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CSE 5810 Biomedical Informatics (Spring 2022)


Implementation Project Final Status

Frank Zappulla


  • For Windows Users Only - install WSL2
    • This will give you a real linux terminal where you can use conda
  • Conda
    • If you don't have Conda, you should install Miniconda instead of Conda
  • Docker
    • If you are on a Windows machine, you must install WSL2 first

Getting Started Instructions

  1. Start your local instance of HAPI FHIR
  2. clone this repository
    • git clone
  3. Change directory into this repository
    • cd cse5810_implementation
  4. Create your conda environment using the included yaml file
    • conda env create --file=hapi_fhir.yaml
    • You should first alter the prefix: /home/frank/miniconda3/envs/hapi_fhir part of the yaml file to reflect your particular conda environment. This will likely be /home/$USER/miniconda3/envs/hapi_fhir
  5. Activate the conda environment you just created
    • conda activate hapi_fhir
  6. Launch jupyter lab
    • jupyter lab
  7. Copy and paste the url in the terminal into your browser
  8. Double click on the hapi_fhir.ipynb file to open the developer's notebook
  9. You should now be using the notebook that was demonstrated during class