论文标题
Biodynamo：基于可扩展代理模拟的一般平台
BioDynaMo: a general platform for scalable agent-based simulation
论文作者
论文摘要
动机：基于代理的建模是研究复杂生物系统的必不可少的工具。但是，现有的模拟器并不总是充分利用现代硬件，并且经常具有特定于现场的软件设计。 结果：我们提出了一个名为Biodynamo的新型仿真平台，可以减轻这两个问题。 Biodynamo具有通用和高性能模拟引擎。我们证明，生物学家可用于模拟以下情况：神经科学，肿瘤学和流行病学。对于每种用例，我们都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。这种改进使得与单个服务器上十亿代理模拟每种用例的可行性，展示了潜在的Biodynamo对计算生物学研究的可能性。 可用性：Biodynamo是Apache 2.0许可下的开源项目，可在www.biodynamo.org上找到。复制结果的说明可在补充信息中获得。 联系人：[email protected]，[email protected]，[email protected]，[email protected] 补充信息：https：//doi.org/10.5281/zenodo.4501515
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators 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 general-purpose 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 baseline. 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. Contact: [email protected], [email protected], [email protected], [email protected] Supplementary information: Available at https://doi.org/10.5281/zenodo.4501515
