cumc-dbmi/omop_notebook

Replicate some reports from Achilles to characterize synthetic OMOP datasets in BQ

Jupyter Notebook

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
```