CBDB Documentation

Welcome to the documentation for the CBDB (Columbia Brain Health DataBank) database, AWS server, and LM notebook chatbot.

AWS Server Storage (S3)

The HPC server is connected to an AWS S3 bucket for large data storage. This storage is accessible directly via the filesystem.

Accessing S3 Storage

To access the S3 bucket storage:

1. Navigate to the S3 directory: Run the following command to change your directory to the mounted S3 folder: bash cd /adrd-s3

2. Create your personal directory: Create a folder using your UNI (University Network ID) to organize your files: bash # Replace 'your_uni' with your actual UNI mkdir /adrd-s3/your_uni

3. Store Files: You can now save your large datasets and files in /adrd-s3/your_uni/.

Available Guides

• Schema Research Doc: Documentation for the research schema.
• Linux R Database Guide: Guide for connecting to the database using R on Linux.
• Python Database Guide: Guide for setting up Python (uv) and connecting to the database.
• Sectioning: Clinical text section extraction guide.