Community Data Portal

Publicly Share Data

If you used VDJServer for immune repertoire analysis, your data and analysis files are already available within VDJServer, and you can skip directly to Step 3 below to publicly share your project. It is not necessary to have performed analysis on VDJServer in order to publicly share your data. Create an account at https://vdjserver.org to get started.

1. Create Project

   Click on the Add Project button to create a new project and give the project a name. To help users identify your project, use a descriptive name such as the title of your study publication. After the project is created, go to the Metadata Entry page and fill out the Project / Study Metadata with a long study description (e.g. abstract of paper), PI and contact information, grant information, publication identifiers (e.g. Pubmed ID), and the BioProject ID. Click the Save Project Metadata button to save your changes. It isn’t necessary to enter metadata for the other sections.

2. Upload Files into Project

   From the Upload and Browse Project Data page, click on the Upload button and select files from your local computer, from Dropbox, or from a URL (ftp/http), to be uploaded; multiple files can be selected. Click the Start button to start uploading.

3. Publish Project

   On the Project Settings page, copy/paste the VDJServer UUID. This is a long identifier with numbers, letters and dashes that uniquely identifies your project. Provide this UUID in the Data Availability section of your publication so users can directly search and find your project. Finally, click the Project Actions button and select Publish Project. This will initiate publishing, and you will receive an email when the project is publicly available. Changes cannot be directly made to a published project, but as the project owner you can unpublish the project at any time to correct information or files. On the Community Data page, find your project and go to the Project Settings page. Click the Project Actions button and select Unpublish Project; you will receive an email when the project has been unpublished. Make the necessary corrections to your project then publish it to make it publicly available again.

Publish AIRR-seq Study in the AIRR Data Commons

Publishing your AIRR-seq study in the ADC with VDJServer is not a completely automated process; there are a number of manual validation steps that need to be performed. Furthermore, loading the data into the repository database can take hours, days or even a week depending upon the size of the data; therefore, the load process is initiated by a VDJServer administrator. The basic requirements include:

1. Study metadata in AIRR Repertoire format.

   Validation scripts are run to verify the metadata is valid and complete. If the study metadata has been provided in VDJServer’s Metadata Entry page, that metadata can be automatically converted into the AIRR Repertoire format.

2. Rearrangement (annotated sequence) data in AIRR TSV format.

   If your rearrangement data is not in the AIRR TSV format, it may need to be converted or run through the IgBLAST tool on VDJServer. Validation scripts are run to verify that the annotations are valid and complete.

3. VDJServer administrator loads the study into VDJServer’s repository.

   Contact VDJServer (vdjserver@utsouthwestern.edu) to initiate publishing your study.

Data Charges for Repository Copies

VDJServer offers the ability to provide a complete copy of the data repository to the customer. This can be a quicker option to acquire large quantities of data versus downloading through the portal. As this requires additional time and resources by VDJServer personnel, we need to impose a data charge for cost recovery. The following options are available:

1. (Price: $2000 USD) Upload data to an Amazon S3 bucket.

   We will upload either to a customer-provided bucket or create a new bucket and provide access. In the case that we create the bucket, it will only be accessible for a pre-determined amount of time (typically one month), so the customer is required to move the data into their own bucket.

2. (Price: $2000 USD) FEDEX/UPS a hard disk drive with the data to the customer.

   We purchase a standard SATA hard drive but can use a customer-provided SATA hard drive if desired. The hard drive becomes the customer’s property and does not need to be returned.

3. (Price: $3000 USD) Both options 1 and 2.

   We will upload data to an Amazon S3 bucket and provide the customer with a hard disk drive.

4. Yearly update for options 1, 2 or 3.

   The same price as the requested option. A repository copy is sent automatically to the customer every year.

Please contact VDJServer (vdjserver@utsouthwestern.edu) to initiate an order. Other data delivery options can be provided as well as training services about the data and data formats. Payment is processed through an invoice sent by UT Southwestern Medical Center.