# Week 14 — paper 1 full draft [**Full learning notebook: explanations, step-by-step challenges, stashes and evidence**](./learning-notebook.md) · [NotebookLM export](./notebooklm.txt) Status: NOT_STARTED. Calendar dates: not assigned. Owner: Peter Ciancaglini. Planning authority: v5 Part 6 with retained v4 details. Deeper walkthrough: [v6 · Week 14 · Write Paper 1](../../../LABLOOP-Master-Plan-v6.md#week-14--write-paper-1). Active project/repository: fermlit. [Programme](../../README.md) · [Model instructions](../../specs.md) · [Decisions](../../DECISIONS.md) · [Resources](../../SOURCES.md) · [**v6 walkthrough**](../../../LABLOOP-Master-Plan-v6.md#week-14--write-paper-1) · [Previous week review](../week-13-fermlit-release-and-paper-outline/review.md) · [Next week](../week-15-paper-1-review-and-revision/specs.md) ## Outcome and relevance 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. - Scientific/build priority: Write introduction and related work from verified sources, stating novelty or extension accurately. - Public/profile priority: Draft a methods-section learning note and a plain-language explanation of one supported result. - Career/relationship/commercial priority: Schedule the human scientific review now, with scope and return date before week 16. ## Deeper walkthrough (v6) Read [v6 · Week 14 · Write Paper 1](../../../LABLOOP-Master-Plan-v6.md#week-14--write-paper-1) 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](../../../LABLOOP-Master-Plan-v6.md#prologue-3--the-resource-rules-so-you-never-waste-an-evening-on-a-bad-source), [NotebookLM protocol](../../../LABLOOP-Master-Plan-v6.md#prologue-4--the-notebooklm-protocol-one-notebook-per-week-zero-decisions), [chapter anatomy](../../../LABLOOP-Master-Plan-v6.md#prologue-5--how-to-read-a-chapter-the-anatomy-identical-for-all-41). v6 adds depth only; it does not change a goal, gate, output or the 600-minute cap, so this specification still governs execution. **Act IV · Threads: B, M, FL · Next gate: 16** **Where this week sits.** - ← **From:** week 13 skeleton and reviewer list; weeks 5-11 artifacts. - → **Feeds:** week 15 (review and human read), week 16 (submission), week 31 (Paper 3 uses the same writing process), week 36 (journal version). - ⟳ **Returns in:** every future paper: your Methods style becomes your signature. **Goals.** - 🎯 **This week:** full draft of Paper 1 (Intro, Related work, Methods, Data availability, Results, Limitations); multiple-testing correction applied; calibrated judge for fuzzy fields. - 🏁 **Next milestone:** Gate 16 (bioRxiv DOI). - 🌟 **Final:** L3 preprinted, the rung that makes founders answer. **Mentor check.** *"My Methods section lets a stranger rebuild FermLit, and I can explain why I corrected for multiple testing."* ## Required inputs and dependency check - [Week 13](../week-13-fermlit-release-and-paper-outline/specs.md): inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins. - Read [commitment](./commitment.md), [evidence](./evidence.md), [review](./review.md) and the current root TODAY/PROGRESS/QUESTIONS files. - Read this week's chapter, [v6 · Week 14 · Write Paper 1](../../../LABLOOP-Master-Plan-v6.md#week-14--write-paper-1), then the standing sections: [Part 0 · how to use the document](../../../LABLOOP-Master-Plan-v6.md#part-0--how-to-use-this-document-read-this-every-monday-for-the-first-month), [Part 3 · the scientific thesis](../../../LABLOOP-Master-Plan-v6.md#part-3--the-scientific-thesis-explained-twice-like-a-kid-then-like-a-reviewer), [Part 4 · curriculum](../../../LABLOOP-Master-Plan-v6.md#part-4--curriculum-from-zero-four-tracks-all-free-exact-units), [Part 8 · the prompt pack](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets) and [Part 9 · branding and endorsement](../../../LABLOOP-Master-Plan-v6.md#part-9--branding-connection-ladder-endorsement). The same sections exist in the [v5 master](../../../LABLOOP-Master-Plan-v5.md), which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from [v4](../../../AI-Upskilling-Plan-Biotech-v4.md). - Inspect the actual canonical repository state, available data, existing figures and required human/external inputs. Never assume a previous week succeeded from its folder name. - Verify current resource links, versions, dataset rights and any live company/venue information before relying on them. Use [source catalog](../../SOURCES.md); explicitly record inaccessible resources. ## Seven-day plan: 600 minutes maximum 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. | Day | Budget | Work and stopping condition | |---|---:|---| | Monday | 90 min | Write introduction and related work from verified sources, stating novelty or extension accurately. Stop when: Each contribution corresponds to an implemented method or measured result. | | Tuesday | 90 min | MSMB ch. 6 (testing, multiple testing) Produce: Multiple-testing correction applied to a FermLit comparison | | Wednesday | 90 min | Write reproducible corpus, schema, annotation, extraction and evaluation methods with availability statement. Stop when: A reader can identify data versions, splits, prompts, annotators and scoring rules. Reserve the last 10 minutes for the optional Wednesday note. | | Thursday | 90 min | Stanford CS336 lecture 12 (evaluation) — cs336.stanford.edu; CS224N benchmarking lecture (judge biases) Select material/exercise that fits 60 minutes; use the last 30 for the founder paper. | | Friday | 90 min | Write results and limitations, apply the planned multiple-testing correction and evaluate any fuzzy-field judge against humans. Stop when: Effect sizes and denominators accompany comparisons; judge output is not ground truth. | | Saturday | 90 min | Resolve the earliest critical spillover or dependency. Prepare any long-form publication draft from existing figures here if needed. Sandbox only after commitments are met. | | Sunday | 60 min | 20 min build-log draft/publication when authorized; 5 min evidence/checklist; 20 min source-grounded gap review; 15 min next week's