ABI Sustaining: A Web-based Platform-independent Tool for Visualization and Analysis of Microbial Population Structures

Marine Biological Laboratory, Woods Hole MA

Investigators

Abstract

The rapid expansion of massively-parallel sequencing (MPS, or "next-generation sequencing") technology has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. While the advent of MPS methods has allowed microbial ecologists to ask meaningful questions with ever-greater precision, it brings significant challenges to individual small laboratories struggling to manage megabytes or even gigabytes of data. This project will sustain the web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu), which removes the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret MPS data for microbial ecology. VAMPS is a free, open-source database-driven website that allows researchers using MPS data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download analyses and images for publication. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS, and the VAMPS development team is available to assist in all aspects of data processing and analysis. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data. VAMPS currently hosts more than 200 projects encompassing more than 5000 datasets and over 250 million sequence tags, is used by nearly 1000 investigators from around the world, and has supported at least 15 NSF-funded projects. VAMPS provides unique educational opportunities through its combination of data from a variety of environments, its integration of sequence cluster-based and taxonomy-based analytical and visualization tools, and the instruction provided by project developers. VAMPS is designed for visualization, exploration, and analysis of amplicon tag data in a comparative context. Sequence data and associated metadata can be uploaded directly by users or by sending data to the VAMPS project team; MPS reads can be automatically quality filtered and assigned to both taxonomic structures and to taxonomic-independent clusters. These can then be linked to metadata and compared using a wide variety of analytical and visualization tools. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. A major strength of VAMPS is that researchers can compare not only datasets within their own projects but can compare these with datasets from projects such as NSF-funded Long Term Ecological Research projects, the International Census of Marine Microbes, the Human Microbiome Project, and hundreds of other individual projects. The project will support: 1) Active releases of QIIME, OTU clustering methods, oligotyping, and other methods as authors release new versions. 2) A VAMPS administrator to support users in uploading and trimming data and the use of the many VAMPS visualization and analysis tools, exporting data for other analytical methods and images for publication, and facilitating collaborations and adding new portals. 3) Incorporation of new publicly available data. Projects of particular interest include the Earth Microbiome Project, the American Gut Project, and Terra Oceans that have or will have data that would benefit the research community if made available through VAMPS. 4) Adapting analysis capabilities to other appropriate genes as requested by the community. 5) Hardware and software maintenance and data storage. All results of the project can be found at vamps.mbl.edu.