SketchBio: a scientist’s 3D interface for molecular modeling and animation

Waldon, Shawn; Thompson, Peter M.; Hahn, Patrick J.; Taylor, Russell M.

doi:10.1186/1471-2105-15-334

Cited by 10 publications

(4 citation statements)

References 29 publications

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“…This problem could potentially be overcome by using 3D modelling software such as Blender (Waldon et al . ), which contains some collision detection algorithms for video game development. However, harnessing this functionality requires further customization of the software.…”

Section: Outstanding Challenges and Future Directionsmentioning

confidence: 99%

Multibody dynamics analysis (MDA) as a numerical modelling tool to reconstruct the function and palaeobiology of extinct organisms

Lautenschlager

2020

Palaeontology

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Recent advances in computer technology have substantially changed the field of palaeontology in the last two decades. Palaeontologists now have a whole new arsenal of powerful digital techniques available to study fossil organisms in unprecedented detail and to test hypotheses regarding function and behaviour. Multibody dynamics analysis (MDA) is one of these techniques and although it originated as a tool used in the engineering and automotive industry, it holds great potential to address palaeontological questions as well. MDA allows the simulation of dynamic movements in complex objects consisting of multiple linked components. As such, this technique is ideally suited to model biological structures and to obtain quantifiable results that can be used to test the function of musculoskeletal systems rigorously. However, despite these advantages, MDA has seen a slow uptake by the palaeontological community. The most likely reason for this lies in the steep learning curve and complexity of the method. This paper provides an overview of the underlying principles of MDA and outlines the main steps involved in conducting analyses. A number of recent studies using MDA to reconstruct the palaeobiology of fossil organisms are presented and the potential for future studies is discussed. Similar to other computational techniques, including finite element analysis and computational fluid dynamics, the non‐invasive and exploratory power of MDA makes it ideally suited to study the form and function in vertebrates for which no modern analogues exist.

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Section: Outstanding Challenges and Future Directionsmentioning

confidence: 99%

Multibody dynamics analysis (MDA) as a numerical modelling tool to reconstruct the function and palaeobiology of extinct organisms

Lautenschlager

2020

Palaeontology

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“…Since then, a variety of scenarios involving novel input technologies for molecular manipulation have been explored and evaluated. These include improving performance using force feedback in a simplified 6 DOF spring-based energy minimization [Ming, Beard and Brooks, 1989]; bimanual scientist creation of molecular structures and animations [Waldon et al, 2014]; multiple scientists interacting with visualizations using multi-touch tables [Forlines and Lilien, 2008;Logtenberg, 2008;Logtenberg, 2009]; using Kinect and/or Leap Motion, targeted at scientists and learners [Alsayegh, Paramonov and Makatsoris, 2013;Hsiao, Cooper et al, 2014;Hsiao, Sun et al, 2016;Jamie and McRae, 2011;Sabir et al, 2013]; camera control with a separate touchscreen device [Lam and Siu, 2017]; as well as tangible [Sankaranarayanan et al, 2003] and "mixed reality" models [Gillet et al, 2005].…”

Section: Interactive Molecular Manipulationmentioning

confidence: 99%

Comparison of mouse and multi-touch for protein structure manipulation in a citizen science game interface

Muender¹,

Gulani²,

Westendorf³

et al. 2019

JCOM

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We developed a multi-touch interface for the citizen science video game Foldit, in which players manipulate 3D protein structures, and compared multi-touch and mouse interfaces in a 41-subject user study. We found that participants performed similarly in both interfaces and did not have an overall preference for either interface. However, results indicate that for tasks involving guided movement to dock protein parts, subjects using the multi-touch interface completed tasks more accurately with fewer moves, and reported higher attention and spatial presence. For tasks involving direct selection and dragging of points, subjects using the mouse interface performed fewer camera adjustments.

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“…For example, our ePMV plugin [25] allows users to run molecular modeling software directly inside of professional 3D animation applications. SketchBio [44] is another example of a 3D interface for molecular modeling and animation. Lv et al [33] explored the possibility to use game technology in biomolecular visualization, using the Unity3D game engine to develop and prototype a molecular visualization application for subsequent use in research or education.…”

Section: Related Workmentioning

confidence: 99%

Instant Construction and Visualization of Crowded Biological Environments

Klein

Autin

Kozlíková

et al. 2018

IEEE Trans. Visual. Comput. Graphics

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We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.

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SketchBio: a scientist’s 3D interface for molecular modeling and animation

Cited by 10 publications

References 29 publications

Multibody dynamics analysis (MDA) as a numerical modelling tool to reconstruct the function and palaeobiology of extinct organisms

Multibody dynamics analysis (MDA) as a numerical modelling tool to reconstruct the function and palaeobiology of extinct organisms

Comparison of mouse and multi-touch for protein structure manipulation in a citizen science game interface

Instant Construction and Visualization of Crowded Biological Environments

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