# Programme progress

Status: NOT_STARTED. Start Monday: not set. Current week: 00. Current evidence level: not assessed. No existing achievements were assumed during scaffolding.

## Weekly checklist

- [ ] Week 00: [cockpit and positioning](./weeks/week-00-cockpit-and-positioning/specs.md) — NOT_STARTED
- [ ] Week 01: [fermentation simulator](./weeks/week-01-fermentation-simulator/specs.md) — NOT_STARTED
- [ ] Week 02: [indpensim data and baseline](./weeks/week-02-indpensim-data-and-baseline/specs.md) — NOT_STARTED
- [ ] Week 03: [statistical batch monitoring](./weeks/week-03-statistical-batch-monitoring/specs.md) — NOT_STARTED
- [ ] Week 04: [batchlens first release](./weeks/week-04-batchlens-first-release/specs.md) — NOT_STARTED
- [ ] Week 05: [fermlit corpus and schema](./weeks/week-05-fermlit-corpus-and-schema/specs.md) — NOT_STARTED
- [ ] Week 06: [human gold standard](./weeks/week-06-human-gold-standard/specs.md) — NOT_STARTED
- [ ] Week 07: [measured extraction agent](./weeks/week-07-measured-extraction-agent/specs.md) — NOT_STARTED
- [ ] Week 08: [technical report gate](./weeks/week-08-technical-report-gate/specs.md) — NOT_STARTED
- [ ] Week 09: [fermlit scale up](./weeks/week-09-fermlit-scale-up/specs.md) — NOT_STARTED
- [ ] Week 10: [annotation agreement and analysis](./weeks/week-10-annotation-agreement-and-analysis/specs.md) — NOT_STARTED
- [ ] Week 11: [fermlit dataset engineering](./weeks/week-11-fermlit-dataset-engineering/specs.md) — NOT_STARTED
- [ ] Week 12: [endorsement and hybrid model](./weeks/week-12-endorsement-and-hybrid-model/specs.md) — NOT_STARTED
- [ ] Week 13: [fermlit release and paper outline](./weeks/week-13-fermlit-release-and-paper-outline/specs.md) — NOT_STARTED
- [ ] Week 14: [paper 1 full draft](./weeks/week-14-paper-1-full-draft/specs.md) — NOT_STARTED
- [ ] Week 15: [paper 1 review and revision](./weeks/week-15-paper-1-review-and-revision/specs.md) — NOT_STARTED
- [ ] Week 16: [paper 1 preprint gate](./weeks/week-16-paper-1-preprint-gate/specs.md) — NOT_STARTED
- [ ] Week 17: [paper 2 complete experiments](./weeks/week-17-paper-2-complete-experiments/specs.md) — NOT_STARTED
- [ ] Week 18: [paper 2 full draft](./weeks/week-18-paper-2-full-draft/specs.md) — NOT_STARTED
- [ ] Week 19: [recruiter portfolio and review](./weeks/week-19-recruiter-portfolio-and-review/specs.md) — NOT_STARTED
- [ ] Week 20: [paper 2 gate and halfway review](./weeks/week-20-paper-2-gate-and-halfway-review/specs.md) — NOT_STARTED
- [ ] Week 21: [protein study and partner scope](./weeks/week-21-protein-study-and-partner-scope/specs.md) — NOT_STARTED
- [ ] Week 22: [protein validation and baselines](./weeks/week-22-protein-validation-and-baselines/specs.md) — NOT_STARTED
- [ ] Week 23: [extremophile candidate ranking](./weeks/week-23-extremophile-candidate-ranking/specs.md) — NOT_STARTED
- [ ] Week 24: [coauthor and validation gate](./weeks/week-24-coauthor-and-validation-gate/specs.md) — NOT_STARTED
- [ ] Week 25: [trialkit field module](./weeks/week-25-trialkit-field-module/specs.md) — NOT_STARTED
- [ ] Week 26: [trialkit plate module](./weeks/week-26-trialkit-plate-module/specs.md) — NOT_STARTED
- [ ] Week 27: [loop audit offer and pipeline](./weeks/week-27-loop-audit-offer-and-pipeline/specs.md) — NOT_STARTED
- [ ] Week 28: [first invoice gate](./weeks/week-28-first-invoice-gate/specs.md) — NOT_STARTED
- [ ] Week 29: [audit delivery or sales recovery](./weeks/week-29-audit-delivery-or-sales-recovery/specs.md) — NOT_STARTED
- [ ] Week 30: [audit readout and validation results](./weeks/week-30-audit-readout-and-validation-results/specs.md) — NOT_STARTED
- [ ] Week 31: [paper 3 coauthor draft](./weeks/week-31-paper-3-coauthor-draft/specs.md) — NOT_STARTED
- [ ] Week 32: [paper 3 gate and career refresh](./weeks/week-32-paper-3-gate-and-career-refresh/specs.md) — NOT_STARTED
- [ ] Week 33: [labdocs ingestion and traceability](./weeks/week-33-labdocs-ingestion-and-traceability/specs.md) — NOT_STARTED
- [ ] Week 34: [labdocs retrieval evaluation](./weeks/week-34-labdocs-retrieval-evaluation/specs.md) — NOT_STARTED
- [ ] Week 35: [labdocs release and local benchmark](./weeks/week-35-labdocs-release-and-local-benchmark/specs.md) — NOT_STARTED
- [ ] Week 36: [journal and joss submissions](./weeks/week-36-journal-and-joss-submissions/specs.md) — NOT_STARTED
- [ ] Week 37: [pilot or job process](./weeks/week-37-pilot-or-job-process/specs.md) — NOT_STARTED
- [ ] Week 38: [scientific talk and proof](./weeks/week-38-scientific-talk-and-proof/specs.md) — NOT_STARTED
- [ ] Week 39: [fund portfolio offer](./weeks/week-39-fund-portfolio-offer/specs.md) — NOT_STARTED
- [ ] Week 40: [final retrospective and career decision](./weeks/week-40-final-retrospective-and-career-decision/specs.md) — NOT_STARTED

