sMolBoxes: Dataflow Model for Molecular Dynamics Exploration

Ulbrich, Pavol; Waldner, Manuela; Furmanová, Katarína; Marques, Sérgio M.; Bednář, David; Kozlíková, Barbora

doi:10.1109/tvcg.2022.3209411

Cited by 6 publications

(3 citation statements)

References 35 publications

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“…Recently, ( Ulbrich et al, 2023 ), presented sMolBoxes featuring a dataflow model designed for exploring and analyzing extended MD simulations. Through the integration of quantitative analysis for user-specified properties and interactive 3D visualizations, it facilitates the visual interpretation of molecular behaviors.…”

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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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: 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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“…More recently, Ulbrich et al 17 ability to visualize each node in the expression tree. sMolBoxes exploits this to plot intermediate results from the operations.…”

Section: ■ Introductionmentioning

confidence: 99%

“…More recently, Ulbrich et al 17 demonstrated the computation of user-defined properties through a visual node-based graph network instead of the typical scripting interface. A benefit of using visual nodes to construct expressions is the ability to visualize each node in the expression tree .…”

Section: Introductionmentioning

confidence: 99%

VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics

Skånberg,

Hotz,

Ynnerman

et al. 2023

J. Chem. Inf. Model.

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The typical workflow in molecular dynamics (MD) analysis requires several separate tools, often resulting in a lack of synergy and interaction between the individual analysis steps. This article presents VIAMD, an application designed to address this issue by integrating a 3D visualization of molecular trajectories with flexible analysis components. VIAMD uses an interactive scripting interface, allowing for property definition and evaluation. The application provides context-aware suggestions and expression feedback through information and visualizations. The user-defined properties can be explored and analyzed through the various components. This enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties such as spatial distribution functions. VIAMD has the potential to advance research in many scientific disciplines and is a promising solution for improving the workflow of MD visualization and analysis.

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MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations

Hnatyshyn,

Zhao,

Perez

et al. 2023

IEEE Trans. Visual. Comput. Graphics

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sMolBoxes: Dataflow Model for Molecular Dynamics Exploration

Abstract: Fig. 1. An overview of the sMolBoxes interface for molecular dynamics exploration, consisting of the 3D View, the Canvas with sMolBox Nodes, and the detailed bigBox View for navigation through the 3D animation.

Cited by 6 publications

References 35 publications

From complex data to clear insights: visualizing molecular dynamics trajectories

From complex data to clear insights: visualizing molecular dynamics trajectories

VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics

MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations

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