WEEK 02 · Mon 28 Sep → Sun 04 Oct 2026
UNDERSTAND · PRACTICE · KEEP EVIDENCE
Read the week in plain language, refresh the foundations, follow each challenge step by step, and check what evidence to keep. Includes worked examples, answer keys and prompts for visual study resources.
Use this within your existing weekly blocks. Your learning completion and research evidence remain in your current tracker and week files.
START HERE · 2 MINUTES
STATUS
| Deliverable | Acceptance | State |
|---|---|---|
data-audit.mdBuild create ＋ |
Record the authoritative IndPenSim source, access terms, checksums and metadata; implement tidy import and count actual available batches. Acceptance: Batch/time/variable/value data and a reproducible manifest exist; benchmark simulated origin is explicit. | |
alignment-protocol.mdBuild create ＋ |
Align and unfold batches with an as-of-time rule, inspect units and missingness, and overlay ten trajectories. Acceptance: Five relevant variables and any use of future information are documented. | |
pca-baseline.mdBuild create ＋ |
Fit exploratory PCA on training normal batches and render held-out projections with labels from metadata. Acceptance: A reproducible scores plot exists even if faulty batches do not separate. | |
study-notes.mdLearning create ＋ |
Selected exact free resources; bounded lesson/exercise; separate solution; quiz and grading rubric; Peter's answers and gaps when executed | |
founder-paper.mdFounder papers create ＋ |
Verified source and P11 digest; authentic question and connection sentence; access limitations | |
branding-pack.mdBranding create ＋ |
Wednesday note, Sunday build log, X adaptation, figure/caption/alt text and the week's special asset; each claim linked to real proof | |
opportunity-actions.mdOpportunities create ＋ |
Qualified target/role, source/date, ladder stage, next action, message/interview/proposal draft and actual status | |
evidence.mdEvidence & review open & edit ↗ |
Actual paths/URLs, versions, checks/metrics, preparation versus execution state and external receipts when applicable | |
review.mdEvidence & review open & edit ↗ |
Checklist, learning assessment, gate status, shortfalls, next actions and carryover |
These filenames are outputs to prepare during this week's execution; this scaffold does not claim they already exist. Drafts and measured results have different states. Technical code/data stay in the canonical project repository and are referenced from these coordinating files.
During preparation, future measured tables get column definitions, input requirements and run instructions with PENDING status. During execution, replace pending values only with measured outputs. Do not create realistic-looking fake evidence.
600 MINUTES MAXIMUM
Target. 📦 Get the real batches. Hook: open the dataset and count the batches yourself. Do: record source, licence and checksums; import IndPenSim into one tidy parquet (batch, time, variable, value); read Goldrick 2015 abstract and figures while it downloads. Done when: the parquet loads and the batch count is written down with its source.
Do these in this order — the plan's own sequence:
Target. 🫁 Why oxygen falls when cells grow. Hook: find DO dropping in one real batch. Learn (30 min): Crash Course 'ATP & Respiration' only, then three lines in notes/bio/B2.md linking respiration to that DO curve. Done when: you can explain why a microbe needs oxygen and sugar in a tank. Then stop studying and continue Monday's import. Chapters 4, 5 and 7 are parked.
Do these in this order — the plan's own sequence:
Target. 📈 Line up the batches. Hook: overlay ten batches and look for the odd one out. Do: align batches on time without using future data, check units and gaps; read the Goldrick 2019 dataset section to learn which batches are faulty. Done when: ten overlaid trajectories exist and five key variables are documented.
Do these in this order — the plan's own sequence:
Target. ∂ Derivatives are rates. Hook: your monod.py already is calculus. Learn: 3Blue1Brown Calculus ch. 1-2 (25 min), then StatQuest PCA (22 min) for Friday. Done when: you can say what dX/dt means in your own code, and what a principal component is. Neural networks are parked until week 8. Last 30 min: founder paper, abstract and figures.
Do these in this order — the plan's own sequence:
Target. 🔭 See all batches in one picture. Hook: will the faulty batches stand out? Do: fit PCA on normal training batches only, project the held-out ones, colour by fault label. Done when: a reproducible scores plot exists, even if the faults do not separate.
