The JBEI Experiment Data Depot

Synthetic Biology research draws on several disciplines and ties together diverse data sets. Collaboration efforts between researchers is often hampered by inaccessible or difficult-to-access data. Results are scattered across instruments, document folders, and email accounts. Discovering whom to ask for a copy of the needed data can be a frustrating and time-consuming process. Deciphering data in varied and exotic spreadsheet layouts and file formats can also add delays.

The Experiment Data Depot (EDD) is a database and associated set of software tools meant to ease the management and organization of "actionable" experimental data sets -- meaning data that can be fed directly into computational models and other analysis tools. The aim of the EDD is explicitly not to be a generic sample-tracking or laboratory information management system (LIMS). Rather, it is designed to be a repository of data in a Design-Build-Test-Learn workflow, focused on capturing information resulting from primarily the Test phase. Data is organized into Studies, with read/write access controls for supervisors, colleagues, and collaborators.  Each Study collects metadata on the experiment setup and measurement protocols used, and links to strain records in the JBEI Inventory of Composable Elements (ICE). Data import from lab instruments - such as mass spectrometers and gene sequencers - is facilitated with custom extensions. The ability to inspect data and metadata is integrated into the user interface, along with exports to SBML, Excel, and CSV files for use in other software packages.