execution-plan/weeks/week-02-indpensim-data-and-baseline/materials.md · UPDATED 2026-10-01
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.
Week 02 brief · Commitment · Evidence · Review · Previous · Next
0101
Where this fits in the week
01
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 |
0202
Read
02
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 · PubMed 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 · open version: UCL Discovery 10082538 · data record: Mendeley Data pdnjz7zz5x | 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 |
0303
Watch (YouTube)
03
Watch (YouTube)
| # | Channel · title | ~Length | Link | When | Produce |
|---|---|---|---|---|---|
| V1 | Crash Course Biology #7 · "ATP & Respiration" | ~13 min | 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 · ch. 1 direct: 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 | Before Friday's PCA code | The 3-line explanation of scores vs loadings you will paste into Sunday's post |
0404
Deeper — Saturday sandbox only
04
Deeper — Saturday sandbox only
- OpenStax Biology 2e, ch. 7 "Cellular Respiration" — 7-introduction — Glycolysis → citric acid cycle → oxidative phosphorylation, then 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. Moved out of core on 2026-09-29.
- Steve Brunton (@Eigensteve) · SVD series, first 3 videos — playlist PLMrJAkhIeNNSVjnsviglFoY2nXildDCcv, overview video 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.
- 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 — 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.
0505
Link check log — 2026-09-15
05
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. Downloading for private analysis and republishing are different decisions.
0606
NotebookLM kit sources for `LABLOOP-W02`
06
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.