Working Quarto book, v0.3. Thirteen one-hour Tuesday meetings for the Denolle Lab, September 8 – December 1, 2026, 1–2 PM America/Los_Angeles.
Published at https://denolle-lab.github.io/metascience-and-AI/
An exploratory quarter: the group reads its way through how experimental, observational, historical, and theoretical research actually proceeds, then asks what follows for the design and evaluation of agents for science. Meeting 12 takes up one such proposal: that agents let a researcher work competently across more fields, making individual polymathy practical again. The seminar puts it as a question and says what would count against it.
| Path | What it is |
|---|---|
index.qmd |
Rationale, schedule, standing questions |
sessions/ |
One chapter per meeting, thirteen of them |
rubrics.qmd |
Inquiry, novelty, advance, and evaluation worksheets |
prior-art.qmd |
Registry of existing science agents and benchmarks, and what their scores do not establish |
reading-library.qmd |
Publisher, DOI, and proceedings links for every assigned paper |
notes.qmd |
The group's meeting record — add yours |
suggested-readings.qmd |
Readings the group adds during the quarter |
contributing.qmd |
How to contribute, and what must never be published here |
references.bib |
39 records: 26 paired papers, 2 discussant papers, 11 optional extensions |
curriculum.json |
Editorial metadata for sessions and references. Kept in step with the .qmd files by hand; validate.py checks that the citation keys agree |
READING-AUDIT.md |
Why the reading selections are what they are |
tools/validate.py |
Source, schedule, link, and citation checks |
tools/check_links.py |
Verifies every DOI against Crossref and fetches every other URL |
tools/stage_site.py |
Fallback: copies a rendered book into a subdirectory of a local Jekyll checkout. Not the current publishing path |
Install the Quarto CLI from https://quarto.org/docs/get-started/. The book has no executable code cells and needs no Jupyter kernel, R, or Julia.
quarto preview # live reload while editing
quarto render # writes _book/The source checks need Python 3 and PyYAML. On a system with an externally managed Python, which covers recent macOS and most Linux distributions, use a virtual environment rather than pip install into the system interpreter:
python3 -m venv .venv
.venv/bin/pip install PyYAML
.venv/bin/python tools/validate.py
.venv/bin/python tools/check_links.py.venv/ is gitignored. validate.py checks that every chapter exists, that local links and
citation keys resolve, that the thirteen meetings fall on consecutive Tuesdays, that references.bib
and curriculum.json describe the same set of works, and that no private material is registered as a
chapter; it then runs a Pandoc citation pass that fails on any warning. check_links.py is slower and
hits the network, so run it when you have changed references rather than on every edit.
Pushing to main triggers .github/workflows/publish.yml, which validates the sources, renders, and
publishes to the gh-pages branch. Pull requests run validation and a render without publishing.
There is nothing to run by hand.
tools/stage_site.py remains for the alternative of copying a rendered build into the group's Jekyll
site at denolle-lab.github.io. That is not how this book is published and the script is kept only as
a fallback.
See CONTRIBUTING.md. Short version: this repository is public, so no journal PDFs,
no unpublished data, nothing a collaborator has not agreed to share, and nothing from private/.
private/ is where the parallel agent analysis lives. It is gitignored, and validate.py fails if
that ignore rule is removed or if private material is registered as a chapter.
Every assigned paper has an external DOI, publisher, repository, or proceedings link, and some full texts require institutional access. No journal PDFs are redistributed here. Free access is not permission to republish; check the license and preserve attribution before adding any third-party asset.
Course content is CC BY 4.0 and tools/ is MIT; see LICENSE. Rights in the cited papers
remain with their holders.
See VALIDATION.md.
- Book structure: https://quarto.org/docs/books/book-structure.html
- Book output: https://quarto.org/docs/books/book-output.html
- GitHub Pages: https://quarto.org/docs/publishing/github-pages.html
- Citations: https://quarto.org/docs/authoring/citations.html