Abstract
BackgroundIn recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological domain due to high demand for a large scale analysis tools for the collection and interpretation of information to solve biological problems. Simulating massive multi-agent systems (i.e. simulations containing a large number of agents/entities) requires major computational effort which is only achievable through the use of parallel computing approaches.ResultsThis paper explores different approaches to parallelising the key component of biological and immune system models within an ABM model: pairwise interactions. The focus of this paper is on the performance and algorithmic design choices of cell interactions in continuous and discrete space where agents/entities are competing to interact with one another within a parallel environment.ConclusionsOur performance results demonstrate the applicability of these methods to a broader class of biological systems exhibiting typical cell to cell interactions. The advantage and disadvantage of each implementation is discussed showing each can be used as the basis for developing complete immune system models on parallel hardware.
Highlights
In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts
The Universal Immune System Simulator (UISS) framework models and simulates immune system related pathologies on Central Processing Units (CPUs) and previously we demonstrated the feasibility of applying Graphic Processing Unit (GPU) to biological cellular model by implementing a very common and necessary biological cell behaviour in FLAME GPU [10]
Using FLAME GPU to simulate the simplified model with only two cell agent types with pairwise interactions, Chimeh et al demonstrated that the technique is computationally more efficient than the serial counterpart and demonstrated the addition of a novel atomic based approach for reproducing equivalent serial behaviour
Summary
This paper explores different approaches to parallelising the key component of biological and immune system models within an ABM model: pairwise interactions. The focus of this paper is on the performance and algorithmic design choices of cell interactions in continuous and discrete space where agents/entities are competing to interact with one another within a parallel environment
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