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.
Massively parallel DNA sequencing has transformed molecular-based studies of free living and host- associated microbes (including the human microbiome) by providing a powerful tool that can inventory changes in community compositions and describe the composite metabolic capacity of microbial communities over temporal and spatial time scales. The increased cost of interpreting ever- larger amounts of omic information has created a large demand for the bioinformatic training of microbiologists and development of novel analytical tools. The STAMPS course seeks to fill this void by taking advantage of lessons learned from unsupported STAMP courses in 2011 and 2012.