## Sunday scorecard

| Week | Blocks / 7 | Commit days / 7 | Sunday log | Wednesday note | Founder conversations cumulative | Evidence level / link | Lost weeks in a row | Gate target / actual / forecast |
|---|---|---|---|---|---|---|---|---|

Use [GATES](./GATES.md) for proof requirements. A completed plan/spec is not a completed execution week.

## Original v5 execution checklist snapshot

The original Parts 6 and 7 are preserved below as a reference snapshot. Treat proposed outcomes and example headlines as targets, with the corrections and status rules in DECISIONS.md. The linked weekly checkboxes above are the working completion checklist.

Weeks 0-20, block by block

Format per week: **Goal** · **Tue (Bio)** · **Thu (AI)** · **Build Mon/Wed/Fri** with done-when · **Sun** output · **Only one thing** (the minimum that keeps the plan alive).
G = GitHub, L-Sun = LinkedIn build log, L-Wed = Wednesday note, M = Medium, Z = Zenodo DOI, HF = Hugging Face, X = preprint.

### Week 0 · Cockpit and positioning
- **Goal:** everything exists and is empty, in the right place.
- **Build:** [ ] `cockpit` repo with the five files; paste Part 6 and 7 into `PROGRESS.md`. [ ] `labloop-notes`, `batchlens`, `fermlit` repos with README skeletons. [ ] Local environment (5.3). [ ] LinkedIn headline and About (Part 9.1). [ ] NotebookLM notebooks created.
- **Tue/Thu:** none. Read Part 0 twice.
- **Sun:** L-Sun post 0: "40 weeks from applied-AI engineer to published AI scientist for biotech, in public, at 10 h/week. First: a fermentation in 80 lines." Write the six `TODAY.md` lines for week 1.
- **Only one thing:** the `cockpit` repo with `TODAY.md` filled for Monday.

### Week 1 · A tank in 80 lines
- **Goal:** a fed-batch simulator that streams like a plant.
- **Tue (B1):** Biology 2e ch. 3 + 6.5. Notes.
- **Thu (M1):** 3Blue1Brown linear algebra ch. 1-7. Notes. Last 30 min: founder paper 1 (Michroma or Levya author).
- **Build:** [ ] Mon: `batchlens/sim/monod.py`: ODEs for biomass X, substrate S, product P, dissolved oxygen; batch and fed-batch. Done when a plot shows lag, log, stationary. [ ] Wed: MQTT publisher (`paho-mqtt`) sending one sample per simulated minute to the Debian box; InfluxDB + Grafana dashboard. Done when you see the curve live. [ ] Fri: 20 batches with random noise and one injected fault (feed pump stops); saved as CSV. Done when `make sim` writes 20 files.
- **Sun:** L-Sun: "A fermentation in 80 lines, streamed like a plant" with the Grafana screenshot. L-Wed (Wednesday): "what a blind bioreactor costs" (archetype note).
- **Only one thing:** `monod.py` with the plot.

