Set up your own bioinformatics server: Chipster in EGI Federated Cloud

K. Mattila, Diego Scardaci, M. Antonacci, C. Condurache
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Abstract

Chipster is an easy to use data analysis platform for bioinformatics. It provides an uniform graphical interface for over 360 commonly used bioinformatics tools including several R/Bioconductor-based tools and standalone programs (i.e. BWA, TopHat). Chipster is based on a client-server system where the user runs locally a Chipster-client that submits analysis tasks to a Chipster server. Even though Chipster is an open source tool, there is no public Chipster server that would be open for everybody. Due to that, a researcher needs to have an access to some of the existing Chipster servers to be able to use this platform. Alternatively, a researcher can set up his own Chipster server. In this paper, we describe how a Chipster server can be launched EGI Federated Could environment, that provides resources for all European researchers. With the instructions provided here, any European researcher can launch and manage his own Chipster server, suited for needs of a small research group or a bioinformatics course. The setup described here is based on a collaboration of several European instances. Chipster is developed by CSC – IT Center for Science Ltd. in Finland. European Grid Infrastructure (EGI) has fitted Chipster to cloud environment and provides the cloud computing resources. Finally, Rutherford Appleton Laboratory hosts the CVMFS server that provides the scientific tools and data sets for the Chipster servers running in EGI federated cloud.
建立您自己的生物信息学服务器:EGI联邦云中的Chipster
Chipster是一个易于使用的生物信息学数据分析平台。它为超过360种常用的生物信息学工具提供了统一的图形界面,包括几个基于R/ bioconductor的工具和独立程序(即BWA, TopHat)。Chipster基于客户端-服务器系统,用户在本地运行一个Chipster-客户端,该客户端向Chipster服务器提交分析任务。尽管Chipster是一个开源工具,但没有一个公共的Chipster服务器可以对所有人开放。因此,研究人员需要访问一些现有的Chipster服务器才能使用这个平台。或者,研究人员可以建立自己的Chipster服务器。在本文中,我们描述了一个Chipster服务器如何启动EGI Federated Could环境,为所有欧洲研究人员提供资源。有了这里提供的说明,任何欧洲研究人员都可以启动和管理他自己的Chipster服务器,适合小型研究小组或生物信息学课程的需要。这里描述的设置基于几个欧洲实例的协作。Chipster是由芬兰CSC - IT科学中心有限公司开发的。欧洲网格基础设施(EGI)将Chipster与云环境相适应,并提供云计算资源。最后,卢瑟福阿普尔顿实验室托管CVMFS服务器,该服务器为运行在EGI联合云中的Chipster服务器提供科学工具和数据集。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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