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.

中文翻译：

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BioDynaMo：用于基于代理的高性能模拟的模块化平台

基于动机代理的建模是研究复杂生物系统不可或缺的工具。然而，现有的仿真平台并不总是能充分利用现代硬件，并且通常具有针对特定领域的软件设计。结果 我们提出了一个名为 BioDynaMo 的新型模拟平台，它可以缓解这两个问题。BioDynaMo 具有模块化和高性能模拟引擎。我们证明 BioDynaMo 可用于模拟以下领域的用例：神经科学、肿瘤学和流行病学。对于每个用例，我们都会使用实验数据或分析解决方案来验证我们的发现。我们的性能结果表明，BioDynaMo 的性能比最先进的基线快三个数量级。这种改进使得在单个服务器上模拟具有 10 亿个代理的每个用例成为可能，展示 BioDynaMo 在计算生物学研究方面的潜力。可用性和实施​​ BioDynaMo 是 Apache 2.0 许可下的开源项目，可从 www.biodynamo.org 获取。补充信息中提供了重现结果的说明。补充信息可在 https://doi.org/10.5281/zenodo.5121618 获得。