### Week 2 · One hundred real batches
- **Goal:** IndPenSim loaded, understood, and one golden-batch picture.
- **Tue (B2):** Biology 2e ch. 4, 5.1-5.2, 7.
- **Thu (M2):** 3Blue1Brown calculus ch. 1-4 + neural networks ch. 1-4. Founder paper 2.
- **Build:** [ ] Mon: `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.
- **Sun:** L-Sun with the overlay plot. **M1** (Medium, thesis piece): "Biotech startups don't have an AI problem" (reuse v4 section 1, archetypes with counts, no names).
- **Only one thing:** the tidy parquet of IndPenSim.

### Week 3 · Golden batch, with statistics
- **Goal:** control limits that are statistics, not thresholds.
- **Tue (B3):** Microbiology ch. 9. Draw the growth curve.
- **Thu (M3):** ISLP ch. 2-3. Redo Lab 3 on IndPenSim.
- **Build:** [ ] Mon: Hotelling T² and SPE with limits from the normal batches (NIST ch. 6.5 as reference). Done when limits are computed, not typed. [ ] Wed: `batchlens monitor --batch 87` replays a batch and prints alarms with time stamps. Done when a faulty batch alarms and a normal one does not. [ ] Fri: tests for the two commands; `make report FAKE=1` works on simulator data. Done when CI is green.
- **Sun:** L-Sun: "Golden batch: what 80 normal fermentations look like as one envelope". L-Wed.
- **Only one thing:** T² limits computed.

### Week 4 · L1: public and reproducible
- **Goal:** first public number and first DOI.
- **Tue (B4):** Microbiology ch. 8.1-8.4.
- **Thu (M4):** ISLP ch. 5. Implement batch-wise CV.
- **Build:** [ ] Mon: hours-to-detection on every faulty batch; false-alarm rate on normal batches; one table. Done when the table regenerates with `make report`. [ ] Wed: README with the headline number, `CITATION.cff`, Zenodo integration. Done when the DOI badge renders. [ ] Fri: release `batchlens v0.1`. Send the repo to your Sumble friend for a 30-minute code review.
- **Sun:** L-Sun: "Deviation detected X hours before harvest on N faulty batches, Y% false alarms". **Z1**. Gauge: **L1**, and L2 for the DOI.
- **Only one thing:** the release with the DOI.

### Week 5 · FermLit begins: the corpus
- **Goal:** 500 open-access fermentation papers on disk and a written schema.
- **Tue (B5):** Biology 2e ch. 14-15; Rosalind 1-4.
- **Thu (M5):** ISLP ch. 6.1-6.2, 8. LightGBM soft sensor v0.
- **Build:** [ ] Mon: Prompt P8 with Semantic Scholar: does a fermentation literature dataset already exist? Write `fermlit/RELATED.md` with what you found (this decides "novel" vs "extension"). Done when the file has ≥ 10 verified references. [ ] Wed: Europe PMC query (`"fed-batch" OR "fermentation" AND ("titer" OR "titre") AND OPEN_ACCESS:y`, refine), download full-text XML for 500 papers. Done when 500 XML files and a manifest exist. [ ] Fri: `schema/fermlit.schema.json` v0: organism, strain, product, reactor type, working volume, mode (batch/fed-batch/continuous), medium carbon source, temperature, pH, DO setpoint, feed strategy, duration, final titer (g/L), yield, productivity, scale, plus a provenance sentence per field. Done when three papers annotated by hand against it fit.
- **Sun:** L-Sun: "500 fermentation papers, one schema: what I want the robot to read". L-Wed.
- **Only one thing:** `RELATED.md`. If someone did it already, you must know now.

