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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

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Lukas Breitwieser

Ahmad Hesam

Jean de Montigny

Vasileios Vavourakis

Alexandros Iosif

Jack Jennings

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Professor of Neuroinformatics

Marco Manca

Alberto Di Meglio

Zaid Al-Ars



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.


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 Instructions to reproduce the results are available in the supplementary information.

Supplementary information

Available at


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.

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
Public URL
Publisher URL


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