Experiment Data Depot (EDD) Study Creation

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Abstract

This protocol details how to create studies in the Experiment Data Depot. Data can be shared with collaborators via exported CSV files or through the REST API.

For more information about the EDD visit: Experiment Data Depot Google Site.

Citation:

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. (link to publication)

Example Links:

https://public-edd.agilebiofoundry.org/

https://public-edd.agilebiofoundry.org/s/example-data-quality-study-2/overview/

Steps

Go to the appropriate EDD for your project (e.g., public-edd.agilebiofoundry.org ). Login with your username and credentials.

Note

For LBNL researchers and affiliates, the EDD can be accessed with your LDAP credentials.

Click on the New Study button on the top right.

In the Add New Study pop-up window, type in your Study Name and Contact . Click Add Study button.

On the Overview page, click on the Example File link in the center box to download a sample experiment description example file. Use this as a template file to fill out your sample experimental conditions. Or, you can click on the Enter Manually button to type in your sample experimental conditions, one by one.

A	B	C	D	E
Line Name	Line Description	Part ID	Media	Replicate Count
181-aceF	Describe your line	JBx_002078	LB	3

Sample Experiment Description Example File Example sample_experiment_description.xlsx

Note

Line Name: Line name should only have dash (-) or underscore (_). While spaces ( ) are not forbidden, they cause issues with various data processing workflows, so spaces should be avoided.Part ID: If you are including Part IDs, make sure that your strains are shared in the ICE that corresponds to the EDD you are using.Part ID: Make sure that your ICE part # is accessible to collaborators and that it is a strain, not a plasmid.Replicate Count: Replicate count of 3 adds -R1 , -R2 , and -R3 . to the end of the Line Name, so additional replicate metadata is unnecessary.For more information about the Experiment Description files, click on the help button on the top right of the grey box or For more information about the Experiment Description files, click on the help button on the top right of the grey box or https://public-edd.agilebiofoundry.org/describe/help/..

Drag-and-drop the Sample Experiment Description Example File into the dropzone on the Overview page.

Click on Permissions to allow collaborators to Read or Write data in the study.

Click on Attachments to attach files to the study.

Once you have acquired the data, go to the EDD Data Import protocol to import data into the EDD study.

Disclaimer

Abstract

Steps

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