3D visualization of concentrations from stochastic agent-based signal transduction simulations

2010 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2010 - Proceedings

Volumn , Issue , 2010, Pages 1301-1304

  Falk, Martin ^a   Klann, Michael ^a   Reuss, Matthias ^a   Ertl, Thomas ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

Agent based simulation; Cellular signal transduction; Direct volume rendering; Protein concentration; Visualization

Indexed keywords

AGENT BASED SIMULATION; CELLULAR SIGNAL TRANSDUCTION; DIRECT VOLUME RENDERING; PROTEIN CONCENTRATION; PROTEIN CONCENTRATIONS;

BACTERIOPHAGES; CELL MEMBRANES; CONCENTRATION (PROCESS); MEDICAL IMAGING; MOLECULES; MONTE CARLO METHODS; PROTEINS; SIGNALING; THREE DIMENSIONAL; VISUALIZATION; VOLUME RENDERING;

SIGNAL TRANSDUCTION;

EID: 77955184375     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISBI.2010.5490235     Document Type: Conference Paper

References (10)

1. Chen W. W., Schoeberl B., Jasper P. J., Niepel M., Nielsen U. B., Lauffenburger D., and Sorger P., "Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data," Molecular Systems Biology, vol. 5, no. 239, pp. 1-19, 2009.
2. Dhillon A. S., Hagan S., Rath O., and Kolch W., "MAP kinase signalling pathways in cancer," Oncogene, vol. 26, no. 22, pp. 3279-3290, 2007.
3. Falk M., Klann M., Reuss M., and Ertl T., "Visualization of signal transduction processes in the crowded environment of the cell," in IEEE Pacific Visualization Symposium (PacificVis '09), 2009, pp. 169-176.
4. Hadwiger M., Ljung P., Salama C. R., and Ropinski T., "Advanced illumination techniques for GPU volume raycasting," in ACM SIGGRAPH Asia 2008 courses, 2008, pp. 1-166.
5. Kholodenko B. N., "Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors," Journal of Experimental Biology, vol. 206, no. 12, pp. 2073-2082, 2003.
6. Klann M. T., Lapin A., and Reuss M., "Stochastic simulation of signal transduction: Impact of the cellular architecture on diffusion," Biophysical Journal, vol. 96, no. 12, pp. 5122-5129, 2009.
7. Levoy M., "Display of surfaces from volume data," IEEE Computer Graphics and Applications, vol. 8, no. 3, pp. 29-37, 1988.
8. Pogson M., Smallwood R., Qwarnstrom E., and Holcombe M., "Formal agent-based modelling of intracellular chemical interactions," Biosystems, vol. 85, pp. 37-45, 2006.
9. Stegmaier S., Strengert M., Klein T., and Ertl T., "A simple and flexible volume rendering framework for graphicshardware-based raycasting," in International Workshop on Volume Graphics 2005, 2005, pp. 187-195.
10. Takahashi K., Arjunan S. N. V., and Tomita M., "Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico," FEBS Letters, vol. 579, no. 8, pp. 1783-1788, 2005.