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First release of Broadsea for deploying the OHDSI technology stack

General
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OHDSI Broadsea is a new way to deploy the OHDSI technology stack.

Use Broadsea to deploy the full OHDSI technology stack at your site so you can use it with your OMOP Common Data model (CDM) database.

Broadsea deploys the following OHDSI developed open source R methods & web tools:

  • The R methods library running in RStudio - including:

  • SqlRender

  • DatabaseConnector

  • FeatureExtraction

  • Cyclops

  • Achilles

  • CohortMethod

  • PatientLevelPrediction

  • The OHDSI Web tools running in Tomcat Apache - including:

  • Atlas

  • Calypso

See the OHDSI/Broadsea GitHub repository for the Broadsea documentation - scroll down to the “Quick Start Broadsea Deployment” section to get started with Broadsea.

Broadsea uses cross-platform Docker container technology. It supports any OS where Docker containers can run, including Windows, Mac OS X and Linux (including Ubuntu, CentOS & CoreOS). The deployed OHDSI methods & tools can be used with any OHDSI supported database including PostgreSQL, Oracle and SQL Server.

Intended usage scenarios:

  • Try-out / demo the OHDSI R packages & web applications (use a SynPUF 1K simulated patient data in the CDM database)
  • Run the Achilles R package for database profiling, database characterization & data quality assessment on your data and view the reports as tables/charts in the Atlas web application
  • Create patient cohorts & determine study feasibility in Calypso
  • Query OMOP vocabularies in Atlas
  • Generate and view patient cohorts in Atlas
  • Run observational studies on your data (including OHDSI Network studies)

Broadsea Dependencies

  • Docker (Version 1.11 or higher)
    • Docker Engine Docker
    • Docker Compose
  • An OMOP Common Data Model (CDM) database populated with the OMOP vocabulary &
    observational data
    • CDM Version 5 database required for the web tools
    • CDM Version 5 database preferred for the R packages but some packages also support CDM Version 4

Broadsea is still under development. If you have any questions about using Broadsea that are not answered by the Broadsea documentation, please post them to the OHDSI forums.

The Broadsea Methods Library Docker container is maintained by Marc Suchard @msuchard
The Broadsea Web Tools Docker container is maintained by Lee Evans @lee_evans (LTS Computing LLC)

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