Announcing the Bedford Workbench Release

We are excited to announce our latest software release! The Bedford Researcher Workbench release includes several highly anticipated new tools and features (detailed below).

  • Dataset builder
    • Data and Analysis tabs: The tabs for ‘Cohorts’, ‘Concepts Sets’ and ‘Notebooks’ that existed previously will be replaced by ‘Data’ and ‘Analysis’. The ‘Data’ tab will let users build Cohorts, Concept Sets and Data Sets. The ‘Analysis’ tab will contain Notebooks.
    • Datasets: Datasets are analysis-ready tables that can be exported to Notebooks. This lets users with limited knowledge of OMOP to quickly build the tables they want for analysis.
  • Cohort Builder
    • Universal Search: The ability to search all source and standard concepts in the Cohort Builder
    • Mutable Cohorts: The ability to edit cohorts once a user has saved a cohort in their work space.
    • Temporal Relationships: A user can link events in the cohort builder temporally to create their inclusion and exclusion criteria.
    • Data Visualizations in Review: Created data visualizations for labs and vitals in review.  Enable sophisticated filtering and sorting functions. 
    • Error Messaging: Display information when an unexpected condition occurs in the application.
  • CAPS Requirements
    • User Registration Steps: New users will be asked to complete the following steps to get access to registered tier data:
    • Set up 2 Factor authentication
    • Complete Compliance training in the Moodle Platform. Though the actual content for the training modules are not developed by NIH, this feature lets us test the integration between workbench and Moodle.
    • Sign-in to eRA commons
    • Data Use Agreement is built but will not be shown to users until Public launch.

***Existing users will not need to go through the above steps.***

  • Capture and retain Research purpose
    • Changes to Research purpose questionnaire: The research purpose questionnaire was modified based on CAPS requirements.
    • Enable users to search and select diseases from disease ontology: As part of the research purpose, users can pick the disease they are studying from the ontology published in http://disease-ontology.org/.
    • Retain workspace description/purpose after deletion: To meet CAPS requirements, workspace metadata such as research purpose will be retained even after a workspace is deleted.
  • Billing project set up
    • All work spaces will have a unique billing project which enables tracking spending at the work space level and changing billing accounts easier.
  • Featured Workspaces
    • All registered users will have access to “Featured” work spaces published by the Data Science team. For Bedford release, we will have Featured work spaces for HIV and Dementia phenotypes. Users can view these work spaces in ‘Read-only’ mode and can clone the work space to edit.
  • Notebooks
    • Read-only view: Users will have a read-only HTML view of the Notebook which will load by default when the cluster is spinning up.
    • Code Snippets: New “Code Snippets” published by the Data Science team will be available in Jupyter Notebooks as a “menu item” that users can select and run in their Notebooks.
    • Copy Notebooks between work spaces: Users can now copy Notebooks between work spaces they have write access to.
    • Notebooks can now be right-clicked and opened in a new tab
    • Notebook names will be shown in the tab’s title so that users having multiple notebooks open in a browser can navigate easily between Notebooks.
  • Data exfiltration prevention
    • Egress rate-limiting in VMs or VPC networks: This feature prevents users from quickly exfiltrating a large amount of data, by slowing down the max internet egress throughput.
    • Reminders of Data use policies: Users will be shown reminders of Data use policies when a Notebook is loading and when a user clicks on the Google bucket in their work space.

 

  • Reminder:  users will be required to have an eRA Commons account for data access. Please find the step-by-step instructions on how to link your eRA Commons account with your @researchallofus.org Workbench account here.

 

  1. New Users: After July 17, all new users will be required to have an eRA Commons account for data access in our production environment (https://workbench.researchallofus.org/).
  2. Existing Users: After August 2, without explicit agreement otherwise, all existing researchallofus.org users will be required to have eRA Commons account for data access in our production environment. If you have concerns about obtaining an eRA commons account by the Aug 2 cutoff, please contact support@researchallofus.org.

If you have any concerns or questions please feel free to contact Research Support in our help forms https://workbench.researchallofus.org/ under “Contact Support” or directly emailing us at support@researchallofus.org.

Thank you, on behalf of the Workbench team, for your continued partnership and feedback.

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