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

Breitwieser, Lukas; Hesam, Ahmad; de Montigny, Jean; Vavourakis, Vasileios; Iosif, Alexandros; Jennings, Jack; Kaiser, Marcus; Manca, Marco; Di Meglio, Alberto; Al-Ars, Zaid

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.

Availability and implementation

BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in the supplementary information.

Supplementary information

Available at https://doi.org/10.5281/zenodo.5121618.

Citation

Breitwieser, L., Hesam, A., de Montigny, J., Vavourakis, V., Iosif, A., Jennings, J., …Al-Ars, Z. (2022). BioDynaMo: a modular platform for high-performance agent-based simulation. Bioinformatics, 38(2), 453-460. https://doi.org/10.1093/bioinformatics/btab649

• Journal Article Type: Article
• Acceptance Date: Sep 13, 2021
• Online Publication Date: Sep 16, 2021
• Publication Date: Jan 15, 2022
• Deposit Date: Oct 23, 2022
• Publicly Available Date: Oct 24, 2022
• Journal: Bioinformatics
• Print ISSN: 1367-4803
• Electronic ISSN: 1460-2059
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 38
• Issue: 2
• Pages: 453-460
• DOI: https://doi.org/10.1093/bioinformatics/btab649
• Public URL: https://nottingham-repository.worktribe.com/output/9085261
• Publisher URL: https://academic.oup.com/bioinformatics/article/38/2/453/6371176