each phase is supported by a specific set of abstracted 2D visual representations of loaded proteins and their loops that are interactively linked with the 3D view onto proteins. By sequentially passing through the individual phases, the user is shaping the list of loops that are potential candidates for loop grafting. In the end, the actual in-silico insertion of the loop candidates from one protein to the other is performed and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. LoopGrafter was designed in tight collaboration with protein engineers, and its final appearance reflects many testing iterations. We showcase the contribution of LoopGrafter on a real case scenario and provide the readers with the experts' feedback, confirming the usefulness of our tool.
Recent graphical interfaces offer direct manipulation mechanisms for authoring visualizations, but are largely restricted to static output. To author interactive visualizations, users must instead turn to textual specification, but such approaches impose a higher technical burden. To bridge this gap, we introduce Lyra 2, a system that extends a prior visualization design environment with novel methods for authoring interaction techniques by demonstration. Users perform an interaction (e.g., button clicks, drags, or key presses) directly on the visualization they are editing. The system interprets this performance using a set of heuristics and enumerates suggestions of possible interaction designs. These heuristics account for the properties of the interaction (e.g., target and event type) as well as the visualization (e.g., mark and scale types, and multiple views). Interaction design suggestions are displayed as thumbnails; users can preview and test these suggestions, iteratively refine them through additional demonstrations, and finally apply and customize them via property inspectors. We evaluate our approach through a gallery of diverse examples, and evaluate its usability through a first-use study and via an analysis of its cognitive dimensions. We find that, in Lyra 2, interaction design by demonstration enables users to rapidly express a wide range of interactive visualizations.
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