XperimentR: painless annotation of a biological experiment for the laboratory scientist.
XperimentR: painless annotation of a biological experiment for the laboratory scientist.
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DOI：
10.1186/1471-2105-14-8
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发表时间：
2013-01-16
影响因子：
3
通讯作者：
Butcher SA
中科院分区：
文献类型：
--
作者：
Tomlinson CD;Barton GR;Woodbridge M;Butcher SA
今天的生物实验往往涉及多学科研究人员利用几个高通量的组学平台进行合作。要求使用标准化的本体论充分描述实验的细节，以便能够保存数据、分析数据并便利将数据输出到公共储存库。然而，用于描述实验的本体、受控词汇和最低标准的数量令人眼花缭乱。需要用户友好的软件工具来帮助实验室科学家获取实验信息。已经开发了一个名为XperentR的网络应用程序，供实验室科学家使用，它由一个基于浏览器的界面和服务器端组件组成，为捕获和共享实验元数据提供了一个直观的平台。记录的信息包括关于生物样本、程序、协议和实验技术的详细信息，所有这些都可以很容易地使用适当的本体进行注释。文件和原始数据可以通过界面从用户的计算机或常用的开源数据存储库导入并与生物样本相关联。实验可以与其他用户共享，并且可以将实验以标准的ISA-Tab格式导出，以便存放在公共数据库中。ExperentR是免费提供的，可以在本地安装，也可以使用提供的预配置的虚拟机进行安装。客户系统也可用于试用目的。我们提供了一个基于Web的软件应用程序，以帮助实验室科学家捕获、描述和共享他们实验的详细信息。
Today’s biological experiments often involve the collaboration of multidisciplinary researchers utilising several high throughput ‘omics platforms. There is a requirement for the details of the experiment to be adequately described using standardised ontologies to enable data preservation, the analysis of the data and to facilitate the export of the data to public repositories. However there are a bewildering number of ontologies, controlled vocabularies, and minimum standards available for use to describe experiments. There is a need for user-friendly software tools to aid laboratory scientists in capturing the experimental information. A web application called XperimentR has been developed for use by laboratory scientists, consisting of a browser-based interface and server-side components which provide an intuitive platform for capturing and sharing experimental metadata. Information recorded includes details about the biological samples, procedures, protocols, and experimental technologies, all of which can be easily annotated using the appropriate ontologies. Files and raw data can be imported and associated with the biological samples via the interface, from either users’ computers, or commonly used open-source data repositories. Experiments can be shared with other users, and experiments can be exported in the standard ISA-Tab format for deposition in public databases. XperimentR is freely available and can be installed natively or by using a provided pre-configured Virtual Machine. A guest system is also available for trial purposes. We present a web based software application to aid the laboratory scientist to capture, describe and share details about their experiments.
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