Human Hippocampus

Welcome to the Human Hippocampus repository, a research project by the UCSC Braingeneers. This repository houses a set of analytical scripts and Jupyter Notebooks designed to analyze and visualize datasets generated by our group. Whether you're a member of our team or an interested collaborator, this repository serves as a hub for active research and data analysis.

Our research team uses Github Codespaces to do research inside of this repository. Codespaces provide a cloud environment where you can work on code for research just like how you usualy do on your personal computer. However, because everything in codespaces happens in the cloud, it provides massive benefits for collaborating on research and sharing your findings with others. Here' we provide a brief introduction to codespace and teach how to get started with doing research...

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Getting Started

To get started with our research and analysis tools, follow these steps:

1. Click the "Open with GitHub Codespaces" button above to launch a fully configured development environment with all the necessary tools and extensions.

2. Once your Codespace is ready, explore the devcontainer.json file for configuration details. It automatically pulls the latest Docker image from ghcr.io/braingeneers/research:latest, installs essential VS Code extensions (Jupyter, Python, LiveShare), and executes the post_create.sh shell script to set up additional features.

3. The post_create.sh script is executed after the Codespace container is built and installs the ./src/human_hip directory as a local library using the command: python3 -m pip install -e ./src/human_hip --no-deps. You can import the fcm.py file from anywhere within the workspace simply by writing import fcm.

4. The docs directory has been set up using sphinx-quickstart to create a base project Documentation structure. You can add inline documentation (NumPy style) to further enrich our project's documentation. To render the documentation locally, navigate to the docs/build/html folder in the terminal and run python3 -m http.server.

Customizing the Devcontainer

The devcontainer.json file allows you to customize your Codespace container and VS Code environment using extensions. You can add more extensions to tailor the environment to your specific needs. Explore the VS Code extensions marketplace for additional tools that may enhance your workflow.

Working with Datasets

Our Docker image contains datasets downloaded from the National Research Platform (NPR) using S3 protocols. These datasets are located in the /home/joyvan/data/ folder within the Docker container. Keep in mind that this folder isn't in the workspace/human_hippocampus/ path, so changes won't be included in GitHub commits.

If you need to commit exported data, make sure to save it to the workspace/human_hippocampus/data/ folder within your Codespace. This way, your data will be included in your GitHub commits and shared with the team.

Project Structure

• src/: This folder contains scripts and notebooks representing completed work by the team.

• dev/: The dev/ folder contains active research by each contributor on the project.

• pyproject.toml: This file follows the guidelines from PyPA for documenting project setup information.

Contributing

We welcome contributions from collaborators and researchers interested in our work. If you have improvements, suggestions, or new findings to share, please submit a pull request. Your contributions help advance our research and analysis efforts.

Thank you for joining us in exploring the fascinating world of the Human Hippocampus! 🧠📊📚

For more information about Braingeneers, visit our website.