### Week 6 · The gold set (the most important week of Half 1)
- **Goal:** 50 papers annotated by hand, guidelines written, second annotator recruited.
- **Tue (B6):** Microbiology ch. 12; Rosalind 5-8.
- **Thu (M6):** Murphy ch. 2 or Statistical Rethinking L1-2.
- **Build:** [ ] Mon: `annotate/GUIDELINES.md` with Prompt P7. Annotate 15 papers. Done when 15 gold JSONs with provenance sentences exist. [ ] Wed: annotate 20 more; refine guidelines with every ambiguity you hit. [ ] Fri: annotate 15 more (50 total). Message two people to annotate 30 of them independently (a founder-scientist, a biology student, or a paid postdoc). Done when one has said yes.
- **Sun:** L-Sun: "I read 50 fermentation papers by hand this week. Here is what they never tell you" (first hint of the reporting finding). L-Wed.
- **Only one thing:** 50 gold JSONs.

### Week 7 · The extraction agent, measured
- **Goal:** first per-field precision and recall.
- **Tue (B7):** MIT 7.016 protein lectures; Michaelis-Menten fitted.
- **Thu (M7):** Statistical Rethinking L3-4.
- **Build:** [ ] Mon: `extract/agent.py`: one paper in, schema JSON out with provenance; Claude via API and local Qwen 7B as two backends; `--fake` backend for tests. Done when 5 papers extract. [ ] Wed: `eval/score.py`: per-field exact and fuzzy match against the gold set, precision/recall/F1, confusion by field. Done when the table prints for 50 papers. [ ] Fri: error analysis: the 5 worst fields, why; one round of prompt and schema fixes; re-score. Log both numbers.
- **Sun:** L-Sun: "An LLM read 50 papers; here is where it was wrong" with the per-field table. L-Wed.
- **Only one thing:** the F1 table, whatever it says.

### Week 8 · GATE 8: technical report and L2
- **Goal:** the first artifact with scientific shape.
- **Tue (B8):** review + 2-page summary; Prompt P3 quiz.
- **Thu (M8):** Karpathy micrograd; rewrite from memory Saturday.
- **Build:** [ ] Mon: soft sensor (titer from online variables), batch-wise CV, error at 25/50/75% of batch time; LightGBM vs PLS. Done when the curve regenerates. [ ] Wed: **Technical report 1** (8-10 pages, Quarto): batchlens on IndPenSim: golden batch, deviation detection, soft sensor; methods reproducible; "where it fails". Prompt P9 for the skeleton, P10 for review. [ ] Fri: release `batchlens v0.2` + report PDF on Zenodo. Send the report to 5 archetype-A founders with the Track F outreach line: "would you tell me in 30 minutes whether this resembles your tank?"
- **Sun:** **M2** deep dive: "What 100 open fermentation batches taught me about early deviation detection". **Z2**. L-Sun. Gauge check: **L2**.
- **Gate 8 passes when:** report on Zenodo with DOI, 5 founders messaged, F1 table public.
- **Only one thing:** the report on Zenodo.

### Week 9 · FermLit at scale
- **Goal:** 2,000 papers extracted with the measured pipeline.
- **Tue (B9):** NPTEL bioreactors 1-3; balances in a notebook.
- **Thu (M9):** Karpathy makemore part 1; bigram on organism names for fun.
- **Build:** [ ] Mon: corpus to 2,000 papers (same query, more years, plus bioRxiv API for preprints). [ ] Wed: batch extraction with the cheapest backend that meets the F1 floor you set in week 7 (cost table with the v3 telemetry schema). Done when 2,000 JSONs exist. [ ] Fri: completeness dashboard: per field, % of papers that report it. This is the seed of the reporting finding.
- **Sun:** L-Sun: "2,000 fermentation papers in one table. X% do not report pH. Y% do not report volume." L-Wed.
- **Only one thing:** the completeness table.

### Week 10 · Inter-annotator agreement and the first real analysis
- **Goal:** kappa reported; first descriptive science.
- **Tue (B10):** NPTEL 4-6; yields on IndPenSim.
- **Thu (M10):** GPML ch. 1-2; GP soft sensor with bands.
- **Build:** [ ] Mon: compute Cohen's kappa per field between you and the second annotator; adjudicate disagreements; freeze gold v1. Done when kappa is in `eval/README.md`. [ ] Wed: descriptive analysis notebook: titer by organism and product, productivity vs scale, reporting completeness by year and journal. [ ] Fri: figures 1-4 of Paper 1 drafted (Plotly to static). Done when `make figs` regenerates them.
- **Sun:** L-Sun: "Two humans, 30 papers, kappa = X: how much can you trust a dataset built by an LLM?" L-Wed.
- **Only one thing:** kappa.

