Collaborative Research: ABI Development: Building a Community Gateway for Cryo-Electron Microscopy Structure Determination

合作研究：ABI 开发：构建冷冻电子显微镜结构测定的社区网关

• 批准号: 1759813
• 负责人: Andres Leschziner
• 金额: $ 56.42万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-15 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759813&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Development; Building

Structural biology, the field devoted to understanding the chemical underpinnings of life, is undergoing a revolution due to the emergence, over the last 4 years, of cryo-electron microscopy (cryo-EM) as a technique capable of producing atomic-resolution structures. This "resolution revolution" has placed within reach structures that were previously inaccessible with other structural biology techniques. As a consequence, there is a growing interest among scientists in the expanded capabilities of cryo-EM. While previous generations of cryo-EM users were familiar with Linux and the HPC tools necessary to process the data, this is not the case with many of the structural biologists now attracted to the technique. We see this as a major barrier to the growth of cryo-EM. In order to remove this barrier, this project will develop an easy-to-use web platform, or "science gateway", that will interface with HPC resources, data processing algorithms, and long-term data storage options, allowing inexperienced users to access the full potential of cryo-EM. A prototype gateway (COSMIC2: Cryo-EM Open Source Multiplatform Infrastructure for Cloud Computing) has been developed in collaboration with the San Diego Supercomputer Center (SDSC), using its substantial HPC resources. This project will turn this early prototype into a resource that will benefit the structural biology community nationwide and outline all the features of a fully-developed gateway. The proposed COSMIC2 gateway will provide a large pool of computing time for cryo-EM users through an XSEDE allocation to the PIs; an easy-to-use web portal allowing users to select cryo-EM analysis routines; novel algorithms to streamline data processing, removing manual user intervention; mechanisms for viewing output data through the web interface; and long-term data storage solutions by connecting COSMIC2 to cloud storage providers (e.g. Google Drive, Box). The COSMIC2 gateway will optimally install and test major cryo-EM data processing software to ensure that they are using computational resources efficiently. The transformative impact of this project will come from the adoption of the COSMIC2 gateway by the broad structural biology community, to which it will bring national HPC resources and the power of cryo-EM while the removing any obstacles in accessing them. The current prototype for the resource may be seen at http://cosmic-cryoem.org/.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

结构生物学，致力于了解生命的化学基础的领域，正在经历一场革命，由于出现，在过去的4年里，低温电子显微镜（cryo-EM）作为一种技术，能够产生原子分辨率的结构。这种“分辨率革命”使以前无法用其他结构生物学技术获得的结构触手可及。因此，科学家对cryo-EM的扩展能力越来越感兴趣。虽然前几代的cryo-EM用户熟悉Linux和处理数据所需的HPC工具，但现在被该技术吸引的许多结构生物学家却并非如此。我们认为这是cryo-EM生长的主要障碍。为了消除这一障碍，该项目将开发一个易于使用的网络平台，或“科学网关”，该平台将与HPC资源，数据处理算法和长期数据存储选项相连接，允许没有经验的用户访问cryo-EM的全部潜力。一个原型网关（COSMIC 2：用于云计算的Cryo-EM开源多平台基础设施）已经与圣地亚哥超级计算机中心（SDSC）合作开发，使用其大量的HPC资源。该项目将把这个早期原型变成一个资源，使全国的结构生物学社区受益，并概述一个完全开发的网关的所有功能。拟议的COSMIC 2网关将通过向PI分配XSEDE为冷冻EM用户提供大量计算时间;一个易于使用的门户网站，允许用户选择冷冻EM分析程序;简化数据处理的新算法，消除用户手动干预;通过网络界面查看输出数据的机制;通过将COSMIC 2连接到云存储提供商（例如Google Drive，Box），提供长期数据存储解决方案。COSMIC 2网关将以最佳方式安装和测试主要的cryo-EM数据处理软件，以确保它们有效地使用计算资源。该项目的变革性影响将来自广泛的结构生物学社区对COSMIC 2网关的采用，它将为国家HPC资源和cryo-EM的力量带来帮助，同时消除访问它们的任何障碍。该资源的当前原型可以在http://cosmic-cryoem.org/.This奖项上看到，反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。