No material for Friday — this is a pure build day. Need something to study instead? →
Target. Catch up, then reward. First: finish the earliest unfinished mission (only its Done when). Then the rabbit-hole slot: anything from PARKING or the Deeper list, guilt-free. Done when: no mission from this week is half-open, or it is logged as moved.
Optional, only if the day went well:
Target. Show it. 20 min: post the PCA scores plot with three lines (what, how, one honest limitation). 5 min: tick evidence. 20 min: write what was hard and why. 15 min: write next Monday's first action, startable in 2 minutes. Done when: the post is drafted and Monday's action is written.
No material for Sunday — this is a pure build day. Need something to study instead? →
Spare pockets, repo exercises and anything the plan lists without a day. Take them in this order when a day finishes early.
The model must turn these into exact physical actions using the observed files and available inputs. Each 90-minute block includes start/stop rituals. All calls, posts, debugging, reading and exercises consume this same capacity.
Each day is one mission: the Hook gets you in, Done when tells you to stop. Study stops at the understanding check. If a piece feels pointless, ask whether Done when needs it: no → skip and log; yes → let AI do the boring part and review it; still stuck → smallest version in 25 minutes.
WHAT TO WATCH, READ AND RUN
Last week you flew the simulator. This week you open the black boxes of 100 real flights. IndPenSim is a benchmark built by researchers from an industrial-scale penicillin fermentation: 100 batches, each hours long, with temperature, pH, oxygen, feeds, and even Raman spectra, some of them with faults. The first feeling will be overwhelm: dozens of variables, thousands of time points. Your job is the job you have don…
0 of 15 finished · give me one to start now → · open in the deck →
In the plan's running order: each card says which block it belongs to and what has to come before it. The seven-day plan lists the same cards under the day that owns them.
Monday build block · Read it inside Monday's build block
This is the paper behind the dataset you are tidying. Paper 2 will cite it
Read exactly: Abstract, all figures, and section 2 (the model)
Produce: Five lines in notes/bio/B2.md: which state variables the simulator actually integrates
In: LABLOOP-W02 Notebook
Tuesday · B2 · Tuesday, first
Produce: Three lines in notes/bio/B2.md: why DO falls when biomass grows
In: LABLOOP-W02 Notebook
Wednesday build block
Your whole week-03 alarm evaluation depends on knowing which batches are the faulty ones — and on the licence for redistribution
Read exactly: Abstract + the dataset section: how many batches, which are faulty, how faults are labelled, what the Raman block is
Produce: A variable table (name, unit, online/offline) and the fault list, with quoted sentences and their page numbers
In: LABLOOP-W02 Notebook
Thursday · M2 · Thursday
Produce: notes/ml/M2.md: what a derivative is, in your own words
In: LABLOOP-W02 Notebook
Thursday · M2 · after 3Blue1Brown · Essence of Calculus · Before Friday's PCA code
Produce: The 3-line explanation of scores vs loadings you will paste into Sunday's post
In: LABLOOP-W02 Notebook
Saturday sandbox
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
In: LABLOOP-W02 Notebook
Saturday sandbox · after OpenStax Biology 2e, ch. 7 "Cellular Respiration"
3Blue1Brown · Neural Networks, ch. 1-2 — Topic page: 3blue1brown.com/topics/neural-networks. Moved out of core on 2026-09-29
In: LABLOOP-W02 Notebook
Saturday sandbox · after 3Blue1Brown · Neural Networks
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
In: LABLOOP-W02 Notebook
Saturday sandbox · after Steve Brunton
Deisenroth, Faisal & Ong, Mathematics for Machine Learning, ch. 10 "Dimensionality Reduction with PCA" — free PDF at mml-book.github.io
In: LABLOOP-W02 Notebook
Saturday sandbox · after Deisenroth, Faisal & Ong, Mathematics for Machine Learning, ch. 10 "Dimensionality Reduction wit…
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
In: LABLOOP-W02 Notebook
Saturday sandbox · after Ninja Nerd · glycolysis and Krebs cycle lectures
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
In: LABLOOP-W02 Notebook
Open IndPenSim_Summary_data_notebook_V3.ipynb in Colab; compare their variable list with your tidy table
In: LABLOOP-W02 Notebook
Colab: 03.08-Aggregation-and-Grouping and 05.09-Principal-Component-Analysis
In: LABLOOP-W02 Notebook
Run the gallery example "PCA example with Iris Data-set", then swap Iris for 20 IndPenSim batches unfolded
In: LABLOOP-W02 Notebook
melt your wide CSVs to long format, save as parquet; time both libraries on the 100 batches
In: LABLOOP-W02 Notebook
READ FIRST
This week delivers the three concrete artifacts below and the supporting learning/branding/opportunity pack. The scientific or commercial outcome follows the preserved source brief, while the acceptance checks make its evidence testable. The career objective is to turn this work into something a scientist, hiring manager or buyer can inspect.
