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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.
We maintain an integrated environment to store, manage and analyze your NGS data seamlessly on the EMBL HPC and GB's big-mem servers.
We administrate and maintain big-mem servers (eg spinoza), scientific libraries (SEPP), analysis platforms (R Studio Server, Galaxy) so you can focus on analyzing your data.
Need help with data analysis, custom data management or data visualization solutions?
We are here for this too!
Documentation, tutorials, seminars, videos, FAQs ... all the resources to understand how all this beauty works!
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