TY - JOUR
T1 - The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization
AU - Morell, William C.
AU - Birkel, Garrett W.
AU - Forrer, Mark
AU - Lopez, Teresa
AU - Backman, Tyler W. H.
AU - Dussault, Michael
AU - Petzold, Christpoher J.
AU - Baidoo, Edward E. K.
AU - Costello, Zak
AU - Ando, David
AU - Alonso-Gutierrez, Jorge
AU - George, Kevin W.
AU - Mukhopadhyay, Aindrila
AU - Vaino, Ian
AU - Keasling, Jay
AU - Adams, Paul D.
AU - Hillson, Nathan J.
AU - Garcia Martin, Hector
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
KW - Database
KW - -omics data
KW - Data standards
KW - Data mining
KW - Flux analysis
KW - Synthetic biology
U2 - 10.1021/acssynbio.7b00204
DO - 10.1021/acssynbio.7b00204
M3 - Journal article
C2 - 28826210
SN - 2161-5063
VL - 6
SP - 2248
EP - 2259
JO - A C S Synthetic Biology
JF - A C S Synthetic Biology
IS - 12
ER -