May 2025 Product Release Notes

The following release notes cover the most recent changes over the last few 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

• Initial credits Expiration update - In February 2025, the All of Us Research Program announced expiration dates to the All of Us initial credits that researchers receive after registering for the Researcher Workbench. These credits now expire 365 days from the date that a researcher obtains access to the Researcher Workbench. Visit this announcement to learn more.
• Google Batch API migration - To keep tools updated with the latest improvements from Google Cloud Platform, we migrated our workflow tools from Google Cloud Life Sciences API (GLS) to Google Batch. Applicable updates were made to our workflow tools such as Cromwell, Nextflow and dsub. See full announcement here.
• Jupyter Image Upgrade - We upgraded the Jupyter image from 2.2.13 to 2.2.16. This upgrade provides substantial improvements to data science and bioinformatics computing, ML capabilities, newer versions of key packages, and support for more advanced GPU computation. Some updates include:
  • • Python upgrade from Python 3.10.12 to 3.10.16
    • Major version upgrades to core machine learning packages (TensorFlow 2.11 → 2.17, Keras 2.11 → 3.5)
    • Addition of NVIDIA CUDA libraries with specific versioning
    • Bioconductor upgrade from 3.19 to 3.21
    • Hail upgrade from Hail 0.2.130 to Hail 0.2.134
    • Better support for large-scale data processing with new packages
    • Removal of some legacy or deprecated packages
• Visit domain tile - We have updated the Cohort Builder and Dataset Builder to include the EHR “Visit” domain allowing users to explore the type of visit (inpatient, outpatient, etc) for a clinical event.

Bug fixes

• Double login - the Researcher Workbench login page had a bug that required multiple login attempts. This has been resolved.
• Excessive egress alerts - some users experienced a bug with triggering subsequent egress events over a 48 hour period, locking them out of their workspace. This has been resolved.

Support resources

• Updated the Smaller Callsets for Analyzing Short Read WGS SNP & Indel Data with Hail MT, VCF, and PLINK to reflect changes applicable to CDR v8.
• Added additional examples in the tutorial notebook, 03_Manipulate Hail VariantDataset, in the Featured Workspace How to Work with All of Us Genomic Data (Hail - Plink)(v8) to demonstrate how to work with phased data in the VDS. Specifically, PLINK does not support phased data and we provided updated examples of how to unphase the data before exporting to a PLINK .bed file.
• The Featured Workspace How to Work with All of Us Survey Data (v8) has additional resources for working with the Emotional Health History and Well-Being & Behavioral Health and Personality surveys.
• New Office Hours informational sessions are available in the “Videos” section to include Cloud Storage Options and an overview of the Exploring the Mind dataset.