Collaborative Research: ABI Development: Extensible, reproducible and documentation-driven microbiome data science

单细胞生物体(微生物)代表着地球上生命多样性的一个巨大组成部分，并执行着一系列令人惊叹的生物功能。它们很少单独生活或行动，而是存在于由许多相互作用的物种组成的复杂群落中，这些物种构成了微生物群。该奖项支持开发下一代微生物生态定量洞察(QIIME，发音为“CHIME”)，这是一个基于DNA测序数据分析微生物群的自由和开源软件平台。微生物组科学正处于从描述性和技术挑战性向假说驱动、可操作和技术直截了当的转变，这在一定程度上是由QIIME实现的。我们现在知道，传统的研究微生物群落的方法依赖于实验室培养微生物，这是不够的，因为我们不知道大多数微生物生长所需的条件。最近的进展是通过“独立于培养”的技术将微生物群与功能过程联系起来，例如对微生物基因组的片段进行测序，然后将这些片段用作“分子指纹”来描述微生物组。微生物组分析的瓶颈不是DNA测序，而是解释产生的大量序列数据。QIIME 2将帮助用户通过交互式探索性分析能力获得洞察力，了解基本方法，并以该领域以外的最终用户(包括迫切需要获得复杂微生物生态系统研究结论的医生、工程师和政策制定者)可以访问的方式报告结果，从而促进对微生物群的了解。社会益处从全球到个人(从了解生物基本营养物质的循环，如环境中的碳和氮，到治愈包括肥胖和癌症在内的疾病)。QIIME已被引用超过4000次，并拥有活跃的用户和开发社区。有关QIIME的教育研讨会大约每月在美国和世界各地教授。其核心是QIIME 2将提供一个稳定的应用程序编程接口(API)，依赖于现有的文档、编码风格和测试社区标准。它将有一个新颖的“文档驱动”的图形用户界面，使用户可以访问QIIME，而不需要高级计算技能。同时，它将帮助用户通过接触基本的生物信息学方法来提高他们的计算技能。QIIME 2将具有完全集成的来源跟踪，这将简化报告和生物信息学工作流程的重现性。一流的插件系统将允许外部开发人员向QIIME 2平台添加新方法，从而分散开发。该API还将支持将QIIME作为其他广泛使用的系统(如Illumina BaseSpace®和QIITA)的组件进行改进的集成，并将为高级用户提供自动生成的命令行界面。QIIME 2将拥有一个完全重新开发的并行框架，它将支持在各种高性能计算资源上的部署，从本地拥有和运营的计算机集群到商业可用的云计算平台。QIIME 2开发的所有阶段都将由用户社区通过QIIME论坛(目前超过2500名活跃用户)和我们的公共GitHub库来推动。有关该项目的更多详细信息，请访问QIIME网站(www.Qiime.org)。

Single-cellular organisms (microbes) represent a vast component of the diversity of life on Earth and perform an amazing array of biological functions. They rarely live or act alone and instead exist in complex communities composed of many interacting species that make up the microbiome. This award supports the development of the next generation of Quantitative Insights Into Microbial Ecology (QIIME, pronounced "chime"), a free and open source software platform for analyzing microbiomes based on DNA sequencing data. Microbiome science is in a transformation from being descriptive and technically challenging, to becoming hypothesis-driven, actionable, and technically straight-forward, in part enabled by QIIME. We now know that the traditional approach for studying microbial communities, which relied on culturing microbes in the lab, is insufficient because we don't know the conditions required for the growth of most microbes. Recent advances link microbiomes to functional processes via 'culture independent' techniques, such as sequencing fragments of microbial genomes, and then using those fragments as 'molecular fingerprints' to profile the microbiome. The bottleneck in microbiome analysis is not DNA sequencing, but in interpreting the large quantities of sequence data generated. QIIME 2 will advance knowledge of microbiomes by helping users derive insight through interactive exploratory analysis capabilities, understand the underlying methods, and report their results in ways accessible to end users from outside of the field, including physicians, engineers and policymakers who urgently need access to conclusions drawn from studies of complex microbial ecosystems. Societal benefits range from global to personal (from understanding cycling of biologically essential nutrients, such as carbon and nitrogen in the environment to curing disease, including obesity and cancer). QIIME has been cited over 4,000 times and has active user and developer communities. Educational workshops on QIIME are taught approximately monthly in the USA and around the world.At its core, QIIME 2 will provide a stable application programming interface (API) relying on existing community standards for documentation, coding style, and testing. It will have a novel 'documentation-driven' graphical user interface that will make QIIME accessible to users without requiring advanced computational skills. At the same time, it will help users improve their computational skills through exposure to the underlying bioinformatics methods. QIIME 2 will have fully integrated provenance tracking, which will simplify reporting and the reproducibility of bioinformatics workflows. A first-class plugin system will decentralize development by allowing outside developers to add new methods to the QIIME 2 platform. The API will also support improved integration of QIIME as a component of other widely used systems, such as Illumina BaseSpace® and Qiita, and an automatically generated command line interface will be provided for power users. QIIME 2 will have a completely redeveloped parallel framework, which will support deployment on diverse high-performance computing resources, from locally owned and operated computer clusters to commercially available cloud computing platforms. All stages of QIIME 2 development will be driven by user community input through the QIIME Forum (currently over 2500 active users) and our public GitHub repository. Further details on this project are on the QIIME website (www.qiime.org).