six physical actions. | The source lists more material than necessarily fits. Select exact excerpts for the learning objective and park the remainder; no full-course completion requirement. ## Learning specification ### Biology/domain unit Source unit: B14 · Statistics for biologists II Material: MSMB ch. 6 (testing, multiple testing) Produce: Multiple-testing correction applied to a FermLit comparison Understanding check: You can defend an effect in Paper 1 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. ### AI/scientific-method unit Source unit: M14 · Evaluation and judges Material: Stanford CS336 lecture 12 (evaluation) — cs336.stanford.edu; CS224N benchmarking lecture (judge biases) Produce: Calibrated judge for FermLit fields Understanding check: You can explain judge-human agreement Use the [prompt pack](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets): 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. ### Founder/scientist paper Select one verified founder/scientific-lead paper relevant to this week's domain. Use [P11](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets); 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. ## Artifact contracts 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. | Artifact | Required content / acceptance | Primary responsibility | |---|---|---| | `paper-1-introduction.md` | Write introduction and related work from verified sources, stating novelty or extension accurately. Acceptance: Each contribution corresponds to an implemented method or measured result. | Model assists; Peter checks and owns the outcome | | `paper-1-methods.md` | Write reproducible corpus, schema, annotation, extraction and evaluation methods with availability statement. Acceptance: A reader can identify data versions, splits, prompts, annotators and scoring rules. | Model assists; Peter checks and owns the outcome | | `paper-1-results.md` | Write results and limitations, apply the planned multiple-testing correction and evaluate any fuzzy-field judge against humans. Acceptance: Effect sizes and denominators accompany comparisons; judge output is not ground truth. | Model assists; Peter checks and owns the outcome | | `study-notes.md` | Selected exact free resources; bounded lesson/exercise; separate solution; quiz and grading rubric; Peter's answers and gaps when executed | Model prepares; Peter learns | | `founder-paper.md` | Verified source and P11 digest; authentic question and connection sentence; access limitations | Model assists; Peter checks | | `branding-pack.md` | Wednesday note, Sunday build log, X adaptation, figure/caption/alt text and the week's special asset; each claim linked to real proof | Model drafts; Peter owns voice/public claims | | `opportunity-actions.md` | Qualified target/role, source/date, ladder stage, next action, message/interview/proposal draft and actual status | Model prepares; Peter owns external relationships | | `evidence.md` | Actual paths/URLs, versions, checks/metrics, preparation versus execution state and external receipts when applicable | Updated after each deliverable | | `review.md` | Checklist, learning assessment, gate status, shortfalls, next actions and carryover | Peter and reviewing model | 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. ## Branding and opportunity execution brief Branding: Draft a methods-section learning note and a plain-language explanation of one supported result. Opportunity action: Schedule the human scientific review now, with scope and return date before week 16. Use [career asset contracts](../../CAREER-ASSETS.md). 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](../../../GridX%20Startups.csv) 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. ## Quality risks and week-specific constraints Do not use an LLM judge to erase strain-level mistakes or support a reporting-completeness claim without manual validation. Unsupported hypotheses stay in limitations or future work. 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. ## Completion and gate review This is an enabling week. Its deliverables feed the next scheduled gate: 16. Complete the acceptance checklist below; do not promote reputation from a draft. - [ ] Monday artifact satisfies: Each contribution corresponds to an implemented method or measured result. - [ ] Wednesday artifact satisfies: A reader can identify data versions, splits, prompts, annotators and scoring rules. - [ ] Friday artifact satisfies: Effect sizes and denominators accompany comparisons; judge output is not ground truth. - [ ] Study pack is prepared; Peter's actual learning/quiz result is recorded separately. - [ ] Branding and opportunity drafts use supported claims and the correct external-action state. - [ ] Reproduction or document checks are recorded with file/version references. - [ ] This week's special gate, if any, has real evidence or remains explicitly pending. - [ ] Review, root progress/log and the next physical action are updated. ## Minimum viable week and recovery Source-preserving minimum: Methods section. Operational first step if stalled: open `paper-1-introduction.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](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets): 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. ## Handoff to the next model 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. ## Ready-to-copy model prompt ```text Prepare Week 14 of this LABLOOP execution plan. Read execution-plan/specs.md, execution-plan/DECISIONS.md, execution-plan/GATES.md and execution-plan/weeks/week-14-paper-1-full-draft/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 14 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. ``` ## Preserved original v5 weekly brief v6 reproduces this brief unchanged inside [v6 · Week 14 · Write Paper 1](../../../LABLOOP-Master-Plan-v6.md#week-14--write-paper-1). The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md. ### 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.