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i2b2-etl-docker

Quick Start for i2B2-etl using docker-compose

Prerequisite

docker-compose on linux machine

install steps

1. git clone https://github.com/i2b2/i2b2-etl-docker
2. cd i2b2-etl-docker/postgres
3. export I2B2_ROOT_PASSWORD=$(openssl rand -base64 14) && docker-compose up -d i2b2-etl;  
Note the password by:
4. echo "I2B2_ROOT_PASSWORD: $I2B2_ROOT_PASSWORD" 
5. verify that webclient is working on http://localhost/webclient (username: demo ,password: from step 4 )

to connect to diffirent data sources for the i2b2 cells

5. docker-compose down
6. modify .env file
7. repeat steps 1 and 2

to use mssql container

8. in step 2 cd to mssql folder

to modify default password

change I2B2_ROOT_PASSWORD in .env file, and run 'docker volume rm -f i2b2-mssql-vol i2b2pg-vol' before step 3

For assistance email: [email protected]

How to Cite

Wagholikar KB, Ainsworth L, Zelle D, et.al. I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform. Bioinformatics. 2022 Oct 14;38(20):4833-4836.

Wagholikar KB, Dessai P, Sanz J, Mendis ME, Bell DS, Murphy SN. Implementation of informatics for integrating biology and the bedside (i2b2) platform as Docker containers. BMC Med Inform Decis Mak. 2018 Jul 16;18(1):66.