Browsing by Author "Alharbi, Naif"

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    Hybrid Visualization of Protein-Lipid and Protein-Protein Interaction
    (The Eurographics Association, 2019) Alharbi, Naif; Krone, Michael; Chavent, Matthieu; Laramee, Robert S.; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
    In the Molecular Dynamics (MD) visualization literature, different approaches are utilized to study protein-lipid interactions (PLI) and protein-protein interaction (PPI) in decoupled contexts. However, the two types of interaction occur in the same space-time domain. It is beneficial to study the PLI and PPI in a unified context. Nevertheless, the simulation's size, length, and complexity increase the challenge of understanding the dynamic behavior. We propose a novel framework consisting of four linked views, a time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. We introduce a selection of visual designs to convey the behavior of PLI and PPI through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, a projected tiled space is used to present both PLI and PPI at the particle level in a heat-map style visual design while glyphs are used to represent PPI at the molecular level. We couple visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately or together in a unified visual analysis framework. We also exemplify its use with case studies focusing on protein clustering and we report domain expert feedback.
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    Spectrum: A C++ Header Library for Colour Map Management
    (The Eurographics Association, 2018) Roberts, Richard C.; McNabb, Liam; AlHarbi, Naif; Laramee, Robert S.; {Tam, Gary K. L. and Vidal, Franck
    The use of colour mapping is fundamental to visualisation research. It acts as an additional layer beyond rendering in the spatial dimensions and provides a link between values in any dataset. When designing and building visualisation research software, the process of creating and managing a colour mapping system can be time-consuming and complex. Existing alternatives offer niche features and require complex dependencies or installations. We present Spectrum; an open source colour map management library that is developer friendly with no installation required, and that offers a wide variety of features for the majority of use cases. We demonstrate the utility of the library through simple snippets of code and a number of examples which illustrate its ease of use and functionality, as well as a video demonstrating the installation and use of the library in under two minutes. It is a very valuable jump-start tool for developers and researchers who need to focus on other tasks.