Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents

Mathieu Le Muzic, Julius Parulek, Anne-Kristin Stavrum, Ivan Viola
Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents
Computer Graphics Forum, 33(3):141-150, June 2014. [ paper] [ video]
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Abstract

In this paper we propose a new type of a particle systems, tailored for illustrative visualization purposes, in particular for visualizing molecular reactions in biological networks. Previous visualizations of biochemical processes were exploiting the results of agent-based modeling. Such modeling aims at reproducing accurately the stochastic nature of molecular interactions. However, it is impossible to expect events of interest happening at a certain time and location, which is impractical for storytelling. To obtain the means of controlling molecular interactions, we propose to govern passive agents with an omniscient intelligence, instead of giving to the agents the freedom of initiating reaction autonomously. This makes it possible to generate illustrative animated stories that communicate the functioning of the molecular machinery. The rendering performance delivers for interactive framerates of massive amounts of data, based on the dynamic tessellation capabilities of modern graphics cards. Finally, we report an informal expert feedback we obtained from the potential users.

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@article{lemuzic-2014-ivm,
  title =      "Illustrative Visualization of Molecular Reactions using
               Omniscient Intelligence and Passive Agents ",
  author =     "Mathieu Le Muzic and Julius Parulek and Anne-Kristin Stavrum
               and Ivan Viola",
  year =       "2014",
  abstract =   "In this paper we propose a new type of a particle systems,
               tailored for illustrative visualization purposes, in
               particular for visualizing molecular reactions in biological
               networks. Previous visualizations of biochemical processes
               were exploiting the results of agent-based modeling. Such
               modeling aims at reproducing accurately the stochastic
               nature of molecular interactions. However, it is impossible
               to expect events of interest happening at a certain time and
               location, which is impractical for storytelling. To obtain
               the means of controlling molecular interactions, we propose
               to govern passive agents with an omniscient intelligence,
               instead of giving to the agents the freedom of initiating
               reaction autonomously. This makes it possible to generate
               illustrative animated stories that communicate the
               functioning of the molecular machinery. The rendering
               performance delivers for interactive framerates of massive
               amounts of data, based on the dynamic tessellation
               capabilities of modern graphics cards. Finally, we report an
               informal expert feedback we obtained from the potential
               users.",
  pages =      "141--150",
  month =      jun,
  number =     "3",
  event =      "EuroVis",
  journal =    "Computer Graphics Forum",
  volume =     "33",
  URL =        "http://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/",
}