PI-FLAME: A parallel immune system simulator using the FLAME graphic processing unit environment
Authored by Paul Richmond, Shailesh Tamrakar, Roshan M D'Souza
Date Published: 2017
DOI: 10.1177/0037549716673724
Sponsors:
United States National Institutes of Health (NIH)
Platforms:
Repast
Model Documentation:
Other Narrative
Pseudocode
Model Code URLs:
Model code not found
Abstract
Agent-based models (ABMs) are increasingly being used to study
population dynamics in complex systems, such as the human immune system.
Previously, Folcik et al. (The basic immune simulator: an agent-based
model to study the interactions between innate and adaptive immunity.
Theor Biol Med Model 2007; 4: 39) developed a Basic Immune Simulator
(BIS) and implemented it using the Recursive Porous Agent Simulation
Toolkit (RePast) ABM simulation framework. However, frameworks such as
RePast are designed to execute serially on central processing units and
therefore cannot efficiently handle large model sizes. In this paper, we
report on our implementation of the BIS using FLAME GPU, a parallel
computing ABM simulator designed to execute on graphics processing
units. To benchmark our implementation, we simulate the response of the
immune system to a viral infection of generic tissue cells. We compared
our results with those obtained from the original RePast implementation
for statistical accuracy. We observe that our implementation has a 13x
performance advantage over the original RePast implementation.
Tags
Agent-based models
differentiation
Dynamics
Model
stochastic simulation
T-cells
Responses
Adaptive immunity
Innate immune system
Adaptive immune system
Flame
gpu
Antigen-presenting cells
Myeloid dendritic cells
Agent-based
simulation