June 2024 Product Release Notes

We have a few updates to share from the past two months. Please see the list below for information about these updates:

Researcher Workbench Features & Updates:

• CDR v7 srWGS Structural Variant supplemental dataset - we recently released a supplemental dataset that contains srWGS SV calls from 97,940 participants. With this release of SV data, we increased the percent of srWGS samples that have SV data to 40%. The data complements the existing genomic data available on the Workbench. To learn more, see the All of Us Short-Read Structural Variant Quality Report. 
• Image Upgrades - we have upgraded our Jupyter Docker images to include upgrades to R 4.4.0, Hail to 0.2.130, Samtools 1.18, Bioconductor to 3.19. We also made an upgrade to the RStudio image to use R 4.4.0, Bioconductor 3.19.
• Variant Search Update in Cohort Builder - the Cohort Builder Variant Search feature now includes a “Select All” feature to select all variants if the result count is less than 10,000. Additionally, this function has been enhanced with an exclusion option that allows the exclusion of certain variants that are not of interest. To learn more see this support article: Variant Search within the Cohort Builder
  
• Application auto-delete option update - starting May 29, Cromwell, SAS Studio, and RStudio environments will auto-delete if left idle. Cromwell applications will auto-delete if left idle for 7 days. SAS Studio and RStudio applications will auto-delete if left idle for 1 day. Your persistent disk will not be deleted when your application is auto-deleted. Please navigate to your cloud analysis environment panel to opt out of this feature. See Overview of applications in the Researcher Workbench to learn more about applications on the Researcher Workbench.

• Researcher Workbench idle time-out increase - we have increased threshold for Researcher Workbench idle time logout. Now, users with Registered Tier access only will be logged out of the Researcher Workbench after 6 hours of idle time. Users with Controlled Tier access will be logged out after 12 hours of idle time.

Bug Fixes

• GPUs were temporarily broken in the Researcher Workbench for Jupyter environments. This bug has been fixed. See instructions here for how to use GPUs in your cloud environment: How to use All of Us GPUs
  
• In some cases, increasing persistent disk (PD) size resulted in loss of saved files on the PD. This has been resolved.

Service Notice

• Beginning Thursday June 27th, 2024 Researcher Workbench users will need to make an annual password change to their @researchallofus.org account. If you have not changed your password within the last year, you will be prompted to update your password on your next login. Please email support@researchallofus.org if you have any questions or concerns with this change. 

Support Resources

• New Office Hours informational sessions are available in the “Videos” section to include Overview of SAS in the Researcher Workbench and Fitbit Device Data Overview. We have updated the tutorial Featured Workspace, How to Work With Wearable Device Data (v7), to include a new notebook on working with the device table data.
  
• We have added support materials for our newly released All by All data, to include Overview of the All by All tables available on the All of Us Researcher Workbench, and a tutorial workspace, All by All, which gives tutorial guides on working with the All by All tables.
• We have a new Featured Workspace, Demo - Pharmacogenomics (PGx) variant frequency and medications, which is a demonstration project that reviews frequencies of pharmacogenomics variants/haplotypes in the All of Us dataset. Specific Controlled Tier CDR paths related to this project can be found here under srWGS PGx Haplotype Calls.

As always, please contact support@researchallofus.org if you have any questions or concerns with our most recent changes. Thank you for your support of the All of Us Research Program and Researcher Workbench!