The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization

Although
recent advances in synthetic biology allow us to produce
biological designs more efficiently than ever, our ability to predict
the end result of these designs is still nascent. Predictive models
require large amounts of high-quality data to be parametrized and
tested, which are not generally available. Here, we present the Experiment
Data Depot (EDD), an online tool designed as a repository of experimental
data and metadata. EDD provides a convenient way to upload a variety
of data types, visualize these data, and export them in a standardized
fashion for use with predictive algorithms. In this paper, we describe
EDD and showcase its utility for three different use cases: storage
of characterized synthetic biology parts, leveraging proteomics data
to improve biofuel yield, and the use of extracellular metabolite
concentrations to predict intracellular metabolic fluxes.