### Week 11 · Dataset engineering and the reporting finding
- **Goal:** FermLit v0.5 as a proper dataset.
- **Tue (B11):** NPTEL kLa and scale-up; kLa estimate.
- **Thu (M11):** Frazier + BoTorch; BO on the simulator feed profile.
- **Build:** [ ] Mon: units normalization (g/L, mg/L, %), organism name normalization (NCBI taxonomy IDs via API), dedup. [ ] Wed: the reporting-completeness analysis as a formal result: which fields are missing, how that changed over 20 years, whether journals differ (with multiple-testing correction from B14 later). [ ] Fri: dataset card draft (HF), license (CC BY 4.0 for the extracted table; papers not redistributed), `dataset/` export.
- **Sun:** L-Sun: "The fermentation literature has a reporting problem, in numbers". L-Wed.
- **Only one thing:** normalized dataset export.

### Week 12 · Endorsement route opens; hybrid model v0
- **Goal:** three routes to an arXiv endorser started; first hybrid model.
- **Tue (B12):** FDA PAT + ICH Q8; glossary.
- **Thu (M12):** Brunton ch. 7; SINDy recovers Monod from simulator data.
- **Build:** [ ] Mon: Part 9.5 routes: (1) message the two most-engaged founders from week 8 with the FermLit completeness figure and ask whether they would co-author or endorse; (2) email two authors you cite heavily (Prompt P13); (3) list three local academics (UBA, UNSAM, Leloir) who publish on arXiv q-bio. Done when three messages are sent. [ ] Wed: `batchlens/hybrid/`: Monod ODE with parameters fitted per batch + GBM on the residual; compare to pure GBM on 10 batches. [ ] Fri: learning-curve harness: train on 5, 10, 20, 50 batches, test on held-out normal and faulty batches, 5 seeds. Done when the curve plots.
- **Sun:** L-Sun: "Does knowing the biology help the model? Hybrid vs pure ML at 5, 10, 20, 50 batches (first look)". L-Wed.
- **Only one thing:** the three endorsement messages.

### Week 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined
- **Goal:** dataset on Hugging Face and Zenodo; Paper 1 skeleton with all figures.
- **Tue (B13):** MSMB ch. 1-2.
- **Thu (M13):** von Stosch review + Neural ODE abstract.
- **Build:** [ ] Mon: HF dataset upload with card, Zenodo DOI, `fermlit v0.5` release. [ ] Wed: Paper 1 skeleton with Prompt P9: title, abstract with numbers, 6 figures placed, methods bullet-pointed. [ ] Fri: Prompt P10 (reviewer 2) on the skeleton; list of every claim without evidence; plan the fixes.
- **Sun:** **M3** deep dive: "FermLit: 2,000 fermentation papers, one table, and what is missing from them". **Z3**, **HF**. L-Sun. Gauge: L2 solid, L3 in sight.
- **Gate 13 passes when:** dataset public with DOI and card; Paper 1 skeleton has every figure; at least one endorsement conversation alive.
- **Only one thing:** the HF dataset.

### Week 14 · Write Paper 1
- **Goal:** full draft.
- **Tue (B14):** MSMB ch. 6; correction applied to the journal comparison.
- **Thu (M14):** CS336 L12 + CS224N judge lecture; calibrated judge for fuzzy fields (does "Yarrowia lipolytica Po1f" match "Y. lipolytica"?).
- **Build:** [ ] Mon: Introduction and Related work (from `RELATED.md`, every citation verified via Semantic Scholar). [ ] Wed: Methods (corpus, schema, guidelines, agents, evaluation, kappa) and Data availability. [ ] Fri: Results (completeness finding, per-field F1, descriptive tables) and Limitations (honest: extraction errors, OA bias, English-only).
- **Sun:** L-Sun: "Writing my first paper at 25 years of career: what a methods section really is". L-Wed.
- **Only one thing:** Methods section.

### Week 15 · Review, revise, human read
- **Goal:** a draft a scientist has read.
- **Tue (B15):** three papers with P11, IMRaD noted.
- **Thu (M15):** Jurafsky & Martin IE chapter; kappa written into Methods.
- **Build:** [ ] Mon: Prompt P10 twice; fix every [VERIFY]. [ ] Wed: send to one human scientist (co-author candidate, endorser, or paid postdoc, USD ~100 for 2 hours). [ ] Fri: figures final; `make paper` builds the PDF from the repo.
- **Sun:** L-Sun: "Reviewer 2 is an LLM and a postdoc; both found things". L-Wed.
- **Only one thing:** human review requested.