READ FIRST
Read v6 · Week 2 · One hundred real batches before Monday. It carries this week's v5 brief unchanged and adds the Welcome analogy, Learn it (▶ core and ＋ deeper sources), Run it (repos with a 20-40 minute exercise), the NotebookLM kit and the mentor check below. Standing v6 rules: resource rules, NotebookLM protocol, chapter anatomy. v6 adds depth only; it does not change a goal, gate, output or the 600-minute cap, so this specification still governs execution.
Verified links, exact scopes and durations for this week's reading and watching: materials.md.
Act I · Threads: B, M, BL · Next gate: 4
Where this week sits. - ← From: week 1 (you know what X, S, P and DO mean because you invented them). - → Feeds: week 3 (PCA scores become Hotelling T² alarms), week 4 (hours-to-detection needs aligned batches), week 8 (soft sensor uses the tidy parquet), weeks 12 and 17 (Paper 2 is built on this dataset). - ⟳ Returns in: Paper 2 "Data" section; you will cite Goldrick et al. 2015 and 2019.
Goals. - 🎯 This week: IndPenSim as a tidy parquet that loads in under a minute; an overlay plot; faulty batches visible in PCA. - 🏁 Next milestone: Gate 4. - 🌟 Final: the dataset under Paper 2; your first Medium thesis piece (M1) positions you before any paper exists.
Mentor check. "I can explain what a faulty batch looks like in a PCA scores plot and why respiration makes oxygen fall when biomass rises."
OPEN WHEN NEEDED
READ FIRST
Source unit: B2 · The cell and energy
Material: Crash Course Biology #7 "ATP & Respiration" (trimmed 2026-09-29; OpenStax ch. 4, 5 and 7 are Deeper)
Produce: three lines linking respiration to a real DO curve
Understanding check: You can explain why a microbe needs oxygen and sugar in a tank
During preparation, write one worked example connected to the week's actual task, one exercise with a separate answer key and five questions. Peter supplies answers; score explanation quality and flag misconceptions in QUESTIONS. Numeric/scientific conclusions require actual data or explicitly synthetic teaching values.
Source unit: M2 · Calculus and the neural network idea
Material: 3Blue1Brown "Essence of Calculus" ch. 1-2 + StatQuest PCA step-by-step (trimmed 2026-09-29; neural networks move to week 8)
Produce: Notes
Understanding check: You can say what dX/dt means in your code and what a principal component is
Use the prompt pack: P1 explanation ladder, P2 concept-to-project bridge and P3 quiz. Coding practice belongs within the allocated study/build block. Where the source asks for a favorable scientific result, substitute an honest measured comparison as explained below.
Select one verified founder/scientific-lead paper relevant to this week's domain. Use P11; save the question, method, numerical result with context, data workflow, three author questions and one connection sentence in founder-paper.md. Keep abstract-only access limitations explicit. On source weeks with no study, prioritize the commercial/submission task and log any skipped digest.
OPEN WHEN NEEDED
Branding: Prepare the first Medium thesis article from v4 and one annotated data figure; label the data simulated.
Opportunity action: Select an initial five-founder feedback list and draft a non-sales question supported by this week's paper digest.
