iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.
iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.
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DOI：
10.1038/ismej.2016.89
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发表时间：
2017-01
期刊：
影响因子：
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通讯作者：
Sullivan MB
中科院分区：
文献类型：
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作者：
Bolduc B;Youens-Clark K;Roux S;Hurwitz BL;Sullivan MB
微生物影响着整个世界生态系统的营养和能量转化，但它们是在病毒的限制下这样做的。在复杂的社区中，病毒宏基因组（病毒组）测序正在改变我们量化病毒多样性和影响的能力。虽然一些瓶颈，例如，很少参考基因组和非定量病毒组学，已被克服，集中的数据集和专门的工具的空白，现在阻止病毒组学被广泛应用于回答基本的生态问题。在这里，我们介绍了iVirus，这是一个社区资源，利用CyVerse网络基础设施提供对病毒学工具和数据集的访问。iVirus Data Commons包含来自全球海洋探险的1866个样本和73个项目的原始和处理数据，以及现有和遗留的公共存储库。通过CyVerse发现环境，用户可以使用现有的分析工具（称为“App”的软件应用程序）来查询这些数据集，以进行组装、开放式阅读框架预测和注释，以及专门为分析病毒组开发的几个新App。由于应用程序基于Web并由CyVerse超级计算资源提供支持，因此它们可以为广泛的用户群提供可扩展的分析。最后，一个用例场景记录了如何将这些进步应用于新数据。这种不断增长的iVirus资源应该有助于研究人员利用病毒组学作为另一种工具来阐明病毒在自然界中的作用。
Microbes affect nutrient and energy transformations throughout the world's ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps') for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.