Self-guided Tutorial

This is a self-guided tutorial released for the Data Submitter’s track of the FaceBase Bootcamp held on September 8, 2021.

It is intended to be used after the bootcamp to apply what you’ve learned about creating records, adding metadata and uploading data. The basic directions are below and it is intended that you refer to the documentation in this wiki for more specific details. If you get stuck, please don’t hesitate to contact the FaceBase Hub at: help@facebase.org

1) Join the “FaceBase Demo” Globus group by going to this link https://app.globus.org/groups/5eebf313-c0b2-11ea-adc2-0ed6a5b292e1/about and following the instructions to join the group.

2) Go to FaceBase Projects (https://www.facebase.org/chaise/recordset/#1/isa:project), login using the same credentials you used to join the group above, and search for the “FaceBase Demo” Project.

3) Create a new Dataset under that Project following the same structure (in terms of Biosamples, Experiments and Replicates) as in the “Bootcamp self-guided tutorial dataset” (https://www.facebase.org/chaise/record/#1/isa:dataset/RID=2-HR74).

4) From the Supplementary Files section of the above dataset, download to your computer the following file: Bootcamp-self-guided-tutorial-data.zip (https://www.facebase.org/chaise/record/#1/isa:file/RID=2-HR94)

5) Unpack the zip file to your computer and change the name of its sub-directories by doing the following replacements:

• Rename the directory “DATASET-RID” to the value of the RID of the Dataset you have created (E.g., for our example dataset, the name of that directory should be “2-HR74”).
• Rename the directory called “Micro-CT-mutant-REPLICATE-RID” to the value of the RID of the micro-CT mutant Replicate. (E., g., for our example dataset, the name of that directory should be “2-HR7Y”).
• Rename the directory called “Micro-CT-control-REPLICATE-RID” to the value of the RID of the micro-CT control Replicate. (E., g., for our example dataset, the name of that directory should be “2-HR7W”).
• Rename the directory called “RNA-seq-REPLICATE-RID” to the value of the RID of the RNA-seq Replicate. (E., g., for our example dataset, the name of that directory should be “2-HR82”).

6) Start the DERIVA Upload Utility and:

• Click the “Options” button to verify that the server value is www.facebase.org .
• Click the “Login” button to authenticate using the same credentials you used above.
• Click the “Browse” button and select the directory that you’ve named with the value of the RID of your new dataset.

7) Once the tool has scanned the content of the directory, click the “Upload” button to start uploading the files.

8) Once the utility is finished, check your dataset to verify that the files have been added (you may need to refresh the browser page). Email us at help@facebase.org if you have any questions.