### Week 16 · GATE 16: Paper 1 on bioRxiv (L3)
- **Goal:** submitted.
- **Tue (B16):** ESM-2 paper + MIT 6.874 protein lecture; ESM-2 running.
- **Thu (M16):** conformal prediction sections 1-2; intervals on the soft sensor.
- **Build:** [ ] Mon: incorporate human review. [ ] Wed: bioRxiv submission (category: Bioengineering or Systems Biology), code and data DOIs in the paper. [ ] Fri: LinkedIn article version of the paper for non-scientists; send the preprint to the 10 founders you have talked to and the 3 scientific-data companies you admire (no ask, just the link).
- **Sun:** L-Sun: the preprint. **X1**. Gauge: **L3**.
- **Gate 16 passes when:** bioRxiv shows the DOI.
- **Only one thing:** the submission.

### Week 17 · Paper 2 experiments, complete
- **Goal:** every number in Paper 2 exists.
- **Tue (B17):** FLIP + Meltome papers; Meltome split loaded.
- **Thu (M17):** ESM-2 embeddings + ridge head on Meltome; baseline number.
- **Build:** [ ] Mon: full learning-curve experiment (mechanistic, pure ML, hybrid × 5/10/20/50 batches × 5 seeds), conformal intervals, coverage. [ ] Wed: transfer to faulty batches; hours-to-detection with each model. [ ] Fri: `paper-2` repo with `make figs`; `batchlens v0.3` + **Z4**.
- **Sun:** L-Sun: "Hybrid wins below 20 batches, loses above 50: the full curve". L-Wed.
- **Only one thing:** the learning curves with seeds.

### Week 18 · Write Paper 2
- **Goal:** full draft.
- **Tue (B18):** two extremophile founder papers; outreach lines.
- **Thu (M18):** Peyton Jones talk + NeurIPS checklist; rewrite.
- **Build:** [ ] Mon: Intro + Related work (hybrid modeling, soft sensors, IndPenSim benchmarks; all verified). [ ] Wed: Methods + Results. [ ] Fri: Limitations (simulated data, one process, no real plant), Reproducibility statement.
- **Sun:** **M4** deep dive: "When does biology help the model? A data-scarcity study on 100 open batches". L-Sun.
- **Only one thing:** Results section.

### Week 19 · Endorsement closed; review; site
- **Goal:** endorser confirmed; draft reviewed; one-screen site.
- **Tue (B19):** scanpy PBMC tutorial.
- **Thu (M19):** effect sizes and intervals across both papers.
- **Build:** [ ] Mon: close the endorsement (Part 9.5); if none yet, bioRxiv fallback prepared. [ ] Wed: Prompt P10 twice + human read (same reviewer as Paper 1, or the endorser). [ ] Fri: one-screen personal site: two preprints, one instrument, one dataset, the gauge level, contact.
- **Sun:** L-Sun. L-Wed. Employee track: 5 applications to scientific-data or bioprocess-AI companies with the two preprints as the cover letter.
- **Only one thing:** the endorser's yes.

### Week 20 · GATE 20: Paper 2 on arXiv, endorsed (L4-endorsed)
- **Goal:** submitted, endorsed; talk proposed; Half 2 planned.
- **Tue (B20):** mock lab meeting (Prompt P3).
- **Thu (M20):** mock ML interview (Prompt P3).
- **Build:** [ ] Mon: arXiv submission (cs.LG, cross-list q-bio.QM) with endorsement; bioRxiv as well if the endorser is late. [ ] Wed: talk proposal to a biotech event in Buenos Aires or Rosario, or an online LATAM one: "Two thousand fermentation papers and a hundred open batches: what the data says". [ ] Fri: public retro (what the gauge says, what slipped); Half 2 `PROGRESS.md` lines written.
- **Sun:** L-Sun retro. **X2**. Gauge: **L4 (endorsed)**.
- **Gate 20 passes when:** arXiv ID exists, or bioRxiv ID exists with an endorsement conversation dated.
- **Only one thing:** the submission.

