BioDynaMo
A modular platform for high-performance agent-based simulation
Lukas Breitwieser (ETH Zürich, CERN)
A.S. Hesam (CERN, TU Delft - Computer Engineering)
Jean De Montigny (CERN)
Vasileios Vavourakis (University College London, University of Cyprus)
Alexandros Iosif (University of Cyprus)
Jack Jennings (Newcastle University)
Marcus Kaiser (University of Nottingham Medical School, Shanghai Jiao Tong University, Newcastle University)
Marco Manca (SCimPulse Foundation)
Alberto Di Meglio (CERN)
Zaid Al-Ars (TU Delft - Computer Engineering)
Fons Rademakers (CERN)
Onur Mutlu (ETH Zürich)
Roman Bauer (University of Surrey)
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Abstract
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology and epidemiology. For each use case, we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baselines. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research.
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