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.

结构生物学是专门理解生命的化学基础的领域，由于过去4年的出现，由于出现了革命，在过去的四年中，冷冻电子显微镜（Cryo-EM）是一种能够生成原子分辨率结构的技术。这种“解决方案革命”已将以前与其他结构生物学技术无法访问的触及结构置于范围内。结果，科学家对Cryo-EM的扩展能力的兴趣越来越大。虽然前几代的低温EM用户熟悉Linux和处理数据所需的HPC工具，但现在许多结构生物学家现在都吸引了该技术，但事实并非如此。我们认为这是冷冻EM增长的主要障碍。为了删除此障碍，该项目将开发一个易于使用的Web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接口，从而使没有经验的用户能够访问Cryo-EM的全部潜力。使用其实质性的HPC资源，已与San Diego SuperComputer Center（SDSC）合作开发了原型网关（COSMIC2：CRYO-EM开源乘出型基础架构）。该项目将把这个早期的原型变成一种资源，该原型将使全国结构生物学社区受益，并概述完整发达的门户的所有功能。拟议的COSMIC2网关将通过XSEDE分配给PIS为Cryo-EM用户提供大量的计算时间；易于使用的Web门户，允许用户选择Cryo-EM分析例程；简化数据处理，删除手动用户干预的新颖算法；通过Web接口查看输出数据的机制；和长期数据存储解决方案通过将COSMIC2连接到云存储提供商（例如Google Drive，Box）。 COSMIC2网关将最佳安装和测试主要的冷冻EM数据处理软件，以确保他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COSMIC2门户的采用，它将带来国家HPC资源和低温EM的力量，同时消除了访问它们的任何障碍。当前的资源原型可以在http://cosmic-cryoem.org/.This奖中看到NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响评估标准，认为NSF的法定任务值得支持。