Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
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DOI：
10.7554/elife.06664
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发表时间：
2015-05-08
期刊：
影响因子：
7.7
通讯作者：
Leschziner, Andres E.
中科院分区：
文献类型：
--
作者：
Cianfrocco, Michael A.;Leschziner, Andres E.
新一代电子显微镜和直接电子探测器的出现已经实现了单粒子低温电子显微镜（cryo-EM）作为一种生成高分辨率结构的技术的潜力。计算这些结构需要高性能计算集群，这是一种可能限制许多可能的cryo-EM用户的资源。为了解决这一限制并促进低温EM的传播，我们在亚马逊的弹性云计算基础设施上开发了一个公开可用的“现成”计算环境。该环境为用户提供了单粒子cryo-EM软件包，并能够创建具有16-480+ CPU的计算集群。我们使用公开的80 S酵母核糖体数据集测试了我们的计算环境，并估计实验室可以在与本地集群相当的时间范围内以每个结构50至1500美元的价格确定高分辨率的cryo-EM结构。我们的分析表明，亚马逊的云计算环境可以为cryo-EM提供一个可行的计算环境。
The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16-480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.