# Week 02 — 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 2 "Learn it" block (units **B2** cellular respiration, **M2** calculus and gradients), expanded into exact locators per the [source contract](../../SOURCES.md).

[Week 02 brief](./specs.md) · [Commitment](./commitment.md) · [Evidence](./evidence.md) · [Review](./review.md) · [Previous](../week-01-fermentation-simulator/materials.md) · [Next](../week-03-statistical-batch-monitoring/materials.md)

## Where this fits in the week

| Slot | Budget | Material |
|---|---:|---|
| **Monday build block** | 20 min max | R3 Goldrick 2015 — abstract, figures, section 2, while the data downloads |
| **Tuesday · B2** | 30 min | V1 (13) → three lines in `notes/bio/B2.md` linking respiration to the DO curve in a real batch. The rest of the block is build |
| **Wednesday build block** | 15 min max | R4 Goldrick 2019 — the dataset section, to answer "which batches are faulty, exactly" |
| **Thursday · M2** | 60 min + 30 | V2 calculus ch. 1-2 (~25) → V4 StatQuest PCA (22), before Friday's PCA code; last 30 min founder paper |
| **Saturday sandbox** | optional | "Deeper", after catch-up |

## Read

| # | Source | Exact scope | Min | Why this week | Produce |
|---|---|---|---:|---|---|
| R3 | Goldrick S. et al., "The development of an industrial-scale fed-batch fermentation simulation", *J. Biotechnology* 193:70-82, 2015. DOI [10.1016/j.jbiotec.2014.10.029](https://doi.org/10.1016/j.jbiotec.2014.10.029) · [PubMed 25449107](https://pubmed.ncbi.nlm.nih.gov/25449107/) | Abstract, **all figures**, and section 2 (the model) | 20 | This is the paper behind the dataset you are tidying. Paper 2 will cite it | Five lines in `notes/bio/B2.md`: which state variables the simulator actually integrates |
| R4 | Goldrick S. et al., "Modern day monitoring and control challenges outlined on an industrial-scale benchmark fermentation process", *Computers & Chemical Engineering* 130:106471, 2019. DOI [10.1016/j.compchemeng.2019.05.037](https://doi.org/10.1016/j.compchemeng.2019.05.037) · open version: [UCL Discovery 10082538](https://discovery.ucl.ac.uk/10082538/) · data record: [Mendeley Data pdnjz7zz5x](https://data.mendeley.com/datasets/pdnjz7zz5x/1) | Abstract + **the dataset section**: how many batches, which are faulty, how faults are labelled, what the Raman block is | 15 | Your whole week-03 alarm evaluation depends on knowing which batches are the faulty ones — and on the licence for redistribution | A variable table (name, unit, online/offline) and the fault list, with quoted sentences and their page numbers |

## Watch (YouTube)

| # | Channel · title | ~Length | Link | When | Produce |
|---|---|---:|---|---|---|
| V1 | Crash Course Biology #7 · "ATP & Respiration" | ~13 min | [youtube.com/watch?v=00jbG_cfGuQ](https://www.youtube.com/watch?v=00jbG_cfGuQ) | Tuesday, first | Three lines in `notes/bio/B2.md`: why DO falls when biomass grows |
| V2 | 3Blue1Brown · *Essence of Calculus*, ch. 1-2 | ~25 min | Topic page: [3blue1brown.com/topics/calculus](https://www.3blue1brown.com/topics/calculus) · ch. 1 direct: [watch?v=WUvTyaaNkzM](https://www.youtube.com/watch?v=WUvTyaaNkzM) | Thursday | `notes/ml/M2.md`: what a derivative is, in your own words |
| V4 | StatQuest · "Principal Component Analysis (PCA), Step-by-Step" | ~22 min | [youtube.com/watch?v=FgakZw6K1QQ](https://www.youtube.com/watch?v=FgakZw6K1QQ) | **Before Friday's PCA code** | The 3-line explanation of scores vs loadings you will paste into Sunday's post |

## Deeper — Saturday sandbox only

- OpenStax *Biology 2e*, ch. 7 "Cellular Respiration" — [7-introduction](https://openstax.org/books/biology-2e/pages/7-introduction) — Glycolysis → citric acid cycle → oxidative phosphorylation, then [7.5 Metabolism without Oxygen](https://openstax.org/books/biology-2e/pages/7-5-metabolism-without-oxygen). Moved out of core on 2026-09-29.
- OpenStax *Biology 2e*, ch. 4 (cell structure) and 5.1-5.2 (membranes/transport) — **Skim only** — headings and figures. Moved out of core on 2026-09-29.
- 3Blue1Brown · *Neural Networks*, ch. 1-2 — Topic page: [3blue1brown.com/topics/neural-networks](https://www.3blue1brown.com/topics/neural-networks). Moved out of core on 2026-09-29.
- Steve Brunton (@Eigensteve) · SVD series, first 3 videos — playlist [PLMrJAkhIeNNSVjnsviglFoY2nXildDCcv](https://www.youtube.com/playlist?list=PLMrJAkhIeNNSVjnsviglFoY2nXildDCcv), overview video [watch?v=gXbThCXjZFM](https://www.youtube.com/watch?v=gXbThCXjZFM). PCA's engine explained by an engineer; you will want this again in weeks 12-17.
- Deisenroth, Faisal & Ong, *Mathematics for Machine Learning*, ch. 10 "Dimensionality Reduction with PCA" — free PDF at [mml-book.github.io](https://mml-book.github.io/).
- Ninja Nerd · glycolysis and Krebs cycle lectures (long, whiteboard) — channel search by title, only if respiration is still abstract. **(verify)** no fixed video ID recorded.
- [industrialpenicillinsimulation.com](https://www.industrialpenicillinsimulation.com/) — the original IndPenSim site. **(verify)**: it was unreachable in the 2026-09-12 check; prefer the UCL/Mendeley routes in R4 and record whichever one actually served the data, with its licence.

## Link check log — 2026-09-15

- Verified today: R1, R3 (DOI + PubMed), R4 (DOI + UCL + Mendeley), V1, V2 ch. 1, V4, Brunton playlist and overview.
- Not re-checked today: R2 chapter pages (same book as R1), V2/V3 topic pages, mml-book, Ninja Nerd **(verify)**, industrialpenicillinsimulation.com **(verify, known unreachable 2026-09-12)**.
- Dataset rights are a hard gate: before any redistribution, record the licence text and its source URL in [`evidence.md`](./evidence.md). Downloading for private analysis and republishing are different decisions.

## NotebookLM kit sources for `LABLOOP-W02`

(1) this file; (2) the Week 2 chapter from the v6 master; (3) R3 PDF; (4) R4 PDF; (5) R1 page; (6) V1 URL; (7) V2 ch. 1 and V3 ch. 1 URLs; (8) V4 URL; (9) your overlay plot description + "5 variables that matter"; (10) `notes/ml/M2.md`.

Focus line: `Focus: what IndPenSim measures and why, how cellular respiration explains the oxygen and substrate curves, and PCA as an executive summary of 100 batches.`

Studio extra (Data Table): `Table of every IndPenSim variable: name, unit, online or offline, what biology or engineering it reflects.`

Custom question: `From the Goldrick papers, which faults exist in the 100 batches and how are they labelled? Quote the sentences.`