execution-plan/weeks/week-01-fermentation-simulator/materials.md · UPDATED 2026-10-01
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.
Week 01 brief · Commitment · Evidence · Review · Previous · Next
0101
Where this fits in the week (600-minute cap respected)
01
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.
0202
Read
02
Read
| # | Source | Exact scope | Min | Why this week | Produce |
|---|---|---|---|---|---|
| R2 | OpenStax Biology 2e, 6.5 Enzymes | Whole section, plus the chapter-6 review questions reachable from Ch. 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 |
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 README | "Publish a single message" example | 10 | Wednesday's telemetry hop, nothing more | The publisher in the Wednesday artifact |
0303
Watch (YouTube)
03
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 · chapter 1 direct: 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 | Monday, before coding | A hand-sketched growth curve taped next to the screen |
0404
Deeper — Saturday sandbox only
04
Deeper — Saturday sandbox only
- OpenStax Biology 2e, ch. 3 "Biological Macromolecules" — 3-introduction, start at 3.1 Synthesis of Biological Macromolecules — 3.1 and the protein section; skim carbohydrates and lipids; finish on Chapter Summary. Moved out of core on 2026-09-29.
- Khan Academy, Energy and enzymes → Activation energy (article) — 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. Moved out of core on 2026-09-29.
- Khan Academy (MCAT) · "Enzymes and activation energy" — khanacademy.org/…/v/enzymes-and-activation-energy. Moved out of core on 2026-09-29.
- LearnChemE · "Washout Derivation in CSTR Bioreactor (Bio)" — 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. Only if 3Blue1Brown leaves you wanting proofs.
- NPTEL Bioreactors (Suraishkumar, IIT Madras), lecture 1 — nptel.ac.in/courses/102106053. A preview of week 09. (verify) course numbering.
- Pioreactor 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.
0505
Link check log — 2026-09-15
05
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. If a video is gone, search the exact title on the same channel and log the substitution.
0606
NotebookLM kit sources for `LABLOOP-W01`
06
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?