BioDynaMo: a general platform for scalable agent-based simulation
Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios, Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca,, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer
TL;DR
BioDynaMo is a high-performance, general-purpose agent-based simulation platform that leverages modern hardware to enable large-scale biological modeling across various fields, significantly outperforming existing simulators.
Contribution
It introduces BioDynaMo, a novel scalable simulation platform optimized for modern hardware, capable of simulating one billion agents, and validated across multiple biological use cases.
Findings
BioDynaMo performs up to three orders of magnitude faster than existing simulators.
It enables simulation of one billion agents on a single server.
Validated with experimental data and analytical solutions across neuroscience, oncology, and epidemiology.
Abstract
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…
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.