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

大规模并行测序(MPS，或称下一代测序)技术的快速发展使复杂群落随时间和空间的详细分析成为小型研究小组易于处理的研究目标，从而彻底改变了分子微生物生态学。虽然MPS方法的出现使微生物生态学家能够以越来越高的精度提出有意义的问题，但它给难以管理兆字节甚至几十亿字节数据的单个小型实验室带来了巨大的挑战。该项目将支持网络服务VAMPS(微生物种群结构可视化和分析，http://vamps.mbl.edu)，)，使各个研究小组不需要在计算基础设施和生物信息支持方面进行大量投资，否则处理、分析和解释微生物生态学的MPS数据是必要的。VAMPS是一个免费的开源数据库驱动的网站，允许研究人员使用MPS数据分析微生物群落的多样性和群落之间的关系，在直观的视觉环境中探索这些分析，并下载分析和图像以供发布。任何具有网络功能的设备都可以用于上传、处理、浏览和提取来自VAMPS的数据和结果，并且VAMPS开发团队可以在数据处理和分析的所有方面提供协助。VAMPS鼓励研究人员共享序列和元数据，并促进来自不同生物群的研究人员之间的合作，他们识别共享数据中的共同模式。VAMPS目前托管着200多个项目，包括5000多个数据集和超过2.5亿个序列标签，被来自世界各地的近1000名研究人员使用，并支持了至少15个NSF资助的项目。VAMPS通过组合来自各种环境的数据、集成基于序列聚类和基于分类的分析和可视化工具以及项目开发人员提供的指导来提供独特的教育机会。VAMPS旨在比较环境中对扩增标记数据进行可视化、探索和分析。序列数据和相关的元数据可以由用户直接上传，也可以通过向VAMPS项目团队发送数据来上传；MPS读取可以自动进行质量过滤，并分配给分类结构和分类独立的集群。然后可以将这些链接到元数据，并使用各种分析和可视化工具进行比较。每个结果都与其他分析和可视化选项建立了广泛的超链接，从而促进了数据探索并导致了对数据关系的更好理解。VAMPS的一个主要优势是，研究人员不仅可以比较他们自己项目中的数据集，而且可以将这些数据集与NSF资助的长期生态研究项目、国际海洋微生物普查、人类微生物组项目和数百个其他单独项目的数据集进行比较。该项目将支持：1)随着作者发布新版本，QIIME、OTU集群方法、寡核苷酸和其他方法的活跃版本。2)支持用户上传和修剪数据、使用多种VAMPS可视化和分析工具、为其他分析方法和图像导出数据以供发布、促进协作和添加新门户的VAMPS管理员。3)纳入新的公开数据。特别令人感兴趣的项目包括地球微生物组项目、美国GUT项目和Terra Ocean，这些项目已经或将拥有数据，如果通过VAMPS提供，这些数据将使研究界受益。4)根据社区的要求调整分析能力以适应其他适当的基因。5)硬件和软件维护及数据存储。该项目的所有结果都可以在vamps.mbl.edu上找到。

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.