cryoEDU: An online curriculum and software platform for hands-on learning in single-particle cryoEM and cryoET

CryoEDU：用于单粒子 CryoEM 和 CryoET 实践学习的在线课程和软件平台

基本信息

批准号：
10222983
负责人：
Michael Cianfrocco
金额：
$ 12.28万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-01 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10222983
关键词：
3-Dimensional Address Algorithms Biochemistry Cells Classification Cloud Computing Communities Comprehension Computer software Data Data Analyses Data Set Data Storage and Retrieval Databases Decision Making Development E-learning Education Educational Curriculum Educational process of instructing Educational workshop Electron Microscope Electron Microscopy Electrons Ensure Environment Evaluation Face Feedback Funding Hour Image In Situ In Vitro Instruction Integral Membrane Protein Internet Interview Investments Knowledge Learning Learning Module Macromolecular Complexes Mainstreaming Motion Occupations Outcome Persons Physics Preparation Process Publications Publishing Resolution Resources Running Sampling Schools Scientist Specimen Structure Surveys Techniques Technology Time Training United States National Institutes of Health Universities cloud based community engagement complex data computer framework computerized data processing computing resources cryogenics electron tomography evidence base experience gigabyte hands-on learning in vivo learning materials next generation online course particle programs protein complex structural biology web site

项目摘要

cryoEDU: An online curriculum and software platform for hands-on learning in single- particle cryoEM and cryoET SUMMARY Single-particle cryogenic electron microscopy (cryoEM) has become a mainstream structural biology technique due to reduced burden of sample preparation, the capacity to solve integral membrane protein complex structures, and the ability to visualize large structurally heterogeneous macromolecular complexes at high resolution. As cryoEM expands, the nascent field of cryogenic electron tomography (cryoET) continues to achieve milestones – such as structure determination in situ – indicating that cryoET will soon become a core technology for structural and cell biologists for both in vitro and in vivo structural characterizations. In both cryoEM and cryoET, new users face a significant educational barrier: practitioners must understand concepts that range from biochemistry to physics of electron microscopes to computational image alignment algorithms. Although there are cryoEM workshops currently available address these concepts with hands-on training, the limited capacity and intimate format results in substantial oversubscription and an inability to train new cryoEM users en masse. As such, there exists a significant gap in training materials and resources that help users understand, analyze, interpret, and validate cryoEM data and structure determination. Towards this end, we propose to build an online educational platform focused on cryoEM/ET data processing called ‘cryoEDU’. The cryoEDU platform is built on three pillars: 1) self-paced online modular curricula; 2) hands-on data analysis in a cloud desktop environment; and 3) community engagement to facilitate information exchange related to cryoEM/ET data analysis. Online educational curricula will incorporate real cryoEM/ET data into learning modules on specific topics in addition to evaluations that highlight best practices and common pitfalls to help train learners in rigor for cryoEM/ET analysis. To ensure adequate data analysis training, we will allow users to submit simulated jobs and interact with cryoEM software using a cloud desktop environment. Importantly, users will not be running real time algorithms, but instead, we will pull results from a precalculated results database containing nearly all conceivable outcomes. The cloud desktop will enable users to make parameter choices and receive immediate results feedback, creating a new paradigm in cryoEM/ET data analysis learning. Finally, we will engage with the cryoEM/ET community by including testimonials on our website, highlighting decisions made by experts when analyzing data, and recording live conversations with primary authors on important cryoEM/ET publications. We recognize that cryoEM and cryoET continue to grow at a fast pace, which is why we expect our content to evolve with changes in the field and with user feedback via learning assessment and surveys. We believe that the cryoEDU platform will facilitate training data analysis and interpretation for cryoEM/ET by combining web content with interactive software job submission and practitioner interviews. The online training platform cryoEDU provides allows us to engage more learners, in particular small remote schools and universities, than achievable through in-person workshops without significant additional investment of resources.

CryoEDU：一个在线课程和软件平台，用于单人实践学习粒子冷冻电镜和冷冻电子显微镜概括单颗粒低温电子显微镜（cryoEM）已成为主流结构生物学技术由于减少了样品制备的负担，因此能够解决完整的膜蛋白复合物结构，以及在高温下可视化大型结构异质大分子复合物的能力随着冷冻电镜分辨率的不断提高，低温电子断层扫描 (cryoET) 的新兴领域不断发展。实现里程碑——例如原位结构确定——表明冷冻电子断层扫描将很快成为核心为结构和细胞生物学家提供体外和体内结构表征的技术。 CryoEM 和 CryoET，新用户面临重大的教育障碍：从业者必须理解概念其范围从生物化学到电子显微镜物理学再到计算图像对齐算法。尽管目前有冷冻电镜研讨会通过实践培训来解决这些概念，但有限的容量和亲密的格式导致大量超额认购并且无法训练新的冷冻电镜因此，在帮助用户的培训材料和资源方面存在巨大差距。为了实现这一目标，我们理解、分析、解释和验证冷冻电镜数据和结构测定。建议建立一个专注于 CryoEM/ET 数据处理的在线教育平台，称为“cryoEDU”。 CryoEDU 平台建立在三个支柱之上：1) 自定进度的在线模块化课程；2) 实践数据分析；在云桌面环境中；3) 社区参与以促进相关信息交换 CryoEM/ET 数据分析在线教育课程将把真实的 CryoEM/ET 数据纳入学习中。除了突出最佳实践和常见陷阱的评估之外，还提供有关特定主题的模块以提供帮助对学习者进行严格的冷冻EM/ET 分析培训为了确保充分的数据分析培训，我们将允许用户：重要的是，用户可以使用云桌面环境提交模拟作业并与 CryoEM 软件交互。将不会运行实时算法，而是从预先计算的结果数据库中提取结果包含几乎所有可以想象的结果，云桌面将使用户能够做出参数选择和接收即时结果反馈，创建冷冻EM/ET 数据分析学习的新范例。将通过在我们的网站上发布感言来与 CryoEM/ET 社区互动，强调所做的决定由专家在分析数据时进行，并记录与主要作者关于重要的冷冻电镜/电子断层扫描（cryoEM/ET）的实时对话我们认识到 CryoEM 和 CryoET 继续快速增长，这就是我们期望我们的出版物的原因。内容随着领域的变化以及通过学习评估和调查的用户反馈而发展。相信 CryoEDU 平台将通过以下方式促进 CryoEM/ET 的培训数据分析和解释将网络内容与交互式软件工作提交和从业者访谈相结合。 CryoEDU 提供的平台使我们能够吸引更多学习者，特别是小型偏远学校和大学，而不是通过面对面的研讨会来实现，而无需大量额外的资源投资。