Anne Jeannin-Girardon, Pascal Ballet and Vincent Rodin.
A Software Architecture for Multi-Cellular System Simulations on
Graphics Processing Units.
Acta Biotheoretica, Springer, 61(3):317-327, September 2013.
Abstract:
The first aim of simulation in virtual environment is to help biologists to
have a better understanding of the simulated system. The cost of such
simulation is significantly reduced compared to that of in vivo simulation.
However, the inherent complexity of biological system makes it hard to
simulate these systems on non-parallel architectures: models might be made of
sub-models and take several scales into account; the number of simulated
entities may be quite large. Today, graphics cards are used for general
purpose computing which has been made easier thanks to frameworks like CUDA or
OpenCL. Parallelization of models may however not be easy: parallel computer
programing skills are often required; several hardware architectures may be
used to execute models. In this paper, we present the software architecture we
built in order to implement various models able to simulate multi-cellular
system. This architecture is modular and it implements data structures adapted
for graphics processing units architectures. It allows efficient simulation of
biological mechanisms.
Keywords:
Virtual biology, Simulation, Multi-cellular systems, Parallel architecture,
GPU, OpenCL.
[doi:10.1007/s10441-013-9187-3]
[Jeannin13a.pdf]