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

• 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
• 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

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，用于在单一环境中进行实践学习。 粒子冷冻电镜和冷冻ET 总结 单粒子低温电子显微镜（cryoEM）已成为结构生物学的主流技术 由于样品制备的负担降低， 结构，以及在高分辨率下可视化大型结构异质大分子复合物的能力。 分辨率随着cryoEM的扩展，低温电子断层扫描（cryoET）的新生领域继续发展， 实现里程碑-例如原位结构测定-表明cryoET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。无论是 cryoEM和cryoET，新用户面临着一个重大的教育障碍：从业者必须了解概念 从生物化学到电子显微镜的物理学，再到计算图像对齐算法。 尽管目前有cryoEM研讨会通过实践培训来解决这些概念， 有限的容量和亲密的格式导致大量超额认购，无法训练新的cryoEM 全体用户。因此，在帮助用户的培训材料和资源方面存在很大差距。 理解、分析、解释和验证cryoEM数据和结构确定。为此，我们 建议建立一个在线教育平台，专注于cryoEM/ET数据处理，称为“cryoEDU”。的 cryoEDU平台建立在三个支柱上：1）自定进度的在线模块课程; 2）动手数据分析 在云桌面环境中;以及3）社区参与，以促进与 冷冻EM/ET数据分析。在线教育课程将把真实的cryoEM/ET数据纳入学习 除了强调最佳实践和常见陷阱以提供帮助的评估之外，还提供有关特定主题的模块 严格培训学员进行cryoEM/ET分析。为了确保足够的数据分析培训，我们将允许用户 提交模拟作业并使用云桌面环境与cryoEM软件进行交互。重要的是，用户 我不会运行真实的时间算法，而是从预先计算的结果数据库中提取结果 包含几乎所有可能的结果。云桌面将使用户能够进行参数选择， 接收即时结果反馈，在cryoEM/ET数据分析学习中创建新的范例。最后我们 我将通过在我们的网站上提供推荐信，突出所做的决定，与cryoEM/ET社区互动。 在分析数据时由专家进行，并记录与主要作者就重要的cryoEM/ET进行的现场对话 出版物。我们认识到cryoEM和cryoET继续快速增长，这就是为什么我们希望我们的 内容随着实地的变化以及通过学习评估和调查获得的用户反馈而发展。我们 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职位提交和从业者面试相结合。在线培训 cryoEDU提供的平台使我们能够吸引更多的学习者，特别是小型偏远学校， 这比通过面对面的研讨会实现的更容易，而无需大量额外的资源投资。