Use career asset contracts. Publish at most the agreed cadence; one figure and one supported number or admitted failure can support multiple drafts. In long-form weeks, prepare a 1,500–2,500-word article from existing evidence within the build/buffer allocation. In release/demo weeks, prepare a 60-second script: problem, input, command/action, result, limitation and proof link.
Verify individuals, jobs and affiliations at execution time. The GridX list and v4 company map are research seeds, not current facts. Do not reveal named company weaknesses or employer/client confidential information. Keep drafted/sent/replied/booked/held statuses separate. The planning request alone does not authorize external messages or publication; honor explicit authorization in the execution session.
OPEN WHEN NEEDED
Do not call these real plant batches or require a visually favorable result. The historical download site may fail; use an author-linked source and preserve provenance.
Apply the root scientific evidence contract: provenance; meaningful independent splits; no future-data leakage; baseline comparison; actual denominators/uncertainty; failed cases; human review where required. State whether data are simulated, public experimental, synthetic or partner-provided.
Keep source gates intact, and log scope/time conflicts in review. Missing people, money, access or results must not be replaced with invented evidence. Reduce optional polish first. A specific essential external dependency stays pending while independent preparation continues.
READ FIRST
This is an enabling week. Its deliverables feed the next scheduled gate: 4. Complete the acceptance checklist below; do not promote reputation from a draft.
READ FIRST
Source-preserving minimum: the tidy parquet of IndPenSim.
Operational first step if stalled: open data-audit.md, write the required inputs and produce the smallest checkable example in ten minutes. If a more urgent missing gate dependency controls the week, use the source minimum above.
If the full week does not fit, use P14: retain one gate-critical deliverable and one directly supporting study exercise; record what is skipped versus moved. Do not mark the original full gate passed merely because the minimum was completed. After a missed week, reforecast from actual evidence and avoid a second unexamined lost week.
OPEN WHEN NEEDED
In review, state exactly what exists, what was verified, what Peter can now explain, which external events remain pending, where the canonical code/data live, and the next file/function or draft paragraph to touch. Link each fact to evidence. Carry scientific assumptions, split definitions and rights constraints forward explicitly.
OPEN WHEN NEEDED
Prepare Week 02 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-02-indpensim-data-and-baseline/specs.md, commitment.md, evidence.md and review.md.
Read prior prerequisite reviews and inspect actual repository/data state.
Use v5 as the governing sequence, the v6 Week 02 chapter
(LABLOOP-Master-Plan-v6.md) as the deeper walkthrough, and v4 only for
retained details.
Produce the full local preparation pack and the exact week-specific files named
in the artifact table. Give me a bounded lesson with exercises/answer key,
daily physical actions, technical runbook or draft, branding drafts and
career/commercial actions. Keep the total to 600 minutes.
Separate prepared artifacts from measured results and my learning completion.
Verify sources and do not invent metrics, citations, papers, people or outcomes.
Do not execute external communications, publication or spending unless the
current session already authorizes the specific action.
Finish by updating evidence/review and TODAY with the next physical action.
OPEN WHEN NEEDED
v6 reproduces this brief unchanged inside v6 · Week 2 · One hundred real batches. The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.
data/download.py for IndPenSim with checksums; load into a tidy long table (batch, time, variable, value). Done when 100 batches load in under a minute from parquet. Wed: batch unfolding and time alignment; plot every variable for 10 batches overlaid. Done when you can name the 5 variables that matter. Fri: PCA on the "normal" batches, scores plot, first look at the faulty ones. Done when the faulty batches are visibly outside.WEEK FILES
State: UNCONFIRMED. Owner: Peter Ciancaglini. Specification
Start date: not set. End date: not set. Available hours: confirm (planned ceiling 10). Primary outcome: indpensim data and baseline. Minimum that keeps the next gate alive: the tidy parquet of IndPenSim.
