Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing
Cloud CPFP: A Shotgun Proteomics Data Analysis Pipeline Using Cloud and High Performance Computing
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DOI：
10.1021/pr300694b
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发表时间：
2012-12-01
影响因子：
4.4
通讯作者：
Mirzaei, Hamid
中科院分区：
文献类型：
--
作者：
Trudgian, David C.;Mirzaei, Hamid
我们扩展了中央蛋白质组设施管道 (CPFP) 的功能，以允许使用远程云和高性能计算 (HPC) 资源进行鸟枪式蛋白质组数据处理。 CPFP 已被修改为包括用于数据处理作业的模块化本地和远程调度。该管道现在可以在单台 PC 或服务器、本地集群、远程 HPC 集群和/或 Amazon Web Services (AWS) 云上运行。我们提供公共映像，允许在 AWS 云中轻松部署整个 CPFP。这显着减少了使用该软件所需的工作量，并允许蛋白质组学实验室支付临时计算时间的费用，而不是获取和维护昂贵的本地服务器集群。或者，根据需要，可以使用 Amazon 云来增加 CPFP 本地安装的吞吐量。我们证明，云 CPFP 允许用户以比本地安装更高的速度处理数据，但成本相似且员工要求更低。除了计算方面的改进之外，CPFP 的 Web 界面也得到了简化，并且其他功能也得到了增强。该软件正在两个领先机构的积极开发中，并继续在 http://cpfp.sourceforge.net 上的开源许可证下发布。
We have extended the functionality of the Central Proteomics Facilities Pipeline (CPFP) to allow use of remote cloud and high performance computing (HPC) resources for shotgun proteomics data processing. CPFP has been modified to include modular local and remote scheduling for data processing jobs. The pipeline can now be run on a single PC or server, a local cluster, a remote HPC cluster, and/or the Amazon Web Services (AWS) cloud. We provide public images that allow easy deployment of CPFP in its entirety in the AWS cloud. This significantly reduces the effort necessary to use the software, and allows proteomics laboratories to pay for compute time ad hoc, rather than obtaining and maintaining expensive local server clusters. Alternatively the Amazon cloud can be used to increase the throughput of a local installation of CPFP as necessary. We demonstrate that cloud CPFP allows users to process data at higher speed than local installations but with similar cost and lower staff requirements. In addition to the computational improvements, the web interface to CPFP is simplified, and other functionalities are enhanced. The software is under active development at two leading institutions and continues to be released under an open-source license at http://cpfp.sourceforge.net.