Strategies and Techniques for Analyzing Microbial Population Structures

分析微生物种群结构的策略和技术

• 批准号: 9273561
• 负责人: JOCELYN E MALAMY
• 金额: --
• 依托单位: MARINE BIOLOGICAL LABORATORY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-15 至 2019-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9273561
• 关键词: Address; Bioinformatics; Biological; Communities; Complex; Computer Architectures; Computer software; Computers; DNA sequencing; Data; Data Analyses; Data Set; Development; Ecology; Educational workshop; Equipment and supply inventories; Faculty; Genes; Genomics; Goals; Health; High-Throughput DNA Sequencing; Human; Human Microbiome; Investigation; Laboratories; Libraries; Marines; Massive Parallel Sequencing; Metabolic; Metadata; Metagenomics; Methodology; Microbe; Molecular; Pathway Analysis; Population; Postdoctoral Fellow; Preparation; Quality Control; RNA; Research; Research Personnel; Schedule; Series; Shotguns; Statistical Models; Structure; Students; Taxonomy; Techniques; Technology; Time; Training; Ursidae Family; Wood material; analytical tool; base; cost; design; graduate student; high end computer; laboratory experiment; laptop; lectures; microbial; microbial community; next generation; novel; posters; public health relevance; theories; tool

DESCRIPTION (provided by applicant): Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) - A workshop at the Marine Biological Laboratory in Woods Hole. This proposal describes a new, 10-day emersion course that will focus on design and analysis of marker gene and shotgun metagenomic projects for advanced graduate students, postdoctoral fellows and established investigators who seek to leverage the power of massively-parallel DNA sequencing technologies for investigations of microbial communities including the human microboime and host associated microbes. The format will include a series of lectures and computer laboratory exercises on the theory, application and experimental strategies for analysis of microbial communities through massively parallel, high-throughput DNA sequencing technology. Topics will include: current technologies for massively parallel sequencing (MPS) of DNA and RNA, experimental strategies for using MPS in studies of microbial communities, library preparation techniques, organization of next generation sequence data and associated meta-data, principles of quality control of sequence data, the theory of clustering sequences by similarity and rarefaction analyses, taxonomic assignments for high-throughput data, statistical models for estimating microbial diversity, microbial community comparison methodology and metrics, network analyses, and the annotation and interpretation of shotgun metagenomic data. Authors of analytical tools for analysis of marker gene and shotgun metagenomic data will challenge the students with tutorials that address real world problems that bear on human health and well- being. Using their laptops, students will gain access to the high-performance computer architecture in the Josephine Bay Paul Center at the MBL for analysis of large data sets. As importantly, this new course will promote a dialogue and exchange of ideas between experts who seek to guide the development of new analytical paradigms for the rapidly evolving field of molecular microbial ecology. Early in the course schedule, students will have the opportunity to present research posters in order to promote interactions with other students and with faculty who can offer advice about data analysis.

描述(由申请人提供)：分析微生物种群结构的战略和技术(STAMP)-伍兹霍尔海洋生物实验室的研讨会。这项建议描述了一个为期10天的新的再现课程，该课程将侧重于为高级研究生、博士后研究员和寻求利用大规模并行DNA测序技术的力量来调查微生物群落(包括人类微生物和宿主相关微生物)的高级研究生、博士后研究员和知名研究人员设计和分析标记基因和猎枪元基因组项目。该形式将包括一系列讲座和计算机实验室练习，内容涉及通过大规模并行、高通量DNA测序技术分析微生物群落的理论、应用和实验策略。主题将包括：DNA和RNA的大规模并行测序(MPS)的当前技术，在微生物群落研究中使用MPS的实验战略，文库准备技术，下一代序列数据和相关元数据的组织，序列数据的质量控制原则，通过相似性和稀疏性分析进行序列聚类的理论，高通量数据的分类分配，估计微生物多样性的统计模型，微生物群落比较方法和度量，网络分析，以及鸟枪式元基因组数据的注释和解释。分析标记基因和散弹枪元基因组数据的分析工具的作者将向学生提供教程，解决与人类健康和福祉有关的现实世界问题。学生们将使用他们的笔记本电脑访问位于MBL的约瑟芬湾保罗中心的高性能计算机体系结构，用于分析大型数据集。同样重要的是，这门新课程将促进专家之间的对话和思想交流，这些专家试图指导为快速发展的分子微生物生态领域开发新的分析范式。在课程安排的早期，学生将有机会展示研究海报，以促进与其他学生和能够提供数据分析建议的教职员工的互动。