June 2024 Product Release Notes

The following release notes cover the most recent changes over the last two months. If you have any questions, email the All of Us Researcher Workbench support team at support@researchallofus.org.

All of Us Researcher Workbench features and updates

• Curated Data Repository (CDR) version 7 (v7) short-read whole genome sequencing (srWGS) structural variant (SV) supplemental dataset - We 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 in the Researcher Workbench. Learn more in the All of Us Short-Read Structural Variant Quality Report. 
• Image upgrades - We 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 images 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. The variant search feature has also been enhanced with an exclusion option that allows the exclusion of certain variants that are not of interest. Learn more about the variant search feature in the Cohort Builder.
• Application auto-delete option update - Starting May 29, 2024, Cromwell, SAS Studio, and RStudio environments auto-delete if left idle.
  • Cromwell applications auto-delete if left idle for 7 days.
  • SAS Studio and RStudio applications auto-delete if left idle for 1 day.
  • Your persistent disk will not be deleted when your application auto-deletes. To opt out of this feature, navigate to your cloud analysis environment panel. Read more about the applications in the Researcher Workbench.

• Researcher Workbench idle timeout increase - We increased threshold for Researcher Workbench idle time logout. Researchers with Registered Tier access only are logged out of the Researcher Workbench after 6 hours of idle time. Researchers with Controlled Tier access are logged out after 12 hours of idle time.

Bug fixes

• Graphics Processing Units (GPUs) were temporarily non-functional in the Researcher Workbench for Jupyter Notebook analysis environments. This bug has been resolved. Read more about using All of Us GPUs.
• Some researchers experienced a loss of saved files on their persistent disk (PD) when increasing their PD. This issue has been resolved.

Service notice

• Starting Thursday, June 27, 2024, researchers using the Researcher Workbench 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.

Support resources

• New Office Hours informational sessions are available in the Video Library, including an overview of SAS in the Researcher Workbench and a Fitbit device data overview.
• We updated the How to Work With Wearable Device Data (v7) featured workspace to include a new notebook on working with the device table data.
• We added support materials for our newly released All by All data, including an overview of the All by All tables available on the All of Us Researcher Workbench and a All by All tutorial workspace, which provides 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. The specific Controlled Tier Curated Data Repository (CDR) paths related to this project can be found under srWGS PGx Haplotype Calls.