Afgan Enis, Chapman Brad, Jadan Margita, Franke Vedran, Taylor James
Center for Informatics and Computing, Ruder Bošković Institute (RBI), Zagreb, Croatia.
Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia.
Curr Protoc Bioinformatics. 2012 Jun;Chapter 11:11.9.1-11.9.20. doi: 10.1002/0471250953.bi1109s38.
Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.
云计算彻底改变了计算和存储资源的可用性及访问方式，只需在网页浏览器中点击几下，就能配置大型计算基础设施。然而，这些资源通常以底层基础设施组件的形式提供，使用前需要采购和配置。在本单元中，我们展示了如何利用云计算资源进行开放式生物信息学分析，并对底层云基础设施进行全自动管理。通过将CloudBioLinux、CloudMan和Galaxy这三个项目整合为一个紧密的单元，我们使研究人员能够在灵活的云计算基础设施之上，访问100多个预配置的生物信息学工具和千兆字节的参考基因组。该协议展示了如何设置可用的基础设施，以及如何通过图形桌面界面、并行命令行界面和基于网络的Galaxy界面使用这些工具。
