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Introductory Session, 09/26/2023

Slides available

Download a PDF of this session's slides at the bottom of this post to follow along. 


Click here to view recording in a new tab on YouTube.

Working Session Info and Homework

1. Create your own project/sandbox on BDC-Seven Bridges.

A project is where all data, as well as any analysis results, will be accessible securely. You can think of projects as private containers for your data, scientific software, and your analysis results.

For detailed information about Projects, refer to Create a Project in the Seven Bridges documentation. 

To create a project:

  1. Log into BDC-Seven Bridges using

  2. Click the Projects tab on the top navigation bar, then select Create a project from the drop-down menu. 

  3. The Create a Project modal will appear. Fill out the fields, with the following settings:

    • Name: PCGC_[FirstName]_[LastName]

    • Billing Group: Pilot Funds

      • Note: The Billing Group field will automatically populate to Pilot Funds, even if you have not yet requested Pilot Credits or if your Pilot Credits request is still under review. 

    • Location: aws-us-east-1

    • Spot instances: On

    • Memoization: Off

    • Network Access: Allow Network Access

  4. Click Create.

2. Add the following four BDC reps or other PCGC Fellows to the project:

  • alvoght


  • dave

  • emhughes1

3. Copy files, apps, and JupyterLab from the main project

  • Copy some of the 1000G cram files from the Pediatric Cardiac Genomics Consortium Project (non-controlled) project to your new project.
  • Copy one or more apps that interest you to your new project. You can search for apps using the BDC Public Apps Gallery. This gallery is a repository of tools optimized for the cloud and developed by the scientific community to help with biomedical analyses.
  • Start a JupyterLab or RStudio Data Studio environment in the Pediatric Cardiac Genomics Consortium Project (non-controlled) project.

4. Post any questions as well as your responses to the following discussion topics below, or bring your thoughts to a Seven Bridges Office Hours:

  • What software do you need to run on BDC for your research? Example: GWAS will require different software than RNA-Seq differential expression
  • What is your timeline?

Feel free to ask any questions!

1 Comment

One small correction! My username is cfisher_gmail if you are adding me to a project with controlled access data. :) 

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