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BioDynaMo: a modular platform for high-performance agent-based simulation
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 BioDy...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723141/ https://www.ncbi.nlm.nih.gov/pubmed/34529036 http://dx.doi.org/10.1093/bioinformatics/btab649 |
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author | Breitwieser, Lukas Hesam, Ahmad de Montigny, Jean Vavourakis, Vasileios Iosif, Alexandros Jennings, Jack Kaiser, Marcus Manca, Marco Di Meglio, Alberto Al-Ars, Zaid Rademakers, Fons Mutlu, Onur Bauer, Roman |
author_facet | Breitwieser, Lukas Hesam, Ahmad de Montigny, Jean Vavourakis, Vasileios Iosif, Alexandros Jennings, Jack Kaiser, Marcus Manca, Marco Di Meglio, Alberto Al-Ars, Zaid Rademakers, Fons Mutlu, Onur Bauer, Roman |
author_sort | Breitwieser, Lukas |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8723141 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87231412022-01-05 BioDynaMo: a modular platform for high-performance agent-based simulation Breitwieser, Lukas Hesam, Ahmad de Montigny, Jean Vavourakis, Vasileios Iosif, Alexandros Jennings, Jack Kaiser, Marcus Manca, Marco Di Meglio, Alberto Al-Ars, Zaid Rademakers, Fons Mutlu, Onur Bauer, Roman Bioinformatics Original Paper 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. Oxford University Press 2021-09-16 /pmc/articles/PMC8723141/ /pubmed/34529036 http://dx.doi.org/10.1093/bioinformatics/btab649 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Paper Breitwieser, Lukas Hesam, Ahmad de Montigny, Jean Vavourakis, Vasileios Iosif, Alexandros Jennings, Jack Kaiser, Marcus Manca, Marco Di Meglio, Alberto Al-Ars, Zaid Rademakers, Fons Mutlu, Onur Bauer, Roman BioDynaMo: a modular platform for high-performance agent-based simulation |
title | BioDynaMo: a modular platform for high-performance agent-based simulation |
title_full | BioDynaMo: a modular platform for high-performance agent-based simulation |
title_fullStr | BioDynaMo: a modular platform for high-performance agent-based simulation |
title_full_unstemmed | BioDynaMo: a modular platform for high-performance agent-based simulation |
title_short | BioDynaMo: a modular platform for high-performance agent-based simulation |
title_sort | biodynamo: a modular platform for high-performance agent-based simulation |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8723141/ https://www.ncbi.nlm.nih.gov/pubmed/34529036 http://dx.doi.org/10.1093/bioinformatics/btab649 |
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