Practical AI for Scientists — FutureHouse Tutorial Series

Interactive tutorials for scientists who want to use AI in research: core concepts, large language models in biology, and LLM agents. Content is written in Markdown and Jupyter notebooks and published with Jupyter Book.

Repository: github.com/Future-House/tutorial-series

View the book

After deployment, the site is served with GitHub Pages. Open:

https://future-house.github.io/tutorial-series/

If the URL differs (fork, custom domain), check Settings → Pages for the live address.

Run notebooks in Google Colab

Coding tutorials can also be opened directly in Colab (replace main if you use another default branch). The published site also includes Colab and Binder launch buttons (🚀) in the notebook header via _config.yml.

Notebook	Open in Colab
LLMs for biology (2.2)	Colab
External databases (2.3)	Colab
Aviary agent implementation (3.2)	Colab
Ant agent implementation (3.3)	Colab
Agent MCP example (3.4)	Colab
Python basics (4.2)	Colab

Before running notebooks that call LLM APIs, set your keys in a .env file or Colab Secrets. See index.md for details.

Build locally

Requires Python 3.11+ (CI uses 3.13).

python -m venv .venv
source .venv/bin/activate   # Windows: .venv\Scripts\activate
pip install -r requirements.txt
jupyter-book build .

Output: _build/html/. Open _build/html/index.html in a browser to preview.

Repository layout

Path	Contents
_config.yml	Book config, launch buttons (Colab/Binder), theme, analytics
_toc.yml	Table of contents
index.md	Landing page
chapter_1/	Introduction — background, AI models, LLMs in biology
chapter_2/	Applications in biology — background, LLM notebooks, external databases
chapter_3/	LLM agents — concepts, Aviary, Ant, and MCP examples
resources/	Glossary, Python basics notebook, submit-your-work page
.github/workflows/deploy.yml	Build and deploy to GitHub Pages on push to main

Table of contents

1. Introduction — evolution of AI, model overview, LLMs in biology
2. Applications of AI in Biology — LLM workflows and external database queries
3. LLM Agents — agent concepts, Aviary and Ant implementations, MCP tooling
4. Resources — glossary, Python basics, project submissions

License and copyright

Copyright 2026 FutureHouse. See repository settings for license terms if applicable.