Programme progress

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

Use GATES for proof requirements. A completed plan/spec is not a completed execution week.

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.

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.

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.