Experiment Data Depot (EDD)

What is EDD?

The Experiment Data Depot (EDD) is an interactive online tool that serves as a standardized repository of experimental data.

EDD provides a standardized description of experiments: from the strains and plasmids involved, to the protocols used, the experimental design for sampling, and the data extracted.

This tool significantly facilitates the Learn and Design steps in the DBTL cycle. Below you can find a publication describing EDD, the available EDD services, and tutorials that explain how to get an account and use EDD. You can also find further documentation. You can find some examples of how EDD has been used in the past to facilitate Learn in the DBTL cycle here, here, and here.

Here is the documentation. If you have further questions, please contact Mark Forrer or William Morrell.

EDD publication

EDD sites

There are several EDD sites (a.k.a services or instances):

The "public-" prefix indicates a site that people outside of ESE can access. The other private sites can only be accessed by researchers in the corresponding program (ABF or JBEI). Each site has different data, metadata, units, databases and permissions. Ask your PI which site you should be using.

Accessing EDD sites:

If you are a Berkeley Lab (LBL) employee or affiliate, you can log into any of the sites using your LBL credentials.
Non-LBL collaborators within the ABF or JBEI programs should contact Nathan Hillson to get LBL affiliate status to use EDD.
Private sites require specific LBL LDAP group membership to access.
- edd.jbei.org: ESE group
- edd.agilebiofoundry.org: ABF group
External collaborators should self-register to the "public-" site for the program sponsoring the research, e.g. using a non-LBL account. Self-registration is only allowed in the "public-" instances.

EDD tutorials

This tutorial should provide all you need to get you started using EDD. You can find further written documentation here.

Data import

You can find here the input files needed to do this tutorial:

EDD_import.mp4

Data visualization

No input files needed for this tutorial.

EDD_visualization.mp4

Data export

You can find here the input files needed to do this tutorial:

Jupyter Notebook

And you can use it on any of the jupyter servers.

EDD_export.mp4

For more information, please email ese-robotics@lbl.gov

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