ABI Sustaining: A visualization and analysis resource for comparative microbial ecology

Marine Biological Laboratory, Woods Hole MA

Investigators

Abstract

The Marine Biological Laboratory is awarded a grant for sustaining operation of the web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu). VAMPS is a free, open-source database-driven website that allows researchers using data from massively-parallel sequencing (MPS, or ?next-generation sequencing?) projects 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. VAMPS currently hosts more than 200 projects encompassing more than 5000 datasets and over 250 million sequence tags, and is used by nearly 900 investigators from around the world. The rapid expansion of MPS technologies with the concurrent drastic drop in sequencing costs 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. The ability to generate 104?107 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to analyze data, it is difficult to compare datasets, which may represent spatial or temporal community gradients, changes to a community in response to nutrients or stress, the response of a biota to its host, or other relationships, in an intuitive and interactive manner that leads to hypothesis generation. VAMPS was developed to address these challenges and to facilitate research by individuals or collaborating groups working on projects of any scale. Sequence data and associated metadata can be uploaded directly to VAMPS 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. 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. VAMPS obviates 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. 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 has been used in more than 50 publication and at least 13 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. In addition to uncounted students among its registered users, the VAMPS website is used by graduate students in the Brown-MBL IGERT Reverse Ecology: Computational Integration of Genomes, Organisms and Environments; in the MBL's graduate/postdoctoral level Microbial Diversity summer course, and in the MBL Special Topics course Strategies and Techniques for Analysis of Microbial Population Structures, which draws graduate students, postdocs and principle investigators from around the world.