DocumentCode :
3302170
Title :
Visualization of signal transduction processes in the crowded environment of the cell
Author :
Falk, Martin ; Klann, Michael ; Reuss, Matthias ; Ertl, Thomas
Author_Institution :
VISUS - Visualization Res. Center, Univ. Stuttgart, Stuttgart, Germany
fYear :
2009
fDate :
20-23 April 2009
Firstpage :
169
Lastpage :
176
Abstract :
In this paper, we propose a stochastic simulation to model and analyze cellular signal transduction. The high number of objects in a simulation requires advanced visualization techniques: first to handle the large data sets, second to support the human perception in the crowded environment, and third to provide an interactive exploration tool. To adjust the state of the cell to an external signal, a specific set of signaling molecules transports the information to the nucleus deep inside the cell. There, key molecules regulate gene expression. In contrast to continuous ODE models we model all signaling molecules individually in a more realistic crowded and disordered environment. Beyond spatiotemporal concentration profiles our data describes the process on a mesoscopic, molecular level, allowing a detailed view of intracellular events. In our proposed schematic visualization individual molecules, their tracks, or reactions can be selected and brought into focus to highlight the signal transduction pathway. Segmentation, depth cues and depth of field are applied to reduce the visual complexity. We also provide a virtual microscope to display images for comparison with wet lab experiments. The method is applied to distinguish different transport modes of MAPK (mitogen-activated protein kinase) signaling molecules in a cell. In addition, we simulate the diffusion of drug molecules through the extracellular space of a solid tumor and visualize the challenges in cancer related therapeutic drug delivery.
Keywords :
cancer; cellular transport; data visualisation; digital simulation; drug delivery systems; genetics; medical computing; stochastic processes; cancer; cellular signal transduction processes visualization; continuous ODE models; diffusion simulation; drug molecules; gene expression; intracellular events; mitogen-activated protein kinase signaling molecules; nucleus; signaling molecules transports; solid tumor; spatiotemporal concentration profiles; stochastic simulation; therapeutic drug delivery; transport modes; virtual microscope; wet lab experiments; Analytical models; Data visualization; Focusing; Gene expression; Humans; Image segmentation; Signal analysis; Signal processing; Spatiotemporal phenomena; Stochastic processes; I.3.3 [Computer Graphics]: Picture/Image Generation; I.3.7 [Computer Graphics]: Three-Dimensional Graphics and Realism; I.3.8 [Computer Graphics]: Applications; I.6.8 [Simulation and Modeling]: Types of Simulation—Discrete Event; J.3 [Life and Medical Sciences]: Biology and Genetics;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Visualization Symposium, 2009. PacificVis '09. IEEE Pacific
Conference_Location :
Beijing
Print_ISBN :
978-1-4244-4404-5
Type :
conf
DOI :
10.1109/PACIFICVIS.2009.4906853
Filename :
4906853
Link To Document :
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