Week 31 — paper 3 coauthor draft

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 methods from the versioned protein-study protocol, splits, embeddings and any partner assay protocol.
• Public/profile priority: Prepare a writing-process note and an evidence-backed protein-ML portfolio bullet.
• Career/relationship/commercial priority: Update qualified hiring contacts on concrete work; prepare co-author review requests and close audit acceptance issues.

Read v6 · Week 31 · Write Paper 3 before Monday. It expands this week's one-row v5 brief into daily build steps 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.

Act VI · Threads: EL, R · Next gate: 32

Where this week sits. - ← From: weeks 21-30 (model, candidates, validation); weeks 14-18 writing craft. - → Feeds: week 32 (preprint), week 36 (journal choice), week 38 (talk), Part 9 headline ("co-author with [lab]"). - ⟳ Returns in: the relationship: co-authors refer clients, students and future papers.

Goals. - 🎯 This week: Paper 3 draft with co-author comments incorporated; P10 run; co-author's lab has read it. - 🏁 Next milestone: Gate 32. - 🌟 Final: L4 co-authored.

The plan (from v5 Part 7, expanded; gate and output unchanged).

v5 row: 31 | Write Paper 3 | Research craft refresher | Draft with co-author; Prompt P10; co-author's lab reads it | Draft to co-author - Goal: a draft both authors are proud of. - Tue (study): research craft refresher (Gopen & Swan re-read; Writing in the Sciences module on discussion sections). - Build: [ ] Mon: skeleton (P9) with the partner's section preferences; Methods (computational) by you, Methods (wet lab) by the partner. [ ] Wed: Results and Discussion draft; P10 twice. [ ] Fri: draft to co-author; CRediT statement; data and code availability agreed. - Sun: no public post about unpublished results. - Only one thing: draft sent to the co-author.

Mentor check. "A biologist and I wrote the same paper, and both of us would defend every sentence."

• Week 22: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 23: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 24: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 30: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Read commitment, evidence, review and the current root TODAY/PROGRESS/QUESTIONS files.
• Read this week's chapter, v6 · Week 31 · Write Paper 3, then the standing sections: Part 0 · how to use the document, Part 3 · the scientific thesis, Part 4 · curriculum, Part 8 · the prompt pack and Part 9 · branding and endorsement. The same sections exist in the v5 master, which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from v4.
• 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; explicitly record inaccessible resources.

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.

Half 2: Tuesday is the formal study block unless this is a selling/submission/decision week. Thursday supports applied review, partner work or the market task; do not add another full course.

Biology/domain unit

Material: Review the research-writing checklist and one closely related protein study's methods/limitations.

Produce: One concise applied note, a worked decision/example and unresolved questions.

Understanding check: The note directly supports this week's experiment, collaboration, delivery or career action.

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

Material: Work through model/human review issues and co-author questions; retain 30 minutes for a directly relevant paper.

Produce: One concise applied note, a worked decision/example and unresolved questions.

Understanding check: The note directly supports this week's experiment, collaboration, delivery or career action.

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.

Founder/scientist paper

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.

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.

Branding: Prepare a writing-process note and an evidence-backed protein-ML portfolio bullet.

Opportunity action: Update qualified hiring contacts on concrete work; prepare co-author review requests and close audit acceptance issues.

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.

Without a contributing scientist, prepare a computational manuscript and disclose the missed co-authorship gate. Models cannot supply human authorship or approval.

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.

This is an enabling week. Its deliverables feed the next scheduled gate: 32. Complete the acceptance checklist below; do not promote reputation from a draft.

• Monday artifact satisfies: Produce Paper 3 methods/results draft from actual evidence and prepare the co-author review request.
• Wednesday artifact satisfies: No computational candidate is described as wet-lab validated without evidence.
• Friday artifact satisfies: Review requests and returned author decisions are separately tracked.
• 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.

Expanded minimum derived from the source goal: Produce Paper 3 methods/results draft from actual evidence and prepare the co-author review request.

Operational first step if stalled: open paper-3-methods-draft.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.

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.

Prepare Week 31 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-31-paper-3-coauthor-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 31 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.

v6 expands this row into a full brief, with the gate and output unchanged, inside v6 · Week 31 · Write Paper 3. The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.