emBASE

 

As of June 2020, the emBASE project is retired.  All the NGS data have been migrated to STOCKS.

 

emBASE is a web-application to store and describe NGS, microarray and ISH data. You can describe and annotate your samples and protocols, associate sample to assays, experiments (=studies) and projects.  

emBASE models your data in a fully MIAME compliant way, including with the use of adequate controlled vocabulary, and is a bridge to EBI ArrayExpress data submission, which is mandatory upon publication (export of experiment in the MAGE-TAB format). In emBASE, your data remains private until you decide otherwise. After project publication, data can be copied to tape in a single click for long term archiving (and to free expensive on-line disk space).  emBASE facilitates finding the right data, even long after collaborators have left the lab or when data is archived on tape. Other components of emBASE:

  • A fully customizable and extentable controlled vocabulary framework,
  • The MAGE-TAB exporter is also a JAVA program developped locally. It allows to produce so-called MAGE-TAB spreadsheets ready for EBI's ArrayExpress submission or data sharing with collaborators. Note that submiting your experimental data to EBI's ArrayExpress is mandatory for publication in most scientific journals.
  • Full NGS data storage module, supporting single and paired data, multiplexing, sharing of sequencing lanes (for multiplexed libraries)
  • Many batch operations (batch upload, batch sample annotations, manipulation of items rights in batch ...) to ease your work in the system
  • One click experiment/project archiving to tape
  • A decentralized NGS data storage library : your files remains on your file server and are directly accessible, while being fully managed by emBASE 
  • A command line API to allow computational biologists to work with the data managed in emBASE directly (direct access to files)
  • Improved documentation and howtos.

N.B. : emBASE is based on the open-source PHP application BASE, Bio Array Software Environment. emBASE is locally developed since 2005.