OMOP Notebook (experimental)

Analyses on the OMOP Common Data Model using Jupyter and Google Cloud Platform

Note: This is experimental and may not be actively maintained

Requirements

• Python 3.5+
• gcloud command-line tool

Getting Started on Linux

• Create an isolated Python environment (recommended)

   python3 -m .venv
   source .venv/bin/activate
   python3 -m pip install --upgrade pip  # upgrade pip if needed
  

• Install the dependency packages in your Python environment

   pip install -r requirements.txt
  

• An environment variable GOOGLE_APPLICATION_CREDENTIALS should point to a file that defines the credentials (see Google Application Default Credentials)

• Start the notebook server

   jupyter notebook