Centre for Integrated Systems Biology and Bioinformatics, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK.
BMC Bioinformatics. 2013 Jan 16;14:8. doi: 10.1186/1471-2105-14-8.
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.
如今的生物实验通常涉及多学科研究人员的合作，他们利用多个高通量“组学”平台。需要使用标准化的本体充分描述实验细节，以实现数据保存、数据分析，并便于将数据导出到公共存储库。然而，有大量的本体、受控词汇和最小标准可供用于描述实验。需要用户友好的软件工具来帮助实验室科学家捕获实验信息。
开发了一个名为 XperimentR 的 Web 应用程序，供实验室科学家使用，它由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直观的平台。记录的信息包括有关生物样本、程序、协议和实验技术的详细信息，所有这些信息都可以使用适当的本体轻松注释。通过界面，可以从用户的计算机或常用的开源数据存储库中导入和关联文件和原始数据与生物样本。可以与其他用户共享实验，并且可以以标准的 ISA-Tab 格式导出实验以在公共数据库中进行存储。XperimentR 是免费提供的，可以通过本机安装或使用提供的预配置虚拟机进行安装。还提供了一个试用版的访客系统。
我们提出了一个基于 Web 的软件应用程序，帮助实验室科学家捕获、描述和共享他们实验的详细信息。
