execution-plan/NOTEBOOKS.md · UPDATED 2026-10-01

LABLOOP — full weekly learning notebooks

5 parts1,373 words

There is one full notebook for every week: Week 00 setup plus Weeks 01–40. Each lives beside the original brief, commitment, evidence and review. Existing study notes and tracked achievements remain in place.

Start with your current week below, or use Open learning notebook on its cockpit page. Each notebook explains the week in plain language, connects the foundations to the milestone, gives numbered challenge steps, links the resource stash, includes worked examples and an exercise/answer key, and shows how to retain research evidence. The explanations assume dormant mathematics/science foundations while respecting your systems, software and AI experience.

01

01

Export to NotebookLM

  1. Download all 41 weekly text files as a ZIP and extract it, or download one week from the table below.
  2. Create a separate notebook named LABLOOP-WNN · week focus and upload its LABLOOP-WNN.txt. The same text is available as notebooklm.txt in the weekly folder. You can also upload learning-notebook.md or paste its contents. Upload one version, not duplicate copies.
  3. Add the selected external reading pages or permitted PDFs separately. Links in a source do not import all their destination content; local cockpit links work only with your app running. Google’s source-import guidance documents supported source types and import limitations.
  4. Use Section 10 of that week’s notebook for its specific diagram brief and copy-ready prompts for a concept map, visual lesson/slides, audio/video script, flashcards and research review. Use available Studio features or request the equivalent text outline in chat.
  5. Add your actual notes and results as separate sources when you execute. Check generated explanations and visuals against sources, especially units, assumptions and planned versus achieved outcomes.

Each notebook is a reference of roughly 5,000–6,000 words. Read it in sections during the existing 600-minute week; the extra detail does not add compulsory hours. Preparation is complete, but learning, experiments, publications and external events still require their own actual evidence.

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02

02

How stashes and the original plan fit

The cockpit now has 41 resource stashes named LABLOOP-W00 Notebook through LABLOOP-W40 Notebook, containing that week’s existing resource cards. Core/run/deeper labels remain visible. Existing completed cards, wins, focus history and other stashes are preserved. A saved resource is not a completed lesson. Sources with only search locators remain marked for resolution, and the source-check log records targeted checks rather than claiming universal link verification.

The original weekly specifications and gate requirements still govern acceptance. Notebooks explain the work and its scientific limits; they do not rewrite milestones or fill evidence registers with invented results. Each challenge names the original artifact, its acceptance condition and what proof to retain.

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03

03

How the essentials become research milestones

Essential First practical use Where it returns Evidence you should be able to explain
Units and ratios W01 states and rates; W02 data columns W11 normalization; W25–26 experiment reports Why two values can or cannot be compared or converted
Derivatives and integrals W01 changing tank states; W02 calculus refresher W08 gradients; W09 balances; W12 hybrid model; Paper 2 How rates accumulate into a trajectory and why the units balance
Vectors and matrices W01 measurement vectors; W02 PCA W03 monitoring; W21 protein embeddings What each row/column means and what the transformation does
Probability and uncertainty W03 alarms; W04 release metrics; W06 Bayesian update W10 agreement; W16 calibration; W22 protein validation A denominator, an interval’s meaning, and when its assumptions fail
Independent experimental units W02 batch splits; W06 human reference labels W17 comparisons; W22 family splits; W25–26 replicates Why extra rows do not automatically create more independent evidence
Data provenance and measurement W05 paper/experiment schema Paper 1; W23 candidates; W33–35 document retrieval How a claim traces to an exact source/version and verification
Reproducible software W00 environment; W04 release All three instruments; W36 software submission A command, inputs, configuration, result and known failure
Scientific communication W08 report W16/20/32 preprints; W38 talk; W40 profile A question, method, measured result and appropriately limited conclusion

The early concepts are tools you reuse. You do not need to relearn an entire university curriculum before beginning; repair the concept needed for the current artifact, apply it, and revisit it when the next milestone makes it useful again.

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04

04

The full programme

Week Notebook Text upload Resource stash
00 cockpit and positioning TXT W00 stash
01 fermentation simulator TXT W01 stash
02 indpensim data and baseline TXT W02 stash
03 statistical batch monitoring TXT W03 stash
04 batchlens first release TXT W04 stash
05 fermlit corpus and schema TXT W05 stash
06 human gold standard TXT W06 stash
07 measured extraction agent TXT W07 stash
08 technical report gate TXT W08 stash
09 fermlit scale up TXT W09 stash
10 annotation agreement and analysis TXT W10 stash
11 fermlit dataset engineering TXT W11 stash
12 endorsement and hybrid model TXT W12 stash
13 fermlit release and paper outline TXT W13 stash
14 paper 1 full draft TXT W14 stash
15 paper 1 review and revision TXT W15 stash
16 paper 1 preprint gate TXT W16 stash
17 paper 2 complete experiments TXT W17 stash
18 paper 2 full draft TXT W18 stash
19 recruiter portfolio and review TXT W19 stash
20 paper 2 gate and halfway review TXT W20 stash
21 protein study and partner scope TXT W21 stash
22 protein validation and baselines TXT W22 stash
23 extremophile candidate ranking TXT W23 stash
24 coauthor and validation gate TXT W24 stash
25 trialkit field module TXT W25 stash
26 trialkit plate module TXT W26 stash
27 loop audit offer and pipeline TXT W27 stash
28 first invoice gate TXT W28 stash
29 audit delivery or sales recovery TXT W29 stash
30 audit readout and validation results TXT W30 stash
31 paper 3 coauthor draft TXT W31 stash
32 paper 3 gate and career refresh TXT W32 stash
33 labdocs ingestion and traceability TXT W33 stash
34 labdocs retrieval evaluation TXT W34 stash
35 labdocs release and local benchmark TXT W35 stash
36 journal and joss submissions TXT W36 stash
37 pilot or job process TXT W37 stash
38 scientific talk and proof TXT W38 stash
39 fund portfolio offer TXT W39 stash
40 final retrospective and career decision TXT W40 stash
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05

05

Refresh exports after editing a notebook

The authored learning-notebook.md is the source of truth. TXT files and the ZIP are generated copies. After editing a notebook, run from the project root:

python3 execution-plan/notebooks/export_notebooks.py
python3 execution-plan/notebooks/export_notebooks.py --check

The exporter uses only Python’s standard library, verifies that all 41 weeks exist, writes a SHA-256 manifest and checks exact TXT/ZIP contents. It does not edit the notebooks, stashes, progress or evidence. Re-upload an updated source to your study notebook as needed; downloaded local exports do not automatically refresh themselves.

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