Rapid: Collaborative Research: Agile and effective responses to emerging pathogen threats through open data and open analytics

在每一次突发性病毒爆发期间，都会出现关于其起源、演变、传播方式以及如何检测和缓解的相同类型的问题，其中许多（如果不是全部）问题取决于多个实验室对不同病毒样本序列进行快速可靠的基因组分析。早期的病毒调查往往因缺乏可重复性、严谨性和数据/分析共享而受损;目前对COVID-19的调查也不例外。如果研究人员不能信任/复制源数据和分析方法，则无法可靠地回答基本问题，例如宿主内基因组变异的程度（指示适应或多重感染），病毒进化（选择，重组），传播（遗传和地理传播）。该奖项的目标是开发，部署和不断更新病毒基因组分析工作流程，以分析和监测SARS-CoV-2的病毒进化和动态，并利用所吸取的经验教训为未来的爆发做好准备。将开发用于调查COVID-19和未来病毒爆发的关键任务的生物信息学工作流程，并将通过Galaxy和Datamonkey公开分析和共享COVID-19深度测序数据，以促进和加速进化发现，并使研究和应对不可避免的未来传染病爆发成为可能。在数字连接的时代，开放和可访问的共享数据和分析平台有可能改变生物医学研究的方式，为“全球研究市场”开辟道路，在全球研究市场中，竞争来自理解而不是访问样本和数据。通过使任何有互联网连接的研究人员能够进行与资源丰富国家的顶级研究小组所做的相同的分析，该奖项将为资源有限的环境提供关键组件，这一奖项反映了NSF的法定使命，并被认为是值得通过评估使用基金会的智力价值和更广泛的影响审查标准。

The same types of questions arise during every emergent viral outbreak regarding its origin, its evolution, the manner of spread, and how to detect and mitigate it. Many, if not all, of these questions depend on rapid and reliable genomic analysis of diverse viral sample sequences by multiple laboratories. Early viral investigation is often impaired lack of reproducibility, rigor, and data/analytic sharing; the current investigation of COVID-19 is no different. Essential questions such as the extent of intra-host genomic variability (indicative of adaptation or multiple infection), viral evolution (selection, recombination), transmission (phylogentic and phylogeographic) cannot be answered reliably if researchers cannot trust/replicate the source data and analytical approaches. The goal of this award is to develop, deploy, and continuously update viral genomic analysis workflows to enable the analysis and monitoring of viral evolution and dynamics for SARS-CoV-2, and to use the lessons learned to prepare capacity for future outbreaks. Bioinformatics workflows for critical tasks in investigating COVID-19 and future viral outbreaks will be developed and COVID-19 deep sequencing data will be analyzed and shared openly via Galaxy and Datamonkey to facilitate and accelerate evolutionary discovery and enable the study of and response to inevitable future infectious disease outbreaks. In an age of digital connectivity, open and accessible shared data and analysis platforms have the potential to transform the way biomedical research is done, opening the way to ‘global research markets’, where competition arises from deriving understanding rather than access to samples and data. By enabling any researcher with an Internet connection to perform the same analyses as are done by top-flight research groups in resource-rich countries, this award will deliver critical components to resource limited settings, which are often those that are first and disproportionately affected by viral outbreaks.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.