Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

XperimentR: painless annotation of a biological experiment for the laboratory scientist

Chris D Tomlinson*, Geraint R Barton, Mark Woodbridge and Sarah A Butcher

Author Affiliations

Centre for Integrated Systems Biology and Bioinformatics, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK

For all author emails, please log on.

BMC Bioinformatics 2013, 14:8  doi:10.1186/1471-2105-14-8

Published: 16 January 2013

Abstract

Background

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.

Results

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.

Conclusion

We present a web based software application to aid the laboratory scientist to capture, describe and share details about their experiments.

Keywords:
Experimental annotation; Ontologies; Biological data management