Running Your Own Jupyter Environment

Running Your Own Jupyter Environment#

Complete Setup Guide for Applied Biostatistics

Set Up Your Local Environment đŸ’»

Follow these step-by-step instructions to install Anaconda Python, launch Jupyter notebooks, and install the course helper package on your computer.

Perfect for: Students who prefer working locally or need offline access to course materials.

Why Use a Local Environment?#

🚀 Better Performance

Local installations typically run faster than cloud-based solutions and don’t require internet connectivity for computation.

🔒 Data Privacy

Keep your data and analyses completely private on your own machine without uploading to cloud services.

đŸ’Ÿ No Storage Limits

Work with large datasets without worrying about cloud storage quotas or session timeouts.

đŸ› ïž Full Control

Install additional packages, customize your environment, and integrate with other local tools as needed.

Installation Instructions by Operating System#

Select your operating system below for detailed installation instructions:

Step 1: Download Anaconda

  1. Visit the Anaconda website

  2. Click “Download” under the Windows section

  3. Choose the 64-bit installer (recommended for most modern computers)

  4. The download file will be named something like Anaconda3-2024.02-1-Windows-x86_64.exe

Step 2: Install Anaconda

  1. Run the installer by double-clicking the downloaded .exe file

  2. Click “Next” on the welcome screen

  3. Accept the license agreement and click “Next”

  4. Choose “Just Me (recommended)” and click “Next”

  5. Keep the default installation location (usually C:\Users\YourName\anaconda3)

  6. Important: Check “Add Anaconda3 to my PATH environment variable”

    • ⚠ The installer warns against this, but it makes using conda much easier

  7. Click “Install” and wait for completion (this may take 10-15 minutes)

  8. Click “Finish” when installation is complete

Step 3: Launch Jupyter

Option 1: Using Anaconda Navigator (Recommended for beginners)

  1. Open Anaconda Navigator from the Start Menu

  2. Click “Launch” under Jupyter Notebook

  3. Your web browser will open with the Jupyter interface

Option 2: Using Command Prompt

  1. Press Win + R, type cmd, and press Enter

  2. Type jupyter notebook and press Enter

  3. Your web browser will open with the Jupyter interface

Step 4: Install Course Helper Package

In a new Jupyter notebook cell, run:

!pip install applied-biostats-helper

You’ll only need to do this once.

Step 1: Download Anaconda

  1. Visit the Anaconda website

  2. Click “Download” under the macOS section

  3. Choose the appropriate installer for your Mac:

    • Apple Silicon (M1/M2/M3): 64-bit ARM installer

    • Intel processors: 64-bit Intel installer

  4. The download file will be named something like Anaconda3-2024.02-1-MacOSX-arm64.pkg

Step 2: Install Anaconda

  1. Run the installer by double-clicking the downloaded .pkg file

  2. Click “Continue” through the introduction screens

  3. Accept the license agreement

  4. Select your installation location (default is recommended)

  5. Click “Install” and enter your password when prompted

  6. Wait for installation to complete (this may take 10-15 minutes)

  7. Click “Close” when installation is finished

Step 3: Launch Jupyter

Option 1: Using Anaconda Navigator (Recommended for beginners)

  1. Open Anaconda Navigator from Applications or Spotlight search

  2. Click “Launch” under Jupyter Notebook

  3. Your web browser will open with the Jupyter interface

Option 2: Using Terminal

  1. Open Terminal (Cmd + Space, type “Terminal”)

  2. Type jupyter notebook and press Enter

  3. Your web browser will open with the Jupyter interface

Step 4: Install Course Helper Package

In a new Jupyter notebook cell, run:

!pip install applied-biostats-helper

You’ll only need to do this once.

Troubleshooting for macOS:

  • If you get a “command not found” error, you may need to add conda to your PATH:

    echo 'export PATH="$HOME/anaconda3/bin:$PATH"' >> ~/.zshrc
source ~/.zshrc

Step 1: Download Anaconda

  1. Visit the Anaconda website

  2. Click “Download” under the Linux section

  3. Choose the 64-bit (x86) installer

  4. The download file will be named something like Anaconda3-2024.02-1-Linux-x86_64.sh

Step 2: Install Anaconda

  1. Open a terminal (Ctrl + Alt + T)

  2. Navigate to your downloads folder:

    cd ~/Downloads

  3. Make the installer executable:

    chmod +x Anaconda3-2024.02-1-Linux-x86_64.sh

  4. Run the installer:

    ./Anaconda3-2024.02-1-Linux-x86_64.sh

  5. Follow the prompts:

    • Press Enter to review the license

    • Type “yes” to accept the license

    • Press Enter to confirm the installation location (default recommended)

    • Type “yes” when asked to initialize Anaconda3

  6. Restart your terminal or run:

    source ~/.bashrc

Step 3: Launch Jupyter

Option 1: Using Anaconda Navigator

  1. Type anaconda-navigator in terminal

  2. Click “Launch” under Jupyter Notebook

  3. Your web browser will open with the Jupyter interface

Option 2: Using Terminal (Recommended)

  1. Open a new terminal

  2. Type jupyter notebook and press Enter

  3. Your web browser will open with the Jupyter interface

Step 4: Install Course Helper Package

In a new Jupyter notebook cell, run:

!pip install applied-biostats-helper

You’ll only need to do this once.

Troubleshooting for Linux:

  • If conda commands don’t work, ensure your PATH is set correctly:

    echo 'export PATH="$HOME/anaconda3/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

Troubleshooting Common Issues#

Problem: “conda: command not found” or “jupyter: command not found”

Solution: The installation directory isn’t in your system PATH.

Windows:

  • Restart your command prompt or computer

  • If still not working, manually add C:\Users\YourName\anaconda3\Scripts to your PATH

macOS/Linux:

echo 'export PATH="$HOME/anaconda3/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc
Problem: Jupyter opens in the wrong directory

Solution: Navigate to your desired folder before launching Jupyter.

cd /path/to/your/course/folder
jupyter notebook
Problem: Package installation fails with permission errors

Solution: Use the --user flag to install packages in your user directory.

pip install --user git+https://github.com/DamLabResources/applied-biostats-helper.git
Problem: Browser doesn’t open automatically

Solution: Jupyter will display a URL in the terminal. Copy and paste it into your web browser.

Look for something like: http://localhost:8888/?token=abc123...

Setup Guide ‱ Last Updated: 2025

Contents