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MI-Lab-E05-Data-Analysis

Installation

Open a terminal in the Setup folder and run docker-compose up.

Browser

After TranSMART has been installed with Docker, the interface is available in the browser at http://localhost:80.
The login credentials are:
user: admin
password: admin

Study Import

Import of the study "MIMIC" into TranSMART for the exercise. This can only be imported once the Docker containers are running.

Copy Study Data

Copy the MIMIC folder from /Material/MIMIC into the volume.
The folder is copied using an additional Docker image Busybox. The container therefore has access to the volume.

Open a terminal in the Material folder and run the following:

  1. docker run -v tm_umg_tm_opt:/data --name helper busybox true
  2. docker cp ./MIMIC helper:/data
  3. docker rm helper

The volume should now contain the MIMIC folder. See the volume in Docker Desktop:
grafik

Import

Once the folder with data has been copied into the volume, run the following in a terminal:
docker-compose exec tmbatch /opt/git/transmart-batch/transmart-batch.jar -c /opt/git/transmart-batch/batchdb.properties -n -p /opt/MIMIC/clinical.params

Docker Desktop: This can also be executed directly in Docker Desktop.

  1. Click on the container tm-batch and select the "Exec" tab:
    grafik
  2. Run the following: /opt/git/transmart-batch/transmart-batch.jar -c /opt/git/transmart-batch/batchdb.properties -n -p /opt/MIMIC/clinical.params
    grafik

The MIMIC study should now be imported into TranSMART.