cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets

Muzic, Mathieu Le; Autin, Ludovic; Parulek, Július; Viola, Ivan

doi:10.2312/vcbm.20151209

Cited by 28 publications

(14 citation statements)

References 25 publications

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“…This amount of detail is not possible to render at interactive rates. With LOD optimizations, such as the creation of super-atoms for distant elements, cellVIEW could process 15 • 10 9 atoms at 60 Hz [30]. This amount of detail does not seem to be necessary in our case.…”

Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

“…The cellVIEW framework [30] also employs a similar level-of-detail (LOD) principle using advanced GPU methods for proteins in the HIV. It also removes detail to depict internal structures, and procedurally generates the needed elements.…”

Section: Multi-scale Visualization By Means Of Leaving Out Detailmentioning

confidence: 99%

“…To show more detail, we use the single nucleosome example in the data, which consists of 292 nucleotides and then create the ≈ 24 • 10 6 instances for the semantic nucleosome scale. Here we fully use of Le Muzic et al's [30] technique of employing the tessellation stages on the GPU, which dynamically injects the atoms of the nucleosome. We apply a similar instancing approach for transitioning to an atomistic representation, based on the 1AOI model from the PDB.…”

Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

“…We apply a similar instancing approach for transitioning to an atomistic representation, based on the 1AOI model from the PDB. To visually represent the elements, we utilize 2D sphere impostors instead of sphere meshes [30]. Specifically, we use triangular 2D billboards (i. e., only three vertices) that always face the camera and assign the depth to each fragment that it would get if it had been a sphere.…”

Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

“…The recent advances in visualization have allowed us to depict and understand many aspects of the structure and composition of the living cell. For example, cellVIEW [30] provides detailed visuals for viewers to understand the composition of a cell in an interactive exploration tool and Lindow et al [35] created an impressive interactive illustrative depiction of RNA and DNA structures. Most such visualizations only provide a depiction of components/processes at a single scale level.…”

Section: Introductionmentioning

confidence: 99%

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Scale Trotter: Illustrative Visual Travels Across Negative Scales

Halladjian

Miao

Kouril

et al. 2020

IEEE Trans. Visual. Comput. Graphics

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NucleusChromosomes Chromosomes with detail Nucleosomes Nucleotides Atoms Fibers Fig. 1. Steps along the voyage into the genomic detail as enabled by ScaleTrotter, showing the semantic scale levels. ScaleTrotter and its visual embedding allow us to seamlessly transition between independent representations and interactively explore them.Abstract-We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels-the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out-instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.

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Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

Section: Multi-scale Visualization By Means Of Leaving Out Detailmentioning

confidence: 99%

Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Scale Trotter: Illustrative Visual Travels Across Negative Scales

Halladjian

Miao

Kouril

et al. 2020

IEEE Trans. Visual. Comput. Graphics

Self Cite

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The modality effect reverses in a virtual reality learning environment and influences cognitive load

Albus

Seufert

2023

Instr Sci

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When Virtual Reality (VR) is used to present learning content, the three-dimensional image is often not sufficient and additional text is required, either in the form of visual or auditory text. Such additional instructional text could be particularly beneficial due to the many visual stimuli and the risk of visual working memory overload. Relieving working memory by using both channels in the audio-visual presentation, there might be more cognitive capacity available to invest in germane processes for learning. In addition, the image and the text can be processed simultaneously, supporting deeper learning processes. Based on the modality effect, it is therefore assumed that an audio-visual presentation in VR, compared to a visual-only presentation, can lead to higher learning outcomes (recall, comprehension and transfer). In a between-subjects design we analysed the modality principle in VR with 61 subjects (69% female). We hypothesized that when verbal information in VR is given auditorily instead of visually, it leads to overall higher learning outcomes. For intrinsic cognitive load we assumed no differences, but lower extraneous cognitive load and higher germane cognitive load for the audio-visual condition. However, results show a reverse modality effect. The visual-only condition showed higher learning outcome scores for recall, comprehension and transfer. As expected, the conditions showed no differences with regard to the intrinsic cognitive load. However, we also found no differences in extraneous cognitive load. Contrary to our hypothesis we found higher germane cognitive load for the visual-only condition compared to the audio-visual condition, which may be attributed to repeated reading, reading strategies or other self-regulatory strategies. Future research could focus on the use of strategies or evaluate relevant process data.

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Molecular Illustration in Research and Education: Past, Present, and Future

Goodsell

Jenkinson

2018

Journal of Molecular Biology

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Two-dimensional illustration is used extensively to study and disseminate the results of structural molecular biology. Molecular graphics methods have been and continue to be developed to address the growing needs of the structural biology community, and there are currently many effective, turn-key methods for displaying and exploring molecular structure. Building on decades of experience in design, best-practice resources are available to guide creation of illustrations that are effective for research and education communities.

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cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets

Cited by 28 publications

References 25 publications

Scale Trotter: Illustrative Visual Travels Across Negative Scales

Scale Trotter: Illustrative Visual Travels Across Negative Scales

The modality effect reverses in a virtual reality learning environment and influences cognitive load

Molecular Illustration in Research and Education: Past, Present, and Future

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