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Understanding how genetically encoded rules drive and guide complex neuronal growth processes is essential to comprehending the brain's architecture, and agent-based models (ABMs) offer a powerful simulation approach to further develop this understanding. However, accurately calibrating these models remains a challenge. Here, we present a novel application of Approximate Bayesian Computation (ABC) to address this issue. ABMs are based on parametrized stochastic rules that describe the time evolution of small components -- the so-called agents -- discretizing the system, leading to stochastic simulations that require appropriate treatment. Mathematically, the calibration defines a stochastic inverse problem. We propose to address it in a Bayesian setting using ABC. We facilitate the repeated comparison between data and simulations by quantifying the morphological information of single neurons with so-called morphometrics and resort to statistical distances to measure discrepancies between populations thereof. We conduct experiments on synthetic as well as experimental data. We find that ABC utilizing Sequential Monte Carlo sampling and the Wasserstein distance finds accurate posterior parameter distributions for representative ABMs. We further demonstrate that these ABMs capture specific features of pyramidal cells of the hippocampus (CA1). Overall, this work establishes a robust framework for calibrating agent-based neuronal growth models and opens the door for future investigations using Bayesian techniques for model building, verification, and adequacy assessment., Comment: 32 pages, 12 Figures

Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low performance of the underlying simulation engines. To overcome this limitation, we present a novel high-performance simulation engine. We identify three key challenges for which we present the following solutions. First, to maximize parallelization, we present an optimized grid to search for neighbors and parallelize the merging of thread-local results. Second, we reduce the memory access latency with a NUMA-aware agent iterator, agent sorting with a space-filling curve, and a custom heap memory allocator. Third, we present a mechanism to omit the collision force calculation under certain conditions. Our evaluation shows an order of magnitude improvement over Biocellion, three orders of magnitude speedup over Cortex3D and NetLogo, and the ability to simulate 1.72 billion agents on a single server. Supplementary Materials, including instructions to reproduce the results, are available at: https://doi.org/10.5281/zenodo.6463816, Comment: Accepted to PPoPP '23: The 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming

Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low performance of the underlying simulation engines. To overcome this limitation, we present a novel high-performance simulation engine. We identify three key challenges for which we present the following solutions. First, to maximize parallelization, we present an optimized grid to search for neighbors and parallelize the merging of thread-local results. Second, we reduce the memory access latency with a NUMA-aware agent iterator, agent sorting with a space-filling curve, and a custom heap memory allocator. Third, we present a mechanism to omit the collision force calculation under certain conditions. Our evaluation shows an order of magnitude improvement over Biocellion, three orders of magnitude speedup over Cortex3D and NetLogo, and the ability to simulate 1.72 billion agents on a single server. Supplementary Materials, including instructions to reproduce the results, are available at: https://doi.org/10.5281/zenodo.6463816, Computer Engineering

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., Computer Engineering

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., Computer Engineering

Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to alleviate researchers from the intricacies that go into the development of high-performance computing. Through a high-level interface, researchers can implement their models on top of BioDynaMo's multi-threaded core execution engine to rapidly develop simulations that effectively utilize parallel computing hardware. In biological agent-based modeling, the type of operations that are typically the most compute-intensive are those that involve agents interacting with their local neighborhood. In this work, we investigate the currently implemented method of handling neighborhood interactions of cellular agents in BioDynaMo, and ways to improve the performance to enable large-scale and complex simulations. We propose to replace the kd-tree implementation to find and iterate over the neighborhood of each agent with a uniform grid method that allows us to take advantage of the massively parallel architecture of graphics processing units (GPUs). We implement the uniform grid method in both CUDA and OpenCL to address GPUs from all major vendors and evaluate several techniques to further improve the performance. Furthermore, we analyze the performance of our implementations for models with a varying density of neighboring agents. As a result, the performance of the mechanical interactions method improved by up to two orders of magnitude in comparison to the multithreaded baseline version. The implementations are open-source and publicly available on Github., Comment: 8 pages, 12 figures

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: lukas.breitwieser@inf.ethz.ch, a.s.hesam@tudelft.nl, omutlu@ethz.ch, r.bauer@surrey.ac.uk Supplementary information: Available at https://doi.org/10.5281/zenodo.4501515, Comment: 8 pages, 6 figures

Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be executable on hybrid cloud computing systems. This paper describes challenges and lessons learnt during the early stages of the software development process, in the context of implementation issues and the international nature of the collaboration., Comment: 4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4), 2016

This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as well as its numerous applications to the computational biology and nanoscience communities., Comment: The paper contains inaccurate content and claims that need to be verified

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems (such as the human brain) comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project (\url{https://biodynamo.web.cern.ch/}) aims at a general platform for computer simulations for biological research. Since the scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This paper describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learnt by the team during these first stages.