论文标题

使用云中的NetworkIt对蛋白Rins的交互式可视化

Interactive Visualization of Protein RINs using NetworKit in the Cloud

论文作者

Angriman, Eugenio, Brandt-Tumescheit, Fabian, Franke, Leon, van der Grinten, Alexander, Meyerhenke, Henning

论文摘要

网络分析已应用于不同的应用领域。在本文中,我们考虑了蛋白质动力学,特别是残基相互作用网络(RIN)的示例。在这种情况下,我们使用NetworkIT(用于网络分析的已建立的软件包)来构建一个基于云的环境,该环境使域科学家能够在大型计算服务器上运行其可视化和分析工作流,而无需大量的编程和/或系统管理知识。为了证明这种方法的多功能性,我们使用它来构建一个基于自定义的jupyter的小部件进行RIN可视化。与现有的RIN可视化方法相反,我们的小部件可以通过简单的Python代码轻松自定义,同时支持良好功能集并提供接近实时速度。它也很容易地集成到分析管道中(例如,使用Python将RIN数据馈送到下游机器学习任务中)。

Network analysis has been applied in diverse application domains. In this paper, we consider an example from protein dynamics, specifically residue interaction networks (RINs). In this context, we use NetworKit -- an established package for network analysis -- to build a cloud-based environment that enables domain scientists to run their visualization and analysis workflows on large compute servers, without requiring extensive programming and/or system administration knowledge. To demonstrate the versatility of this approach, we use it to build a custom Jupyter-based widget for RIN visualization. In contrast to existing RIN visualization approaches, our widget can easily be customized through simple modifications of Python code, while both supporting a good feature set and providing near real-time speed. It is also easily integrated into analysis pipelines (e.g., that use Python to feed RIN data into downstream machine learning tasks).

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