3D Visualization and Virtual Exploration of Genomic Sequences

Hérisson, Joan; Férey, Nicolas; Gros, Pierre-Emmanuel; Magneau, Olivier; Gherbi, Rachid

doi:10.2481/dsj.4.82

Cited by 4 publications

(3 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The potential of VR for immersive 3D visualization of DNA structures was also exploited in the area of genomics [64]. ADN Viewer [28] is an application for the visualization and exploration of genomic 3D structures that also integrates VR capabilities to enable stereoscopic visualization on large screens [27]. 3DGV [67] is a newer approach that focuses on manipulating data in two-controller immersive environments, but again it does not support modeling tasks.…”

Section: Molecular Modeling and Visualization In Vrmentioning

confidence: 99%

Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures

Kuťák

Selzer

Ganuza

et al. 2022

IEEE Trans. Visual. Comput. Graphics

View full text Add to dashboard Cite

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design of such structures. However, as such structures are often spatially complex, their assembly and analysis are complicated. Since virtual reality (VR) was proven to be advantageous for such spatial-related tasks and there are no existing VR solutions focused on this domain, we propose Vivern, a VR application that allows domain experts to design and visually examine DNA origami nanostructures. Our approach presents different abstracted visual representations of the nanostructures, various color schemes, and an ability to place several DNA nanostructures and proteins in one environment, thus allowing for the detailed analysis of complex assemblies. We also present two novel examination tools, the Magic Scale Lens and the DNA Untwister, that allow the experts to visually embed different representations into local regions to preserve the context and support detailed investigation. To showcase the capabilities of our solution, prototypes of novel nanodevices conceptualized by our collaborating experts, such as DNA-protein hybrid structures and DNA origami superstructures, are presented. Finally, the results of two rounds of evaluations are summarized. They demonstrate the advantages of our solution, especially for scenarios where current desktop tools are very limited, while also presenting possible future research directions.

show abstract

Section: Molecular Modeling and Visualization In Vrmentioning

confidence: 99%

Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures

Kuťák

Selzer

Ganuza

et al. 2022

IEEE Trans. Visual. Comput. Graphics

View full text Add to dashboard Cite

show abstract

“…Previous work on DNA visualization has appeared in [3,4], but the techniques pose limitations regarding the visual comparison between multiple DNA sequences. A technique that allows the comparison between different sequences in terms of their common subsequences has been presented in [1].…”

Section: Introductionmentioning

confidence: 99%

Visual Exploration of Genomic Data

Vlachos

Taneri

Keogh

et al. 2007

Knowledge Discovery in Databases: PKDD 2007

View full text Add to dashboard Cite

Abstract. In this study, we present methods for comparative visualization of DNA sequences in two dimensions. First, we illustrate a transformation of gene sequences into numerical trajectories. The trajectory visually captures the nucleotide content of each sequence, allowing for fast and easy visualization of long DNA sequences. Then, we project the relative placement of the trajectories on the 2D plane using a spanning-tree arrangement method, which allows the efficient comparison of multiple sequences. We demonstrate with various examples the applicability of our technique in evolutionary biology and specifically in capturing and visualizing the molecular phylogeny between species.

show abstract

“…We selected a sample of 22 users from biology, medicine and other related fields. To better understand our users, we carried out usability inquiries in the form of field studies and user observations on two Bioinformatics visualization tools, Cn3D (Cn3D, 2005) and ADN-Viewer (Hérisson et al, 2005). For each participant, a complete set of user variables was recorded (see Tables 4 and 7).…”

Section: The Second Study: Designing With the P2p Mappermentioning

confidence: 99%

P2P Mapper: From User Experiences to Pattern-Based Design

Javahery¹,

Ahmed²

2012

THCI

View full text Add to dashboard Cite

User experience is an umbrella term referring to a collection of information that covers the user's behavior and interaction with a system. It is observed when the user is actively using a service or interacting with information, includes expectations and perceptions, and is influenced by user characteristics and application or service characteristics. User characteristics include knowledge, experience, personality and demographics. We propose a process and supporting software tool called Persona to Pattern (P2P) Mapper, which guides designers in modeling user experiences and identifying appropriate design patterns. The three-step process is: Persona Creation (a representative persona set is developed), Pattern Selection (behavioral patterns are identified resulting in an ordered list of design patterns for each persona), and Pattern Composition (patterns are used to create a conceptual design). The tool supports the first two steps of the process by providing various automation algorithms for user grouping and pattern selection combined with the benefit of rapid pattern and user information access. Persona and pattern formats are augmented with a set of discrete domain variables to facilitate automation and provide an alternative view on the information. Finally, the P2P Mapper is used in the redesign of two different Bioinformatics applications: a popular website and a visualization tool. The results of the studies demonstrate a significant improvement in the system usability of both applications.

show abstract

3D Visualization and Virtual Exploration of Genomic Sequences

Cited by 4 publications

References 6 publications

Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures

Vivern–A Virtual Environment for Multiscale Visualization and Modeling of DNA Nanostructures

Visual Exploration of Genomic Data

P2P Mapper: From User Experiences to Pattern-Based Design

Contact Info

Product

Resources

About