Data-parallel techniques for agent-based tissue modeling on graphics processing units

Agent-Based Modeling has been recently recognized as a method for in-silico multi-scale modeling of biological cell systems. Agent-Based Models (ABMs) allow results from experimental studies of individual cell behaviors to be scaled into the macro-behavior of interacting cells in complex cell systems or tissues. Current generation ABM simulation toolkits are designed to work on serial von-Neumann architectures, which have poor scalability. The best systems can barely handle tens of thousands of agents in real-time. Considering that there are models for which mega-scale populations have significantly different emergent behaviors than smaller population sizes, it is important to have the ability to model such large scale models in real-time. In this paper we present a new framework for simulating ABMs on programmable graphics processing units (GPUs). Novel algorithms and data-structures have been developed for agent-state representation, agent motion, and replication. As a test case, we have implemented an abstracted version of the Systematic Inflammatory Response System (SIRS) ABM. Compared to the original implementation on the NetLogo system, our implementation can handle an agent population that is over three orders of magnitude larger with close to 40 updates/sec. We believe that our system is the only one of its kind that is capable of efficiently handling realistic problem sizes in biological simulations. Copyright © 2008 by ASME