data-audit.md: Batch/time/variable/value data and a reproducible manifest exist; benchmark simulated origin is explicit.alignment-protocol.md: Five relevant variables and any use of future information are documented.pca-baseline.md: A reproducible scores plot exists even if faulty batches do not separate.| Day | Minutes | Physical action / outcome | Actual slot | Done |
|---|---|---|---|---|
| Mon | 90 | Record the authoritative IndPenSim source, access terms, checksums and metadata; implement tidy import and count actual available batches. | Not set | ☐ |
| Tue | 90 | Notes + a drawing of a cell making ATP | Not set | ☐ |
| Wed | 90 | Align and unfold batches with an as-of-time rule, inspect units and missingness, and overlay ten trajectories. Last ten minutes: optional note. | Not set | ☐ |
| Thu | 90 | Notes Include relevant founder-paper work within this block. | Not set | ☐ |
| Fri | 90 | Fit exploratory PCA on training normal batches and render held-out projections with labels from metadata. | Not set | ☐ |
| Sat | 90 | Resolve critical spillover; long-form draft if due; sandbox only if done. | Not set | ☐ |
| Sun | 60 | Build log, evidence, gap review, next actions. | Not set | ☐ |
Peter's commitment / adjustments: pending. Reviewing model and date: pending.
Execution state: NOT_STARTED. Specification This file is a blank register with planned artifact names; none of the rows prove completion.
| Item | Path / URL / version | State | Verification / actual result | Verified by / date |
|---|---|---|---|---|
| data-audit.md | Not created | NOT_STARTED | Pending: Batch/time/variable/value data and a reproducible manifest exist; benchmark simulated origin is explicit. | — |
| alignment-protocol.md | Not created | NOT_STARTED | Pending: Five relevant variables and any use of future information are documented. | — |
| pca-baseline.md | Not created | NOT_STARTED | Pending: A reproducible scores plot exists even if faulty batches do not separate. | — |
| Learning exercise / Peter's quiz | Not created | NOT_STARTED | Peter's actual answers required | — |
| Founder paper digest | Not created | NOT_STARTED | Source/content and access checked | — |
| Branding pack | Not created | NOT_STARTED | Claims audited; drafted/public status distinct | — |
| Opportunity actions | Not created | NOT_STARTED | Drafted/sent/replied/booked/held distinct | — |
| Question / metric | Dataset, N and unit | Split / seed / config | Command or verification method | Output path and measured value | Uncertainty / limitation |
|---|---|---|---|---|---|
| Date | Action / counterpart | Receipt or private reference | State | Next action / date |
|---|---|---|---|---|
Peter's teach-back / quiz score: not assessed. Scientific assumptions and deviations: none recorded yet. Budget allocated / spent: not assessed / no spend recorded. Missing evidence and responsible owner: pending inspection.
Do not put API keys, source full texts with restricted rights, client data or invoice personal details in a public version of this register. Keep private evidence references private.
Review status: NOT_REVIEWED. Specification · Evidence
What Peter can explain or reproduce now: not assessed. Quiz / teach-back gaps: not assessed. Measured result and limitations: pending. Best evidence link for a scientist/recruiter/buyer: pending. What failed or changed, and why: pending.
Gate requirement: No standalone gate; check this week's acceptance criteria and next gate dependencies. Gate status: NOT_STARTED. Original target week: See next gate in specs. Actual completion date / forecast: not set. Missing external evidence: pending inspection. Blocks completed / 7: not recorded. Days with commits / 7: not recorded. Sunday build log / optional Wednesday note: not recorded. Founder conversations cumulative: not recorded. Earned evidence level and proof: not assessed. Consecutive lost weeks: not assessed.
Week-specific risk to revisit: Do not call these real plant batches or require a visually favorable result. The historical download site may fail; use an author-linked source and preserve provenance.
Continue / recover / blocked: not decided. Retain as the minimum: the tidy parquet of IndPenSim. Skipped permanently with reason: none recorded. Carryover with owner, dependency and target week: none recorded. Canonical repository paths and versions: pending. Data permissions, split definitions or assumptions to preserve: pending. External action authorization that still applies: not assessed. Next physical action, exact file/function/paragraph: pending. Updates to root PROGRESS / LOG / TODAY completed: ☐
YOUR SPACE