The Experiment Data Depot (EDD) is an online tool designed as a repository of standardized biological experimental data and metadata. The EDD can easily uptake experimental data, provide visualization of these data, and produce downloadable data in several standard output formats. See the deployed version at public-edd.jbei.org. An academic article describing the EDD is available at ACS Synthetic Biology: Morrell, et al "The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization". Get the article from the ACS website.

The EDD is available under a BSD 3-Clause License and is actively developed at the Lawrence Berkeley National Lab (LBL) by the Joint BioEnergy Institute (JBEI), supported by the U. S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between LBL and DOE.

The source code of EDD is published on GitHub. Pull requests should adhere to the Contributing Guidelines, and bug reports or feature requests should be directed to the GitHub project.

The EDD is packaged as a collection of Docker container images. With the Docker Compose tool, all the components of EDD are configured to work together, and requires no other installation of dependencies. Docker has installers available for several operating systems here. The Docker for Mac installer includes both Docker and Docker Compose; the installers for Linux environments currently only include Docker, and Docker Compose must be installed separately. EDD does not test with, or support, Docker for Windows at this time. Docker versions should be v.1.13.0 or greater, or v.17.03 or greater for Docker Community Edition. Docker Compose should be v.1.11.2 or greater.

With Docker and Docker Compose installed, launching the entire EDD software stack is as simple as copying the docker_services directory of the code repository and running the following commands from a terminal in that directory:

. init-config
./start-edd.sh

The first time EDD runs, it must complete some setup tasks before the UI is available. You may monitor progress with docker-compose logs -f and wait for Starting production appserver to appear (you can quit viewing logs with Ctrl+c), or simply wait a few minutes. You can then access the EDD through a browser with http://edd.lvh.me, a domain that maps all requests to the localhost IPv4 address of 127.0.0.1. Using this domain allows for your browser to be directed to the correct service, and looks nicer than an IP address.

Without additional configuration, the launched copy of EDD will be using default options. It will only be available on your local computer, and some functions (e.g. TLS support, external authentication, referencing an ICE deployment) will not work. See Deployment for more detailed instructions for installing Docker and configuring EDD for your deployment environment.

You may test the edd installation by following the Public EDD tutorials. If you have not deployed ICE with your EDD installation, eliminate the part ID numbers in the example files in order to complete the tutorial. Creating an account without configuring EDD will send an email from webmaster@localhost, which may get caught by spam filters; be sure to check there if the confirmation message does not appear within a few minutes. Once the email is confirmed, the user name for logging in is the part of your email before the @ sign.

For a more detailed reference for EDD's low-level configuration options, see Configuration. Instructions on administering an EDD instance can be found in the Administration document, and steps to deploy a new instance are in the Deployment document. Getting a development environment set up to modify or contribute to EDD is outlined in the Developer Setup document. The Troubleshooting guide details some commands to diagnose problems.