# Week 04 — Materials: what to read, what to watch

Status: PREPARED 2026-09-15. Links checked on 2026-09-15 unless marked **(verify)**.
Authority: v6 master plan, Week 4 "Learn it" block (units **B4** microbial metabolism, **M4** cross-validation), expanded into exact locators per the [source contract](../../SOURCES.md).

[Week 04 brief](./specs.md) · [Commitment](./commitment.md) · [Evidence](./evidence.md) · [Review](./review.md) · [Gates](../../GATES.md) · [Previous](../week-03-statistical-batch-monitoring/materials.md)

**This is GATE 4 week.** Reading is subordinate to the release. If the DOI is at risk on Friday, cut every optional item below and log the cut in `review.md`.

## Where this fits in the week

| Slot | Budget | Material |
|---|---:|---|
| **Tuesday · B4** | 20 min | V3 Khan fermentation (10) → one paragraph in `notes/bio/B4.md`: "what is a fermentation, really". The rest of the block is build |
| **Wednesday build block** | 15 min max | R3 GitHub citation/Zenodo docs + the `CITATION.cff` format page |
| **Thursday · M4** | 60 min + 30 | V1 (6) → R4 Kapoor & Narayanan, the leakage taxonomy only (20) → batch-wise CV with its test (~35); last 30 min founder paper |
| **Saturday sandbox** | optional | "Deeper", only after the release is out |

## Read

| # | Source | Exact scope | Min | Why this week | Produce |
|---|---|---|---:|---|---|
| R3 | GitHub Docs, ["Referencing and citing content"](https://docs.github.com/articles/referencing-and-citing-content) and ["About CITATION files"](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files); format spec at [citation-file-format.github.io](https://citation-file-format.github.io/) | The Zenodo-integration steps and the minimal `CITATION.cff` fields | 15 | This is the literal procedure for Friday's DOI badge. Read it once, follow it exactly | `CITATION.cff` in the repo root and a rendering DOI badge in the README |
| R4 | Kapoor S. & Narayanan A., "Leakage and the reproducibility crisis in machine-learning-based science", *Patterns* 4(9):100804, 2023. DOI [10.1016/j.patter.2023.100804](https://doi.org/10.1016/j.patter.2023.100804) · open PDF: [hbiostat.org/papers/kap23lea.pdf](https://hbiostat.org/papers/kap23lea.pdf) | The **taxonomy of eight leakage types**; identify which one batch-wise CV prevents | 20 | The single best paper on the exact mistake that would invalidate Paper 2. Cite it in week 08 and week 18 | One paragraph in the README's honest "Where it fails" section naming the leakage type you guarded against |
## Watch (YouTube)

| # | Channel · title | ~Length | Link | When | Produce |
|---|---|---:|---|---|---|
| V1 | StatQuest · "Machine Learning Fundamentals: Cross Validation" | ~6 min | [youtube.com/watch?v=fSytzGwwBVw](https://www.youtube.com/watch?v=fSytzGwwBVw) | Thursday, first | The sentence "why random k-fold is wrong for batch data" in `notes/ml/M4.md` |
| V3 | Khan Academy · "Fermentation and anaerobic respiration" (article + practice) | ~10 min | [khanacademy.org/…/a/fermentation-and-anaerobic-respiration](https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-respiration-ap/a/fermentation-and-anaerobic-respiration) | Tuesday, first | One paragraph in `notes/bio/B4.md`: "what is a fermentation, really" |

## Deeper — Saturday sandbox only, and only after the release is out

- OpenStax *Microbiology*, ch. 8 "Microbial Metabolism", sections 8.1-8.4 — start at [8.1 Energy, Matter, and Enzymes](https://openstax.org/books/microbiology/pages/8-1-energy-matter-and-enzymes), chapter entry [8-introduction](https://openstax.org/books/microbiology/pages/8-introduction), recap [8-summary](https://openstax.org/books/microbiology/pages/8-summary) — 8.1 through 8.4; pay attention to aerobic vs anaerobic. Moved out of core on 2026-09-29.
- ISLP ch. 5 "Resampling Methods" — free PDF at [statlearning.com](https://www.statlearning.com/) — 5.1 cross-validation and 5.2 bootstrap; then the ch. 5 lab. Moved out of core on 2026-09-29.
- Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", *PLOS Comp. Biol.* 9(10):e1003285, 2013. DOI [10.1371/journal.pcbi.1003285](https://doi.org/10.1371/journal.pcbi.1003285) — All ten rules, they are one page each. Moved out of core on 2026-09-29.
- StatQuest · "Bootstrapping Main Ideas!!!" — Channel: [youtube.com/@statquest](https://www.youtube.com/@statquest) — search the exact title. **(verify)**: no stable video ID confirmed on 2026-09-15. Moved out of core on 2026-09-29.
- *The Turing Way* — [book.the-turing-way.org](https://book.the-turing-way.org), chapters on "Version control" and "Research compendia". The grown-up version of what you shipped this week.
- [carpentries-lab/good-enough-practices](https://github.com/carpentries-lab/good-enough-practices) — the hands-on lesson behind week 00's R3.
- [Zenodo help](https://help.zenodo.org/) — versioning and GitHub integration, if the DOI badge misbehaves.
- [JOSS submission guidance](https://joss.readthedocs.io/en/latest/submitting.html) — you submit in **week 36**, not now. Read it once so that today's release history is already the kind reviewers want.

## Link check log — 2026-09-15

- Verified today: R1 (all three pages), R3 (GitHub docs, both pages), R4 (DOI + open PDF), R5 (DOI), V1, V3.
- **Not verified: V2** — the StatQuest bootstrapping video did not resolve to a stable ID in today's search. Find it from the channel, record the URL you actually used in [`evidence.md`](./evidence.md), or skip it; ISLP 5.2 covers the same ground.
- Not re-checked today: R2 statlearning.com (verified 2026-09-12), citation-file-format.github.io, Turing Way, Zenodo help, JOSS docs.
- Gate 4 evidence must name the real DOI, the release tag and the command that regenerates the headline table. A prepared link is not a released artifact.

## NotebookLM kit sources for `LABLOOP-W04`

(1) this file; (2) the Week 4 chapter from the v6 master; (3) R1 pages; (4) ISLP ch. 5 PDF; (5) V1 URL; (6) R4 PDF; (7) R5 article; (8) R3 GitHub docs pages; (9) your README draft with the headline number; (10) [`GATES.md`](../../GATES.md).

Focus line: `Focus: why a result is only finished when a stranger can regenerate it; batch-wise cross-validation as leakage prevention; aerobic versus anaerobic metabolism.`

Custom question: `Given my batch-wise CV implementation and the Kapoor & Narayanan taxonomy, which leakage type am I still exposed to in batchlens v0.1, and what is the cheapest test that would catch it?`