Toward Petascale Simulation of Cellular Microphysiology

Author

Baden, Scott B. ; Sejnowski, Terrence J. ; Bartol, Thomas M. ; Stiles, Joel

Author_Institution

Univ. of California, San Diego, La Jolla

fYear

2007

fDate

14-17 Oct. 2007

Firstpage

628

Lastpage

634

Abstract

MCell is a Monte Carlo simulator of cell microphysiology, and the scalable variant can be used to study challenging problems of interest to the biological community. MCell can currently model a single synapse out of thousands on a single cell. Petascale technology will enable significant advances in the ability to treat larger structures involving many synapses, with correspondingly more complex behavior. However, there are significant challenges to scaling MCell across two orders of magnitude in performance: increased communication delays and uneven workload concentrations. We discuss software solutions currently under investigation that will accompany us on the path to petascale cell microphysiology.

Keywords

Monte Carlo methods; biology computing; cellular biophysics; MCell; Monte Carlo simulator; cellular microphysiology; communication delays; petascale simulation; synapses; uneven workload concentrations; Biological system modeling; Biology computing; Cells (biology); Computational modeling; Computer simulation; Context modeling; Delay; Monte Carlo methods; Petascale computing; Stochastic processes;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on

Conference_Location

Boston, MA

Print_ISBN

978-1-4244-1509-0

Type

conf

DOI

10.1109/BIBE.2007.4375626

Filename

4375626