Johns Hopkins University, Baltimore, Maryland, United States of America.
The Pennsylvania State University, University Park, Pennsylvania, United States of America.
PLoS Pathog. 2020 Aug 13;16(8):e1008643. doi: 10.1371/journal.ppat.1008643. eCollection 2020 Aug.
The current state of much of the Wuhan pneumonia virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies and requires unimpeded access to data, analysis tools, and computational infrastructure. Here, we show that community efforts in developing open analytical software tools over the past 10 years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all SARS-CoV-2 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at https://github.com/galaxyproject/SARS-CoV-2.
目前，武汉肺炎病毒（严重急性呼吸系统综合症冠状病毒 2[简称 SARS-CoV-2]）的许多研究现状表明，人们在数据共享方面令人遗憾地做得不够，且分析工作也相当混乱。这阻碍了全球研究合作，而这种合作对于应对公共卫生突发事件至关重要，它需要无障碍地获取数据、分析工具和计算基础设施。在这里，我们展示了过去 10 年来，社区在开发开放分析软件工具方面所付出的努力，再加上国家对科学计算基础设施的投资，这些努力可以克服这些缺陷，并为以公开和透明的方式应对全球卫生突发事件提供一个可访问的平台。具体来说，我们使用迄今为止公共领域中所有可用的 SARS-CoV-2 基因组数据，（1）强调获取原始数据的重要性，以及（2）表明现有的生物医学软件管理和部署方面的社区工作，可以在全球卫生危机期间可靠地支持快速、可重复的研究。我们所有的分析都在 https://github.com/galaxyproject/SARS-CoV-2 上有完整记录。
