Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments

Alharbi, Ruwayda; Strnad, Ondřej; Luidolt, Laura R.; Waldner, Manuela; Kouril, David; Bohak, Ciril; Klein, Tobias; Groeller, Eduard; Viola, Ivan

doi:10.1109/tvcg.2021.3133592

Cited by 7 publications

(4 citation statements)

References 67 publications

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Section: Visual Abstraction Formalismmentioning

confidence: 99%

“…Subsequently, the visualization adjusts to reveal the internal composition of the chosen subpart, allowing for continued exploration (refer to Figure 5 ). In 2021, Nanotilus, a guided-tour generator for exploring the biological nanoworld in an immersive 3D environment was introduced by ( Alharbi et al, 2021 ). It transforms a 3D model and script (i.e., textual story), into an engaging guided tour, introducing a camera path planning technique and sparsification method to enhance user experience.…”

Section: General Considerations On Visualization Of Complex Molecular...mentioning

confidence: 99%

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From complex data to clear insights: visualizing molecular dynamics trajectories

Belghit,

Spivak,

Dauchez

et al. 2024

Front. Bioinform.

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Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

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Section: Visual Abstraction Formalismmentioning

confidence: 99%

Section: General Considerations On Visualization Of Complex Molecular...mentioning

confidence: 99%

From complex data to clear insights: visualizing molecular dynamics trajectories

Belghit,

Spivak,

Dauchez

et al. 2024

Front. Bioinform.

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“…An exception to this rule is the work of Alharbi et al. [ASL*22], focusing on VR guided‐tours in dense molecular environments. A fundamental question in this context is how much biological context is required to make complex molecular illustrations, that is, to what extent does biological information need to be included, compared to an approach that uses general 3D modelling and painting?…”

Section: Application Domainsmentioning

confidence: 99%

“…Sharing also finds echo in approaches that allow users to create guided tours, as was proposed by Alharbi et al. [ASL*22]. Similarly, VRdeo provides the means to create interactive experiences by recording user actions that can be replayed [BBMK21].…”

Section: Application Domainsmentioning

confidence: 99%

State of the Art of Molecular Visualization in Immersive Virtual Environments

Kuťák

Vázquez

Isenberg

et al. 2023

Computer Graphics Forum

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Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.

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Mesoscale explorer: Visual exploration of large‐scale molecular models

Rose,

Sehnal,

Goodsell

et al. 2024

Protein Science

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The advent of cryo‐electron microscopy (cryo‐EM) and cryo‐electron tomography (cryo‐ET), coupled with computational modeling, has enabled the creation of integrative 3D models of viruses, bacteria, and cellular organelles. These models, composed of thousands of macromolecules and billions of atoms, have historically posed significant challenges for manipulation and visualization without specialized molecular graphics tools and hardware. With the recent advancements in GPU rendering power and web browser capabilities, it is now feasible to render interactively large molecular scenes directly on the web. In this work, we introduce Mesoscale Explorer, a web application built using the Mol* framework, dedicated to the visualization of large‐scale molecular models ranging from viruses to cell organelles. Mesoscale Explorer provides unprecedented access and insight into the molecular fabric of life, enhancing perception, streamlining exploration, and simplifying visualization of diverse data types, showcasing the intricate details of these models with unparalleled clarity.

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Nanotilus: Generator of Immersive Guided-Tours in Crowded 3D Environments

Cited by 7 publications

References 67 publications

From complex data to clear insights: visualizing molecular dynamics trajectories

From complex data to clear insights: visualizing molecular dynamics trajectories

State of the Art of Molecular Visualization in Immersive Virtual Environments

Mesoscale explorer: Visual exploration of large‐scale molecular models

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