DELTA-Topology: A Science Gateway for Experimental and Computational Chemical Data Analysis using Topological Models
DELTA-Topology: A Science Gateway for Experimental and Computational Chemical Data Analysis using Topological Models
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DOI：
10.1145/3437359.3465609
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发表时间：
2021-07
期刊：
影响因子：
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通讯作者：
Sudhakar Pamidighantam;Eric Coulter;Marcus A. Christie;A. Clark
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文献类型：
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作者：
Sudhakar Pamidighantam;Eric Coulter;Marcus A. Christie;A. Clark
化学数据是多样和复杂的，跨越点云数据和流形，并且可能出现大的维度。它们是从实验和计算模型中获得的，并且可以编码粒子/分子构型和动态运动的复杂关联。识别这种相关性，降低维度，识别点云数据和化学衍生表面（例如，化学转化的能量景观）的形状和拓扑结构是一个重大挑战。化学图论和计算拓扑为化学社区提供了强大的新工具，然而，由于缺乏支持基础设施，这些工具相关算法和方法的传播和实现受到了阻碍。在本文中，我们描述了DELTA科学网关，它集成了几种类型的数学和拓扑分析软件，用于化学数据分析。重点是从实验和计算建模技术中获得的能源景观数据，以便了解结构和功能所涉及的原理。DELTA网关由印第安纳大学的SciGaP项目托管，由Apache Airavata网关中间件框架提供支持。该网关为XSEDE资源的模拟和分析提供了一个集成的基础设施，以及通过VNC客户端和使用虚拟集群部署在Jetstream云上的JupyterHub进行交互访问。
Chemical data are diverse and complex, spanning point cloud data and manifolds, and occurring with potentially large dimensions. They are obtained from experimental and computational modeling, and may encode complex correlations of particle/molecular configurations and dynamic motion. It is a significant challenge to identify such correlations, reduce dimensionality, and identify the shapes and topologies of both point cloud data and chemistry-derived surfaces (e.g., energy landscapes of chemical transformation). Chemical graph theory and computational topology offer powerful new tools for the chemistry community, however, dissemination and implementation of the tools’ associated algorithms and methods has been hampered by a lack of supporting infrastructure. In this manuscript, we describe the DELTA Science Gateway, which integrates several types of mathematical and topological analysis software for chemical data analysis. The focus is on energy landscape data derived from experimental and computational modeling techniques in order to understand the principles involved in structure and function. The DELTA gateway is hosted under the SciGaP project at Indiana University and is powered by Apache Airavata gateway middleware framework. The gateway provides an integrated infrastructure for simulations and analysis on XSEDE resources, as well as interactive access through a VNC client and a JupyterHub deployed on the Jetstream cloud using virtual clusters.