CellPathway: A simulation tool for illustrative visualization of biochemical networks

Matthias Reisacher, Ivan Viola, Mathieu Le Muzic

Research output: Contribution to conferencePaperpeer-review

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 publication we propose a reaction system including a collision detection algorithm, which is able to work at the level of single atoms, to enable 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.

Original languageEnglish (US)
Pages99-105
Number of pages7
StatePublished - Jan 1 2016
Externally publishedYes
Event24th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, WSCG 2016 - Plzen, Czech Republic
Duration: May 30 2016Jun 3 2016

Conference

Conference24th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, WSCG 2016
CountryCzech Republic
CityPlzen
Period05/30/1606/3/16

Keywords

  • Collision detection
  • Large data
  • Molecular simulation
  • Particle-based data
  • Visualization system

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Computer Vision and Pattern Recognition

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