nanovisualization

KAUST Cell Visualization Summit 2019

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B9 H2 R2325

You are invited to attend the KAUST Cell Visualization Summit 2019 organized by the Nanovisualization group from the Visual Computing Center (VCC). The summit will focus on the technological advancement that can lead to an in-silico virtual and visual representation by integrating current knowledge into a unified structural and dynamic model of a living cell. Each keynote speaker will relate to one of the technological aspects (modeling, visualization, and interaction). Keynote speakers Arthur Olson Graham Johnson Anders Ynnerman For more information about the summit, please click here. If you

Nanovisualization: Depicting the Tiny World Around Us

Ivan Viola, Associate Professor, Computer Science

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KAUST

Life at micron-scale is inaccessible to the naked eye. To aid the comprehension of nano- and micro-scale structural complexity, we utilize 3D visualization. Thanks to efficient GPU-accelerated algorithms, we witness a dramatic boost in the sheer size of structures that can be visually explored. As of today an atomistic model of the entire bacterial cell can be displayed interactively. On top of that, advanced 3D visualizations efficiently convey the multi-scale hierarchical architecture and cope with the high degree of structural occlusion which comes with dense packing of biological building blocks. To further scale up the size of life forms that can be visually explored, the rendering pipeline needs to integrate runtime construction of the biological structure. Assembly rules define how a body of a certain biological entity is composed. Such rules need to be applied on-the-fly, depending on where the viewer is currently located in the 3D scene to generate full structural detail for that part of the scene. We will review how to construct membrane-like structures, soluble protein distributions, and fiber strands through parallel algorithms, resulting in a collision-free biologically-valid scene. Assembly rules that define how a life form is structurally built need to be expressed in an intuitive way for the domain scientist, possibly directly in the three-dimensional space. Instead of placing one biological element next to another one for the entire biological structure by the modelers themselves, only assembly rules need to be specified and the algorithm will complete the application of those rules to form the entire biological entity. These rules are derived from current scientific knowledge and from all available experimental observations. The Cryo-EM Tomography is on rising and shows that we can already now reach the near-atomistic detail when employing smart algorithms. Our assembly rules extraction, therefore, needs to integrate with microscopic observations, to create an atomistic representation of specific, observed life forms, instead of generic models thereof. Such models then can be used in whole-cell simulations, and in the context of automated science dissemination.

Web-based 3D Visualization

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B9 L2 H2 H2

In this seminar I will present how to create 3D computer graphics and visualization systems for the web, using WebAssmbly and WebGPU language specifications, which are new, bleeding-edge technologies. Previously, accelerated graphics on the web was based on JavaScript libraries, which is still very popular, but they do not offer detailed memory management and code optimization, necessary for systems requiring high memory load and high computational demands. WebAssembly and WebGPU can be compiled from the C++ or Rust code, which also allows the deployment of the same codebase either for web or for the desktop-based applications.

Visiting Slovenian student relishes time at KAUST

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KAUST visiting student Aljaz Bogataj, who spent three months in the NANOVIS research group, shared his impressions of work and life at KAUST.

Ivan Viola

Professor, Computer Science
Professor Viola’s expertise lies in scientific visualization and visual computing. His research focuses on multiscale visualization and modeling of complex biological systems, ranging from cellular organisms to atomistic-level details.

Deng Luo

Ph.D. Student, Computer Science
Deng Luo is a Ph.D. Candidate in the Computer Science program under the supervision of Professor Ivan Viola at the Visual Computer Center (VCC) at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. Education and Early Career Deng Luo earned his Bachelor's degree in Bioinformatics from Southern University of Science and Technology in Shenzhen, China in 2016. He has a multidisciplinary background, including bioinformatics, molecular biology, computer science, and entrepreneurship. He joined KAUST and received his Master's degree in Bioscience in 2019. Deng was trained as