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In Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation

机译:基于3D代理的声带发炎和修复模拟的原位可视化

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摘要

A fast and insightful visualization is essential in modeling biological system behaviors and understanding underlying inter-cellular mechanisms. High fidelity models produce billions of data points per time step, making in situ visualization techniques extremely desirable as they mitigate I/O bottlenecks and provide computational steering capability. In this work, we present a novel high-performance scheme to couple in situ visualization with the simulation of the vocal fold inflammation and repair using little to no extra cost in execution time or computing resources. The visualization component is first optimized with an adaptive sampling scheme to accelerate the rendering process while maintaining the precision of the displayed visual results. Our software employs VirtualGL to perform visualization in situ. The scheme overlaps visualization and simulation, resulting in the optimal utilization of computing resources. This results in an in situ system biology simulation suite capable of remote simulation of 17 million biological cells and 1.2 billion chemical data points, remote visualization of the results, and delivery of visualized frames with aggregated statistics to remote clients in real-time.
机译:快速而有洞察力的可视化对于建模生物系统行为和理解潜在的细胞间机制至关重要。高保真模型每个时间步产生数十亿个数据点,因此原位可视化技术非常理想,因为它们可减轻I / O瓶颈并提供计算控制能力。在这项工作中,我们提出了一种新颖的高性能方案,将原位可视化与声带发炎和修复的模拟相结合,而执行时间或计算资源却很少甚至没有额外的成本。首先使用自适应采样方案对可视化组件进行优化,以加快渲染过程,同时保持所显示视觉结果的精度。我们的软件采用VirtualGL进行原位可视化。该方案重叠了可视化和仿真,从而可以优化利用计算资源。这样就形成了一个原位系统生物学模拟套件,该套件能够对1700万个生物细胞和12亿个化学数据点进行远程模拟,对结果进行远程可视化,并将具有汇总统计信息的可视化框架实时交付给远程客户端。

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