BioDynaMo: A modular platform for high-performance agent-based simulation

Lukas Breitwieser*, Ahmad Hesam, Jean De Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

3 Citations (Scopus)
13 Downloads (Pure)

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.

Original languageEnglish
Pages (from-to)453-460
Number of pages8
JournalBioinformatics
Volume38
Issue number2
DOIs
Publication statusPublished - 2022

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