Dataset Information

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

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.

SUBMITTER: Breitwieser L

PROVIDER: S-EPMC8723141 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Publications

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

Breitwieser Lukas L Hesam Ahmad A de Montigny Jean J Vavourakis Vasileios V Iosif Alexandros A Jennings Jack J Kaiser Marcus M Manca Marco M Di Meglio Alberto A Al-Ars Zaid Z Rademakers Fons F Mutlu Onur O Bauer Roman R

Bioinformatics (Oxford, England) 20220101 2

<h4>Motivation</h4>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.<h4>Results</h4>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: neuro ...[more]

PMID: 34529036

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Dataset Information

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

Motivation

Results

Availability and implementation

Supplementary information

Publications

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

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