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 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 supplementary information. Supplementary information Available at https://doi.org/10.5281/zenodo.5121618.

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“…Straightforward visualizations that plot spikes in signal propagation are relatively common in the domain literature, such as in Rhodes et al [RPR*20]. Microscopy data often provide a structural foundation for visualizing simulations of signal propagation between neurons or in a multi‐neuron network [LHH*12; BHdM*21]. We show an example of a multineuron simulation network from BioDynaMo in Fig.…”

“…Agent‐based simulation of large‐scale pyramidal neuron cell growth with the BioDynaMo platform [BHdM*21]. Reproduced with author permission and under Creative Commons CC BY license.…”

HL-LHC Analysis With ROOT: ROOT Project Input to the HL-LHC Computing Review (Stage 2)

“…This means ROOT is itself an active element of open science. At the same time, ROOT is used also outside HEP, for instance through BioDynamo [16] or in quantitative finance research [17].…”

Hybrid computational models of multicellular tumour growth considering glucose metabolism

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