The JBEI Experiment Data Depot

Ask a dozen researchers for data supporting their results, and you will get data formats numbering an order of magnitude higher. At the Joint BioEnergy Institute (JBEI), we are developing the Experiment Data Depot (EDD) to help reduce the friction in sharing data sets and collaboration. The EDD is a database and set of software tools aiming to organize and annotate actionable data with conditions and other metadata. The aim is not to be a generic laboratory information management system (LIMS); our focus is instead on collating processed results from multiple inputs, and enabling the whole to be exported to computational models, analysis tools, visualization packages, or other applications. The database framework organizes data in a heirarchcal structure for each experiment: multiple samples and conditions, each having multiple assays, each having multiple measurements, each having multiple data points. Additional metadata can be added at each level of heirarchy, and can later be queried; e.g. finding all data linked to a particular strain. Basic access controls are built in, to allow only specific individuals or groups to view or edit data.
Our original use-case for the EDD collected respiration, mass spectrometer, and optical density data for 13-C metabolic flux analysis of host metabolic models. The software is pending an open-source release, allowing the broad framework to be adapted to the needs of individual labs. We have added modules to better support the collection of RNA transcription levels, protein expression levels, flow cytometry, and chromatography data imports. Additional tools extract data to characterize genetic parts or enzymes, or build instructions for robotic measurement of samples. We hope that the framework can be used to handle more types of data, providing a common framework for sharing data.