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

Mathieu Le Muzic, Ludovic Autin, Julius Parulek, Ivan Viola
cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets
In Eurographics Workshop on Visual Computing for Biology and Medicine, pages 61-70. September 2015.
[] [paper]

Information

Abstract

In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.

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BibTeX

@inproceedings{cellVIEW_2015,
  title =      "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering
               of Large Biomolecular Datasets",
  author =     "Mathieu Le Muzic and Ludovic Autin and Julius Parulek and
               Ivan Viola",
  year =       "2015",
  abstract =   "In this article we introduce cellVIEW, a new system to
               interactively visualize large biomolecular datasets on the
               atomic level. Our tool is unique and has been specifically
               designed to match the ambitions of our domain experts to
               model and interactively visualize structures comprised of
               several billions atom. The cellVIEW system integrates
               acceleration techniques to allow for real-time graphics
               performance of 60 Hz display rate on datasets representing
               large viruses and bacterial organisms. Inspired by the work
               of scientific illustrators, we propose a level-of-detail
               scheme which purpose is two-fold: accelerating the rendering
               and reducing visual clutter. The main part of our datasets
               is made out of macromolecules, but it also comprises nucleic
               acids strands which are stored as sets of control points.
               For that specific case, we extend our rendering method to
               support the dynamic generation of DNA strands directly on
               the GPU. It is noteworthy that our tool has been directly
               implemented inside a game engine. We chose to rely on a
               third party engine to reduce software development work-load
               and to make bleeding-edge graphics techniques more
               accessible to the end-users. To our knowledge cellVIEW is
               the only suitable solution for interactive visualization of
               large bimolecular landscapes on the atomic level and is
               freely available to use and extend.",
  month =      sep,
  booktitle =  "Eurographics Workshop on Visual Computing for Biology and
               Medicine",
  editor =     "Katja B{"u}hler and Lars Linsen and Nigel W. John",
  isbn =       "978-3-905674-82-8",
  issn =       "2070-5786",
  location =   "Chester, United Kingdom",
  organization = "EG Digital Library",
  publisher =  "The Eurographics Association",
  pages =      "61--70",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/",
}