Documentation

This site is the source of truth for the Science Jubilee LLM Agent.

All pages here are exactly what the Jubilee LLM Agent can read via its retrieval-augmented generation (RAG) pipeline. When you ask the agent a question, it searches this documentation first and explains its reasoning based on what it finds here.

INFO

If it’s not documented here, the agent will either not know about it or will treat it as uncertain.

What this documentation is for

This documentation is designed for:

• Wet-lab scientists who want to run reliable, repeatable experiments without becoming full-time programmers.
• Protocol authors who maintain reusable scripts and procedures.
• Developers & maintainers extending the Science Jubilee library or the LLM agent itself.

We focus on:

• Clear, copy-pasteable code snippets.
• Explicit pre-conditions and safety notes for physical actions.
• Consistent structure so both humans and the LLM can navigate easily.

How the LLM uses these pages

When you ask the Jubilee LLM Agent something like:

“How do I calibrate XY offsets for my syringe tool with a camera?”

the agent will:

1. Search this documentation (e.g., the Procedures section).
2. Retrieve the most relevant pages.
3. Answer using those pages as its primary reference, quoting steps or code where helpful.

This means:

• Improving the docs directly improves the agent’s answers.
• If you want to change how the agent behaves or what it recommends, you should update or extend these pages.

How the docs are organized

Use the sidebar to explore, or start with one of these major sections:

Classes

• 📚 Classes Reference for the Python API: Machine, Deck, Labware, Tool, Well, Location, and others.
• Each class page follows a standard layout: description, constructor, key properties, important methods, short example, and related concepts.

Examples

• 🧪 Examples End-to-end, copy-pasteable scripts that demonstrate common workflows (e.g., gel printing with a syringe extruder).
• Written for scientists first: minimal assumptions about Python, clear execution order, and safety notes inline.

Procedures

• 🔧 Procedures Step-by-step operational guides that mix:
  • physical steps on the machine,
  • Duet / G-code configuration,
  • and Python code using the Science Jubilee library.
• Ideal for calibration, alignment, and configuration tasks (e.g., XY tool offset calibration with a USB microscope).

More sections may be added over time (e.g., troubleshooting, FAQ, or higher-level guides). The LLM agent will automatically benefit from any new content once it is included here.

How to contribute or report issues

This documentation – and the LLM’s behavior – improves when you report problems or suggest clarifications.

Contribute in one click

If you find a typo, unclear step, or missing detail:

• Click “Edit this page” in the lower-left corner of any page to propose a change directly, or
• Click the GitHub icon in the upper-right corner to open the repository and create an issue.

Even small fixes (better wording, extra warnings, clearer examples) can make the Jubilee LLM Agent significantly more helpful and safer to use.