CellPathway: A Simulation Tool for Illustrative Visualization of Biochemical Networks

Information

• Publication Type: Conference Paper
• Workgroup(s)/Project(s):
  • Visual Computing: Illustrative Visualization
• Date: 2016
• Location: Pilsen, Czech Republic
• Lecturer: Mathieu Le Muzic
• Booktitle: Proceedings of WSCG

Abstract

The molecular knowledge about complex biochemical reaction networks in biotechnology is crucial and has received a lot of attention lately. As a consequence, multiple visualization programs have been already developed to illustrate the anatomy of a cell. However, since a real cell performs millions of reactions every second to sustain live, it is necessary to move from anatomical to physiological illustrations to communicate knowledge about the behavior of a cell more accurately. In this thesis I propose a reaction system including a collision detection algorithm, which is able to work at the level of single atoms, to enable precise simulation of molecular interactions. To visually explain molecular activities during the simulation process, a real-time glow effect in combination with a clipping object have been implemented. Since intracellular processes are performed with a set of chemical transformations, a hierarchical structure is used to illustrate the impact of one reaction on the entire simulation. The CellPathway system integrates acceleration techniques to render large datasets containing millions of atoms in real-time, while the reaction system is processed directly on the GPU to enable simulation with more than 1000 molecules. Furthermore, a graphical user interface has been implemented to allow the user to control parameters during simulation interactively.

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BibTeX

@inproceedings{Reisacher2016,
  title =      "CellPathway: A Simulation Tool for Illustrative
               Visualization of Biochemical Networks",
  author =     "Matthias Reisacher and Mathieu Le Muzic and Ivan Viola",
  year =       "2016",
  abstract =   "The molecular knowledge about complex biochemical reaction
               networks in biotechnology is crucial and has received a lot
               of attention lately. As a consequence, multiple
               visualization programs have been already developed to
               illustrate the anatomy of a cell. However, since a real cell
               performs millions of reactions every second to sustain live,
               it is necessary to move from anatomical to physiological
               illustrations to communicate knowledge about the behavior of
               a cell more accurately. In this thesis I propose a reaction
               system including a collision detection algorithm, which is
               able to work at the level of single atoms, to enable precise
               simulation of molecular interactions. To visually explain
               molecular activities during the simulation process, a
               real-time glow effect in combination with a clipping object
               have been implemented. Since intracellular processes are
               performed with a set of chemical transformations, a
               hierarchical structure is used to illustrate the impact of
               one reaction on the entire simulation. The CellPathway
               system integrates acceleration techniques to render large
               datasets containing millions of atoms in real-time, while
               the reaction system is processed directly on the GPU to
               enable simulation with more than 1000 molecules.
               Furthermore, a graphical user interface has been implemented
               to allow the user to control parameters during simulation
               interactively.",
  location =   "Pilsen, Czech Republic",
  booktitle =  "Proceedings of WSCG",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/",
}