Jan 09, 2024
Experiment Data Depot (EDD) Study Creation
- 1Lawrence Berkeley National Laboratory
External link: https://public-edd.agilebiofoundry.org/
Protocol Citation: Jennifer Gin, Christopher J Petzold 2024. Experiment Data Depot (EDD) Study Creation. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvjxn4xlk5/v1
Manuscript 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.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 04, 2021
Last Modified: January 09, 2024
Protocol Integer ID: 45987
Keywords: EDD, Metadata, Synthetic Biology, Experiment Data Depot, Metabolic Engineering, REST API
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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.
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:
Guidelines
Line Name: Line name should only have dash (-), underscore (_), or space ( ).
Part ID: Make sure that your ICE registry part ID number is accessible to collaborators and that it is a strain, not a plasmid.
Materials
Example study description file:
Example sample_experiment_description.xlsx 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.
Login page
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 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.