# Week 01 — 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 1 "Learn it" block (units **B1** molecules and enzymes, **M1** linear algebra), expanded into exact locators per the [source contract](../../SOURCES.md).

[Week 01 brief](./specs.md) · [Commitment](./commitment.md) · [Evidence](./evidence.md) · [Review](./review.md) · [Previous](../week-00-cockpit-and-positioning/materials.md) · [Next](../week-02-indpensim-data-and-baseline/materials.md)

## Where this fits in the week (600-minute cap respected)

| Slot | Budget | Material |
|---|---:|---|
| **Monday build block** | 20 min max | V4 LearnChemE Monod (6), before coding → R3 SciPy `solve_ivp` examples — this is 70% of `monod.py` |
| **Tuesday · B1** | 35 min | R2 Enzymes (25) → 10 min: five lines in `notes/bio/B1.md`. Stop at the understanding check; the rest of the block is build |
| **Wednesday build block** | 10 min max | R4 paho-mqtt publish example |
| **Thursday · M1** | 60 min + 30 | V2 chapters 1-3 (~30) → one example redone in NumPy (~20); last 30 min: founder paper, abstract and figures only |
| **Saturday sandbox** | optional | Everything under "Deeper", after catch-up |

Rule (trimmed 2026-09-29): study stops at the understanding check, not at the end of the chapter. Anything that pulls you further goes to PARKING and the Saturday rabbit-hole slot.

## Read

| # | Source | Exact scope | Min | Why this week | Produce |
|---|---|---|---:|---|---|
| R2 | OpenStax *Biology 2e*, [6.5 Enzymes](https://openstax.org/books/biology-2e/pages/6-5-enzymes) | Whole section, plus the chapter-6 review questions reachable from [Ch. 6 Introduction](https://openstax.org/books/biology-2e/pages/6-introduction) if time allows | 25 | Enzyme + substrate is literally the shape of the Monod term `S/(Ks+S)` you code on Monday | 5 questions at the end of `notes/bio/B1.md`; answer them yourself next week |
| R3 | SciPy docs, [`scipy.integrate.solve_ivp`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.solve_ivp.html) | The **Examples** section only, especially the Lotka-Volterra style system | 15 | Replace predator-prey with biomass-substrate and Monday's task is mostly done | The working ODE skeleton in `batchlens/sim/monod.py` |
| R4 | [eclipse-paho/paho.mqtt.python](https://github.com/eclipse-paho/paho.mqtt.python) README | "Publish a single message" example | 10 | Wednesday's telemetry hop, nothing more | The publisher in the Wednesday artifact |
## Watch (YouTube)

Durations are approximate.

| # | Channel · title | ~Length | Link | When | Produce |
|---|---|---:|---|---|---|
| V2 | 3Blue1Brown · *Essence of Linear Algebra*, chapters 1-3 | ~30 min | Playlist: [youtube.com/playlist?list=PLZHQObOWTQDPD3MizzM2xVFitgF8hE_ab](https://www.youtube.com/playlist?list=PLZHQObOWTQDPD3MizzM2xVFitgF8hE_ab) · chapter 1 direct: [watch?v=fNk_zzaMoSs](https://www.youtube.com/watch?v=fNk_zzaMoSs) | Thursday, first | `notes/ml/M1.md`: what a matrix does to a vector; one example redone in NumPy |
| V4 | LearnChemE (CU Boulder) · "Monod Cell Growth Example (Bio)" | ~6 min | [youtube.com/watch?v=39kf7YdwNOs](https://www.youtube.com/watch?v=39kf7YdwNOs) | Monday, before coding | A hand-sketched growth curve taped next to the screen |

## Deeper — Saturday sandbox only

- OpenStax *Biology 2e*, ch. 3 "Biological Macromolecules" — [3-introduction](https://openstax.org/books/biology-2e/pages/3-introduction), start at [3.1 Synthesis of Biological Macromolecules](https://openstax.org/books/biology-2e/pages/3-1-synthesis-of-biological-macromolecules) — 3.1 and the protein section; skim carbohydrates and lipids; finish on [Chapter Summary](https://openstax.org/books/biology-2e/pages/3-chapter-summary). Moved out of core on 2026-09-29.
- Khan Academy, [Energy and enzymes](https://www.khanacademy.org/science/biology/energy-and-enzymes) → [Activation energy (article)](https://www.khanacademy.org/science/ap-biology/cellular-energetics/enzyme-structure-and-catalysis/a/activation-energy) — One article + the practice set. Moved out of core on 2026-09-29.
- Crash Course Biology #3 · "Biological Molecules — You Are What You Eat" — [youtube.com/watch?v=H8WJ2KENlK0](https://www.youtube.com/watch?v=H8WJ2KENlK0). Moved out of core on 2026-09-29.
- Khan Academy (MCAT) · "Enzymes and activation energy" — [khanacademy.org/…/v/enzymes-and-activation-energy](https://www.khanacademy.org/test-prep/mcat/biomolecules/enzyme-structure-and-function/v/enzymes-and-activation-energy). Moved out of core on 2026-09-29.
- LearnChemE · "Washout Derivation in CSTR Bioreactor (Bio)" — [watch?v=L_bzv0bbU4M](https://www.youtube.com/watch?v=L_bzv0bbU4M). The engineer's version of what happens when the feed stops — which is exactly Friday's injected fault.
- MIT OCW **18.06 Linear Algebra** (Gilbert Strang), lectures 1-3 — [ocw.mit.edu/courses/18-06-linear-algebra-spring-2010](https://ocw.mit.edu/courses/18-06-linear-algebra-spring-2010/). Only if 3Blue1Brown leaves you wanting proofs.
- NPTEL *Bioreactors* (Suraishkumar, IIT Madras), lecture 1 — [nptel.ac.in/courses/102106053](https://nptel.ac.in/courses/102106053). A preview of week 09. **(verify)** course numbering.
- [Pioreactor](https://pioreactor.com) docs — a real open-source mini bioreactor; read the growth-rate estimation page to see what an online signal actually looks like. No hardware needed.

## Link check log — 2026-09-15

- Verified today: R1, R2, V1, V2 (playlist and ch. 1), V3, V4, and the LearnChemE washout video.
- Not re-checked today, inherited locators: R3, R4, MIT OCW 18.06, NPTEL 102106053 **(verify)**, Pioreactor docs.
- Log the actual URL, access date and sections read in [`evidence.md`](./evidence.md). If a video is gone, search the exact title on the same channel and log the substitution.

## NotebookLM kit sources for `LABLOOP-W01`

(1) this file; (2) the Week 1 chapter from the v6 master; (3) R1 page; (4) R2 page; (5) V1 URL; (6) R5 Khan article; (7) V2 chapters 1 and 3 URLs; (8) R3 SciPy docs page; (9) your `notes/bio/B1.md`; (10) `sim/monod.py` pasted as text after Monday.

Focus line: `Focus: the Monod growth model as a restaurant kitchen (biomass, substrate, product, oxygen), what an enzyme is, and why a matrix is a machine that transforms vectors.`

Custom question: `Look at my monod.py. Which biological assumptions does it make silently (lag phase, maintenance, oxygen limitation), and which one would a bioprocess engineer challenge first?`