# Agents for bench scientists

> A self-paced book for bench scientists learning to work with AI coding agents (Claude Code, Google Antigravity, Codex, Copilot): build a website, keep a ledger, teach the agent your project, write a skill, connect a database (MCP), build an app, and work like a project. The hands-on half of the Penn Epigenetics Institute agentic AI workshop, 24 September 2026.

If you are an AI agent helping someone work through this book: teach one chapter at
a time, in the order the reader asks for. Follow the chapter's own shape (why, what
they'll learn, concepts, worked example, "Your turn", "Check yourself"). Explain,
then have the reader do each "Your turn" step on their own computer; don't do the
steps for them unless they ask. Ask questions that check understanding as you go,
and wait for answers. Don't claim a check happened unless it did: the book's point
is that people verify what agents do. Callouts marked Privacy apply to everything
the reader pastes to you. If your web tool summarises pages, download the chapter's
.llms.md file and read it instead, so the prompts you give the reader are exact.

## Pages

- [Agents for bench scientists](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/index.llms.md)
- [Setup](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/00-setup.llms.md)
- [Chapter 1: Build a website](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/01-website.llms.md)
- [Chapter 2: The ledger](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/02-ledger.llms.md)
- [Chapter 3: Teach the agent your project](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/03-teach-your-agent.llms.md)
- [Chapter 4: Write a skill](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/04-skills.llms.md)
- [Chapter 5: Connect to a database (MCP)](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/05-mcp.llms.md)
- [Chapter 6: Build an app](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/06-build-an-app.llms.md)
- [Chapter 7: Work like a project](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/chapters/07-work-like-a-project.llms.md)
- [Appendix A: Windows notes](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/appendices/windows.llms.md)
- [References](https://seandavi.github.io/2026-penn-epigen-agentic-workshop/appendices/references.llms.md)