HyperLabels: Browsing of Dense and Hierarchical Molecular 3D Models.

David Kouril,M. Eduard Groller,Ivan Viola,Barbora Kozlikova,Miriah Meyer,Tobias Isenberg

doi:10.1109/tvcg.2020.2975583

Abstract

We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment-using clicks on nodes, links, or icons-with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e. g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that-in addition to their annotational role-also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.

Highlights

B IOLOGY as a scientific discipline has reached a point where we begin to understand the essential building blocks of life, on every level of its structural organization
We demonstrate the HyperLabels-enabled spatial and hierarchical browsing using the previously mentioned molecular meso-scale models: a mature Human Immunodeficiency Virus (HIV) embedded in blood plasma and a Mycoplasma genitalium bacterium
We show the HyperLabels interaction in the supplemental video, where the textual labels can be observed in a sufficient size

Summary

Introduction

B IOLOGY as a scientific discipline has reached a point where we begin to understand the essential building blocks of life, on every level of its structural organization. A huge body of work acts as supporting evidence and most of the structural details are digitally available. Visualization plays an important role in this effort [51], [55] Two such complex systems have been modeled at The Scripps Research Institute using cellPACK procedural modeling [36], i. E., a model of HIV [37] (Figure 1) and a draft model of the Mycoplasma bacterium (Figure 9). While these life forms can be considered rather primitive from a biological perspective, their structural detail results in models with a huge geometric complexity

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