Experimental Data Depot
EDD is an online tool designed as a repository of experimental data and metadata. EDD can uptake experimental data, provide visualization of these data, and produce downloadable data in several standard output formats. The input of data to EDD is performed through automated data streams: each of these input streams automatically parses the standard outputs of the instruments most commonly used for bioengineering. New input streams can be easily added to adapt to local data production. EDD provides a quick visualization of imported data that allows for a quality check by showing whether the imported data are within the expected range or not. Since data are stored internally in a relational database, all data output is consistent. Outputs can be provided in terms of different standardized files (Systems Biology Markup Language, SBML, or CSV) or through a representational state transfer (RESTful) Application Programming Interface (API). SBML and CSV files can be used in conjunction with libraries such as COBRApy or Scikit-learn to generate actionable results for metabolic engineering. EDD is the only tool that provides a single data repository for all -omics data types which is able to extract data straight from instrument output, visualize this data, and export the data in formats that are readily applicable to modeling tools and libraries. As all data is collected in a standardized form, EDD enables the application of machine learning and mechanistic models to learn from data and guide the metabolic engineering process in a systematic fashion. Code is available to anyone as part of an open source project. The EDD website is internally available to ABF researchers.
References and Additional Information:
Morrell, William C., et al. “The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization.” ACS synthetic biology 6.12 (2017): 2248-2259.
Lawrence Berkeley National Laboratory
Pacific Northwest National Laboratory
Sandia National Laboratories