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

单细胞生物（微生物）代表了地球上生命多样性的巨大组成部分，并发挥了一系列惊人的生物功能。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。该奖项支持下一代微生物生态学定量洞察（QIIME，发音为“chime”）的开发，这是一个基于DNA测序数据分析微生物组的免费开源软件平台。微生物组学正处于从描述性和技术挑战性向假设驱动、可操作和技术直接性的转变，这在一定程度上是由QIIME实现的。我们现在知道，研究微生物群落的传统方法依赖于在实验室培养微生物，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。最近的进展通过“培养独立”技术将微生物组与功能过程联系起来，例如对微生物基因组片段进行测序，然后使用这些片段作为“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，而是如何解释产生的大量序列数据。QIIME 2将通过帮助用户通过交互式探索性分析功能获得洞察力，了解基本方法，并以该领域以外的最终用户（包括迫切需要从复杂微生物生态系统研究中得出结论的医生、工程师和政策制定者）可访问的方式报告结果，从而提高对微生物组的认识。社会效益范围从全球到个人（从了解生物必需营养素的循环，如环境中的碳和氮，到治疗疾病，包括肥胖和癌症）。QIIME被引用超过4000次，拥有活跃的用户和开发者社区。QIIME每月在美国和世界各地举办一次教育研讨会。在其核心，QIIME 2将提供一个稳定的应用程序编程接口（API），它依赖于现有的文档、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，使用户无需高级计算技能即可访问QIIME。同时，它将帮助用户通过接触潜在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，这将简化生物信息学工作流程的报告和可重复性。一流的插件系统将通过允许外部开发人员向QIIME 2平台添加新方法来分散开发。该API还将支持QIIME作为其他广泛使用的系统（如Illumina BaseSpace®和Qiita）的组件的改进集成，并将为高级用户提供自动生成的命令行界面。QIIME 2将有一个完全重新开发的并行框架，它将支持部署在各种高性能计算资源上，从本地拥有和运营的计算机集群到商用云计算平台。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存储库提供意见。有关该项目的更多细节，请参见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).