index.qmd

---
title: "Working with AI"
format:
  html: default
  revealjs:
    output-file: index-slides.html
  pdf:
    output-file: index-handout.pdf
  docx:
    output-file: index.docx
---

This site collects the UCD-SERG lab's notes on working responsibly and
effectively with AI coding assistants: what they are, how to use them, and
the policies lab members follow when using them.
It was migrated out of the
[UCD-SERG Lab Manual](https://ucd-serg.github.io/lab-manual/)'s "Working with
AI" chapter, which had grown large enough to deserve a dedicated site.
For the lab's broader coding, reproducibility, and collaboration
conventions, see the lab manual itself.

::: {.callout-warning}
## Technology in Rapid Evolution

As of early 2026,
AI coding assistant technology is changing extremely rapidly,
and we are just beginning to figure out how to use these tools effectively ourselves.
All information on this site should be taken with extra caution,
as best practices and capabilities continue to evolve.
:::

## Chapters

- [**Policies for Using AI**](chapters/ai-use-policies.qmd):
  responsibility for validation, disclosure, attribution, and using AI for
  journal articles
- [**Coding Agents**](chapters/coding-agents.qmd):
  what language models and coding agents are; platforms and catalogs;
  when and how to work with them; prompt formats; and benefits, hazards,
  and best practices
- [**Agent and Harness Architecture**](chapters/agent-architecture.qmd):
  how harnesses, agent execution loops, and runtime environments are
  engineered, and the 2026 harness landscape
- [**Configuring and Extending Agents**](chapters/agent-customization.qmd):
  configuring agent environments, instructions, Agent Skills (`SKILL.md`),
  MCP servers, plugins, and developer extensions
- [**Local Models and Offline Agents**](chapters/local-models.qmd):
  running agents offline, connecting open harnesses to local Ollama and
  OpenRouter endpoints, and evaluating small local models
- [**Orchestrating Teams of Agents**](chapters/agent-orchestration.qmd):
  when running several agents at once is worth the cost, what we already use
  for it, outside orchestrators (Agent Teams, Inflexa, TORQCLAW, Oh My OpenCode),
  and multi-agent frameworks
- [**AI for Math and Statistics**](chapters/ai-for-math.qmd):
  reasoning models for mathematics and statistics, formal proof assistants,
  and benchmarks
- [**Grok Bot and Alternatives**](chapters/grok-bot-and-alternatives.qmd):
  persistent teammates with their own computer (Grok Bot, Rakazo, OpenClaw),
  collaborative workspaces (Claude Cowork, Gemini Spark), and hosted agent offices
- [**Data Dictionaries for Humans and Agents**](chapters/data-dict.qmd):
  `data-dict.yaml` for making dataset context accessible to both humans and AI
  agents (see [data-dict.tidyverse.org](https://data-dict.tidyverse.org/))
- [**Benchbook: A Personal Wiki Under Contract**](chapters/benchbook.qmd):
  a plain-markdown, git-versioned wiki that an AI agent maintains under a
  written contract (see [benchbook](https://github.com/Ulef1005/benchbook))
- [**Make: Visual Automation and AI Agents**](chapters/make.qmd):
  visual, no-code canvas for 3,000+ apps, scenarios, and AI agents with Make
  Grid and MCP (see [make.com](https://www.make.com/en))
- [**Pull-Request Workflow with Agents**](chapters/pr-workflow-with-agents.qmd):
  filing issues, claiming work, driving a pull request to a clean,
  mergeable state, and agent-assisted automated code review

The notes are available in multiple formats:

- **HTML Website**: Navigate using the navbar for easy access to all pages
- **RevealJS Slides**: Each chapter can generate a presentation format with `-slides.html` suffix
- **PDF Handouts**: Each chapter can generate a PDF handout with `-handout.pdf` suffix
- **DOCX Documents**: Each chapter can generate a Microsoft Word document with `.docx` extension

## About this website

This website is built with [Quarto](https://quarto.org/), an open-source scientific and technical publishing system, from the
[UCD-SERG `qwt` (Quarto Website Template)](https://github.com/Morrison-Lab/qwt).

That template's structure comes from the
[UCD-SERG Lab Manual](https://ucd-serg.github.io/lab-manual/),
which is in turn adapted from the
[Benjamin-Chung Lab Manual](https://jadebc.github.io/lab-manual/index.html).
This site's own content also began as
the "Working with AI" chapter of the UCD-SERG Lab Manual.

## Building the website

To render the website locally:

```bash
quarto render
```

To preview the website with live reload:

```bash
quarto preview
```

The rendered output will be in the `_site/` directory, which is published to GitHub Pages.

## License

See [`LICENSE`](https://github.com/Morrison-Lab/wai/blob/main/LICENSE).

## References {.unnumbered}

::: {#refs}
:::