CDS&E: Tools to facilitate deeper data analysis, exploration, management, and sharing of ensembles of molecular dynamics trajectory data

犹他大学的Thomas Cheatham获得了化学部化学理论、模型和计算方法奖的支持，以开发一个软件框架和一套工具，以促进跨规模和网络基础设施资源的数据分析和管理。齐塔姆和其他研究人员现在能够运行大量的分子动力学模拟，包括那些通过多维副本交换和以不同分辨率保存的数据来交换信息以增强采样的模拟。该项目的一个重要目标是提供一种简单的方法来深入检查这些模拟生成的数据，可视化结果，并最终指导模拟工作流。化学部和高级网络基础设施部的计算和数据使能科学与工程(CDS&amp；E)计划为该奖项提供资金。该项目涉及开发两个互补的软件环境，特别是iBIOMES和MD弹道分析代码cpptraj。IBIOMES提供了一个框架，允许自动注释、分析、搜索和显示模拟结果。最终目标是扩展和泛化这些环境，以提供允许任何人搜索、探索和分析原始数据、派生数据和/或数据子集的方法。Cpptraj计划将进一步发展，为MD轨迹的分析和数据管理提供新的思维方式，重点是对数据进行更深入的分析，包括更“交互”的分析能力。生物分子模拟提供对生物分子结构、动力学、相互作用和功能的详细洞察。随着对极其强大的计算资源的访问，社区正在被这些模拟的原始数据淹没。不仅管理和处理这些数据很困难，而且理解数据的含义也是具有挑战性的。通过进一步的软件开发，我们的目标是使管理和分析数据变得更容易，并最终将数据注释、搜索和传播到更广泛的社区。

Thomas Cheatham, of the University of Utah is supported by an award from the Chemical Theory, Models and Computational Methods in the Chemistry Division to develop a software framework and set of tools to facilitate data analysis and management across scales and cyberinfrastructure resources. Cheatham and other researchers are now able to run large ensembles of Molecular Dynamics simulations including those exchanging information for enhanced sampling with multidimensional replica-exchange and with data saved at different levels of resolution. An important goal of this project is to provide an easy means to deeply inspect the data generated from these simulations, visualize the results, and ultimately guide the simulation workflow. The Computational and Data-Enabled Science and Engineering (CDS&E) programs in the Chemistry Division and in the Division of Advanced Cyberinfrastructure cofund this award. The project involves the development of two complementary software environments, specifically iBIOMES and the MD trajectory analysis code cpptraj. iBIOMES provides a framework that allows automatic annotation, analysis, searching, and display of the simulation results The ultimate goal is to extend and generalize these environments to provide the means to allow anyone to search, explore, and analyze the raw data, derived data, and/or subsets of the data. The program cpptraj will be further developed by providing new ways of thinking about the analysis of MD trajectories and the management of the data with a focus on deeper analysis of the data, including more "interactive" analysis capabilities.Biomolecular simulations provide detailed insight into biomolecule structure, dynamics, interactions and function. With access to tremendously powerful computational resources, the community is being flooded with raw data from these simulations. Not only is managing and processing this data difficult, understanding the meaning of the data is challenging. Through further software developments we aim to make it easier to manage and analyze the data, and ultimately annotate, search and disseminate the data to the wider community.