A Short Course in Computation, Statistical Analyses, and Interpretation of Microbial Metagenome Data

微生物宏基因组数据的计算、统计分析和解释短期课程

• 批准号: 9119846
• 负责人: Ashley Shade
• 金额: $ 6.2万
• 依托单位: MICHIGAN STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-03 至 2018-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9119846
• 关键词: Address; Algorithms; Animals; Area; Bioinformatics; Biomedical Research; Cloud Computing; Computer software; Creativeness; Data; Data Analyses; Data Set; Databases; Development; Disease; Ecology; Ecosystem; Educational process of instructing; Environment; Equilibrium; Evaluation; Experimental Designs; Faculty; Feedback; Fostering; Foundations; Genbank; Generations; Health; High-Throughput Nucleotide Sequencing; Human; Human Microbiome; Immunity; Language; Lead; Learning; Mental Health; Metagenomics; Michigan; Participant; Pattern; Personal Computers; Plants; Postdoctoral Fellow; Preventive Medicine; Process; Protocols documentation; Pythons; Research; Research Personnel; Role; Running; Science; Shotguns; Statistical Computing; Statistical Data Interpretation; Technology; Testing; Time; Training; Vocabulary; Work; application programming interface; cluster computing; computing resources; data visualization; graduate student; improved; insight; learning materials; lectures; lens; literacy; meetings; metagenome; microbial; microbiome; microbiota; repository; skills; sound; statistics; tool; web site

 DESCRIPTION (provided by applicant): Recently, two important advances have fostered a new era in biomedical research. First, we now recognize that humans, other animals, and plants are important ecosystems for microbial consortia, and that these consortia underpin their hosts' wellness. For example, we are just beginning to understand the role of human microbiota in mental health, immunity, and development. Second, advances in high-throughput sequencing technologies have provided cutting-edge experimental tools for observing the diversity and functions of microbial consortia. For the first time, researchers can grapple with the sheer diversity of microbial consortia associated with hosts, and also can begin to untangle how this diversity contributes to host wellness. Thus, a many biomedical researchers have generated immense, information-rich metagenomic datasets, hoping to realize the promise of these datasets to understand the intricate relationships between microbiota and host. Despite this promise, analyses of metagenomic data present a major challenge. Most biomedical researchers lack the computational, bioinformatic, and statistical training required for appropriate analysis, and also lack a working vocabulary to communicate their analysis needs to statisticians. This is especially concerning in human microbiome research because inaccurate or incomplete analyses can lead to erroneous interpretations that have implications for our approaches to preventative medicine and disease treatment. It also leads to generation of data that ultimately cannot be used to answer research questions because of inadequate statistical power or depth of sequencing in experimental design. We plan to address this need by offering an economical, one-week intensive course to train advanced graduate students, post-docs, and faculty in how to analyze microbial metagenomic data, from raw sequence handling to statistical analyses. Our integrated educational strategy addresses two related training needs. First, we offer general training in the fundamentals of effective computing so that participants will build computing skills needed to execute their analyses independently. We also offer specific training to overcome hurdles particular to microbial metagenome analyses. Participants will develop these skills via practical, hands-on tutorials motivated with real microbial metagenome datasets, and will enrich their learning by engaging in lectures and panel discussions with key leaders in the field. All of our course materials are continually improved and freely available on our course website (edamame-course.org) and disseminated on our GitHub repository. Participant learning will be assessed each year and materials iteratively adapted to best meet course objectives. We successfully ran this course in 2014 and received overwhelmingly positive feedback. Our course evaluation data shows that our educational strategy was effective at increasing skill level, confidence, and analysis sophistication among our participants.

 描述(由申请人提供)：最近，两个重要的进展促进了生物医学研究的新纪元。首先，我们现在认识到，人类、其他动物和植物是微生物群落的重要生态系统，这些群落支撑着宿主的健康。例如，我们刚刚开始了解人类微生物区系在心理健康、免疫和发育中的作用。其次，高通量测序技术的进步为观察微生物群落的多样性和功能提供了尖端的实验工具。第一次，研究人员可以解决与宿主相关的微生物群落的绝对多样性，也可以开始解开这种多样性如何有助于宿主健康的谜团。因此，许多生物医学研究人员已经产生了大量的、信息丰富的元基因组数据集，希望实现这些数据集理解微生物区系和宿主之间复杂关系的前景。尽管有这样的希望，元基因组数据的分析仍然是一个重大挑战。大多数生物医学研究人员缺乏适当分析所需的计算、生物信息学和统计学培训，也缺乏将他们的分析需求传达给统计学家的工作词汇。这在人类微生物组研究中尤其令人担忧，因为不准确或不完整的分析可能会导致错误的解释，从而对我们预防医学和疾病治疗的方法产生影响。它还导致生成的数据最终无法用于回答研究问题，因为实验设计中的统计能力或测序深度不足。我们计划通过提供一门经济的、为期一周的强化课程来满足这一需求，培训高级研究生、博士后和教职员工如何分析微生物元基因组数据，从原始序列处理到统计分析。我们的综合教育战略解决了两个相关的培训需求。首先，我们提供有效计算基础知识的一般培训，以便参与者将建立独立执行他们的分析所需的计算技能。我们还提供特定的培训，以克服微生物元基因组分析所特有的障碍。参与者将通过实际操作的教程来发展这些技能，并通过与该领域的主要领导人进行讲座和小组讨论来丰富他们的学习。我们的所有课程材料都在不断改进，并在我们的课程网站(edamame-Course.org)上免费提供，并在我们的GitHub资源库中传播。将每年对参与者的学习进行评估，并反复调整材料，以最大限度地满足课程目标。我们在2014年成功举办了这门课程，并收到了压倒性的积极反馈。我们的课程评估数据显示，我们的教育策略在提高学员的技能水平、自信心和分析能力方面是有效的。