---

## PART 7 · Weeks 21-40, week by week (Half 2: depth, co-author, money)

Same weekly shape. Study tracks become lighter (one block instead of two) because the build blocks now carry Paper 3 and the instruments. Details for each week can be expanded later with Prompt P15; the gates and outputs here are fixed.

| Week | Goal | Study (Tue) | Build (Mon/Wed/Fri) | Output |
|---|---|---|---|---|
| 21 | Paper 3 scoped with a partner | Meltome and FLIP deep read; extremophile enzyme families of the 3 candidate partners (Puna Bio, Antarka, APEXzymes) | `enzymelens` repo; ESM-2 embeddings for the full Meltome split cached on disk (overnight on the 3050); ridge/GBM/MLP heads; baseline table | Partner call booked with the FermLit + batchlens preprints as the calling card |
| 22 | Baselines beaten honestly | Brady Neal causal inference lecture 1 (for confounders in Paper 3's analysis) | Cross-validation by protein family (no leakage); conformal intervals; compare to FLIP published baselines | L-Sun with the table |
| 23 | Extremophile focus | Partner's organisms and enzyme classes | Filter and enrich: sequences from UniProt for the partner's enzyme class; predict thermostability; ranked candidate list with uncertainty | Candidate list shared with the partner under a simple collaboration note |
| 24 | Co-authorship agreed | How wet-lab validation works (partner explains; you take notes) | Validation plan: which 5-10 candidates the partner can express and test in their lab; what "success" is, pre-registered in the repo | Written co-author agreement (one paragraph, emailed) |
| 25 | Instrument 2 trialkit (field module) | NIST ch. 5 (DoE); statsmodels MixedLM | `trialkit/ingest` and `report` (v4 weeks 9-10 content) | `trialkit v0.1`, Z5 |
| 26 | Instrument 2 (plate module) | Assay statistics (4PL, growth curves, Z′) | `trialkit/plate` (v4 week 11) | L-Sun |
| 27 | Loop Audit offer, built on papers | v4 Part 4 offers, re-read | Offer one-pager rewritten with the two preprints as proof; sent to 10 (5 founders who engaged, 3 established companies, 2 funds) | 3 calls booked |
| 28 | GATE 28: first Loop Audit sold | none (selling week) | Audit scoped and half paid; Paper 3 wet-lab results start arriving | **First invoice** (any amount). If not: week 29 is a second selling week |
| 29 | Audit delivery 1 | Client's domain reading | Loop map, data inventory, cycle-time and readiness numbers, one prototype on their sample | Client readout |
| 30 | Audit delivery 2; Paper 3 results | Statistics for validation results (small n) | Analysis of the partner's validation; figures | Anonymized case study drafted |
| 31 | Write Paper 3 | Research craft refresher | Draft with co-author; Prompt P10; co-author's lab reads it | Draft to co-author |
| 32 | GATE 32: Paper 3 preprint (L4 co-authored) | none | bioRxiv submission with co-author; second audit or pilot proposal sent | **X3**. Case study published with client permission |
| 33 | Instrument 3 labdocs, part 1 | 21 CFR Part 11 + ALCOA+ (v4 catalog 15) | eLabFTW on the Debian box; local VLM extraction; audit log (v4 week 14) | L-Sun |
| 34 | labdocs, part 2 | Retrieval evaluation | "Ask the lab" with citations; 60 labeled Q&A; judge agreement (v4 week 15) | L-Sun |
| 35 | labdocs, part 3 | Privacy basics | Deviation drafting + on-prem benchmark table (v4 weeks 16-17) | `labdocs v0.1`, Z6, M5 deep dive |
| 36 | GATE 36: journal + JOSS | Journal author guides | Paper 1 to Scientific Data or a bioprocess journal; Paper 2 to Computers & Chemical Engineering or Biotechnology and Bioengineering (pick one each); JOSS submission for batchlens | Submissions logged |
| 37 | Pilot delivery or job process | Client or interview prep | Pilot (6-8 weeks) running, or interviews at scientific-data companies with three preprints | Weekly client readout |
| 38 | Talk delivered | Talk rehearsal (Prompt P3) | 20-minute talk at the event accepted in week 20 | Video posted |
| 39 | Fund package | none | Portfolio data-readiness package proposed to one fund (GridX first) | Proposal sent |
| 40 | GATE 40: retro and decision | none | Gauge level, income to date, pipeline, offers. Decide: consultant with retainers, or employee, or both | Public retro |

**Gate 40 passes when:** three preprints (one co-authored), two journal submissions, one JOSS submission, three instruments with DOIs, one talk delivered, at least one paid engagement delivered, and a decision written down.

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