BioDynaMo: a modular platform for high-performance agent-based simulation.
BioDynaMo: a modular platform for high-performance agent-based simulation.
复制标题
DOI：
10.1093/bioinformatics/btab649
复制
发表时间：
2022-01-03
期刊：
影响因子：
--
通讯作者：
Bauer R
中科院分区：
文献类型：
--
作者：
Breitwieser L;Hesam A;de Montigny J;Vavourakis V;Iosif A;Jennings J;Kaiser M;Manca M;Di Meglio A;Al-Ars Z;Rademakers F;Mutlu O;Bauer R
基于智能体的建模是研究复杂生物系统不可缺少的工具。然而，现有的仿真平台并不总是充分利用现代硬件，并且通常具有特定领域的软件设计。我们提出了一种名为BioDynaMo的新型仿真平台，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可以用来模拟用例：神经科学，肿瘤学和流行病学。对于每个用例，我们用实验数据或分析解决方案验证我们的发现。我们的性能结果表明，BioDynaMo的性能比最先进的基线快了三个数量级。这一改进使得在单个服务器上用10亿个代理模拟每个用例变得可行，展示了BioDynaMo在计算生物学研究方面的潜力。BioDynaMo是Apache 2.0许可下的开源项目，可从www.biodynamo.org获得。在补充信息中提供了复制结果的说明。可在https://doi.org/10.5281/zenodo.5121618获得。
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. 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. Available at https://doi.org/10.5281/zenodo.5121618.
登录
查看更多内容
影响因子：
2.1
作者：
Cytowski, Maciej;Szymanska, Zuzanna
通讯作者：
Szymanska, Zuzanna
影响因子：
4.2
作者：
Chowell, G.;Miller, M. A.;Viboud, C.
通讯作者：
Viboud, C.
DOI：
10.1016/s0168-9002(97)00048-x
发表时间：
1997-04-11
影响因子：
1.4
作者：
Brun, R;Rademakers, F
通讯作者：
Rademakers, F
影响因子：
2.5
作者：
Azevedo, Frederico A. C.;Carvalho, Ludmila R. B.;Herculano-Houzel, Suzana
通讯作者：
Herculano-Houzel, Suzana
影响因子：
5.4
作者：
DENNARD, RH;GAENSSLEN, FH;LEBLANC, AR
通讯作者：
LEBLANC, AR