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

海洋生物实验室获得一笔赠款，用于维持网络服务VAMPS（微生物种群结构的可视化和分析，http://vamps.mbl.edu）的运作。 VAMPS是一个免费的开源数据库驱动的网站，允许研究人员使用来自并行测序（MPS，或？下一代测序？）项目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出版。 VAMPS目前拥有200多个项目，包括5000多个数据集和超过2.5亿个序列标签，并由来自世界各地的近900名研究人员使用。MPS技术的快速扩展以及测序成本的大幅下降，通过对复杂群落随时间和空间的详细分析，为小型研究小组提供了易于处理的研究追求，从而彻底改变了分子微生物生态学。 #21040;能力，可？107读取相对容易，带来了许多下游并发症。 除了分析数据所需的计算资源和技能之外，很难以直观和交互的方式比较数据集，这些数据集可能代表空间或时间的群落梯度，群落对营养物或压力的反应，生物群对其宿主的反应或其他关系，从而导致假设生成。VAMPS的开发是为了应对这些挑战，并促进个人或合作团体在任何规模的项目上的研究。 序列数据和相关的元数据可以由用户直接上传到VAMPS或通过将数据发送到VAMPS项目团队; MPS读数可以自动进行质量过滤并分配给分类结构和分类独立的聚类。 然后可以将这些数据链接到元数据，并使用各种分析和可视化工具进行比较。 每个结果都被广泛地超链接到其他分析和可视化选项，促进数据探索并加深对数据关系的理解。 VAMPS的一个主要优势是，研究人员不仅可以比较自己项目中的数据集，还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项目的数据集进行比较。虽然MPS方法的出现使微生物生态学家能够以更高的精度提出有意义的问题，但它给那些难以管理兆字节甚至千兆字节数据的小型实验室带来了重大挑战。 VAMPS消除了单个研究小组在计算基础设施和生物信息学支持方面进行大量投资的需要，否则处理，分析和解释微生物生态学的MPS数据是必要的。 任何支持Web的设备都可以用于上传、处理、探索和提取VAMPS的数据和结果，VAMPS开发团队可以在数据处理和分析的各个方面提供协助。 VAMPS鼓励研究人员共享序列和元数据，并促进不同生物群落的研究人员之间的合作，这些研究人员认识到共享数据中的共同模式。 VAMPS已被用于50多个出版物和至少13个国家科学基金会资助的项目。 VAMPS通过其来自各种环境的数据的组合，其基于序列簇和基于分类学的分析和可视化工具的集成，以及项目开发人员提供的指导，提供了独特的教育机会。 除了注册用户中未统计的学生外，VAMPS网站还被Brown-MBL IGERT反向生态学的研究生使用：基因组、生物和环境的计算整合;在MBL的研究生/博士后水平的微生物多样性夏季课程，并在MBL专题课程的策略和技术，微生物种群结构的分析，这吸引了研究生，来自世界各地的博士后和主要研究人员。

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.