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Module 0 · Environment Setup and Access

White-Label Program

This module is designed for Train-the-Trainer programs built around the OHDSI ecosystem.
It intentionally avoids site-specific branding so it can be cloned and customized by any institution or trainer team.
Replace placeholders and add links for your local environment as needed.

Setup and extraction are site specific

There is no single correct environment. Institutions differ in their data warehouse, SQL client, and extraction tooling. These materials use Databricks and DBeaver as examples, but not everyone uses Databricks. Your site may use Snowflake, Postgres, BigQuery, SQL Server, Posit Workbench, or another stack. The OMOP CDM and OHDSI tools are the same everywhere; only the connection details change. See the Environment Setup Handout for the participant quick guide.

Overview

This module ensures all participants have functional access to the systems, tools, and data sources required before the start of Day 1.
Each participant should complete the environment checklist and verify all access points work correctly.

Objectives

By the end of this module, participants will be able to:

  1. Access all required tools and environments (ATLAS and the CDM database).
  2. Verify permissions for data connections and tool execution.
  3. Install and test required local software (R, RStudio, Git, SQL client).
  4. Document readiness using the provided Environment Checklist Template.

Systems & Tools Setup

ATLAS

  • Confirm login credentials and ability to create/edit cohorts.
  • Test saving and exporting a cohort definition (JSON).
  • Verify cohort characterization jobs can run successfully.

OMOP CDM Access

  • Confirm read access to a sandbox or training CDM database (synthetic or de-identified).
  • Ensure network permissions and ODBC/connection strings are functional.
  • Optional: Test a basic SELECT * FROM PERSON LIMIT 5; query via SQL client (SELECT TOP 5 * on SQL Server).

HADES Environment (Optional — Day 6 Track)

  • Verify R, RStudio (or Posit Workbench), Java, and (on Windows) RTools. The HADES R setup guide names the R version the packages are tested against (R 4.4.1 when the guide was read on 1 October 2026).
  • Set a GitHub personal access token before installing, as the setup guide describes; installing every HADES package anonymously runs into the GitHub download cap.
  • Confirm ability to install and load OHDSI packages:
install.packages("remotes")
remotes::install_github("OHDSI/Hades")
library(Hades)
  • Optional: Test Achilles or DQD on a small sample CDM if permissions allow.

Local Tools

  • Git/GitHub: ability to clone, pull, and push to this repository.
  • SQL client: Databricks, DBeaver, or similar with CDM connectivity.
  • Text editor: VS Code, RStudio, or preferred IDE.

Participants who are new to Git or to a terminal can use the GitHub Starter Kit and the Command Line Starter Kit before the session.

Environment Checklist Template

Trainers may clone and adapt this checklist for local use.
A downloadable Markdown version is available here:
Download environment-checklist-template.md

Area Task Verified (Y/N) Notes
ATLAS Login successful and can save cohorts
CDM Database Confirmed SQL read access
HADES R environment installed and packages load
GitHub Repo cloned and permissions confirmed
SQL Client Connected to CDM successfully

Trainers: copy this table to your local documentation or export it as CSV for tracking participant readiness.

Slides & Kit Materials

File Description
Instructor Deck Full slide deck with speaker notes
Participant Handout Abbreviated handout for participants
Kahoot Quiz Environment setup quiz

Deliverables

  • Completed Environment Checklist uploaded or shared with instructors.
  • Verified tool access and functional test results (ATLAS and the CDM).

Tips for Trainers

  • Keep setup tool-agnostic and site-neutral. Replace institutional URLs and connection details in your fork.
  • Encourage participants to complete setup at least 48 hours before Day 1.
  • Maintain a shared support document or channel for troubleshooting access issues.

Next: Day 1 · OMOP Common Data Model — once all environment checks are complete.