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تسجيل مستخدم جديدThe BioDynaMo Project
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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.
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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 it
s numerous applications to the computational biology and nanoscience communities.
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.
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 presen
t 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
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