Protein study and partner scope

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 Paper 3 question, target quantity, label context, dataset/split choice and available partner capabilities; create the repository plan.
• Public/profile priority: Draft a protein-ML transition post linking the new question to earlier evaluation work.
• Career/relationship/commercial priority: Prepare a call with one of three researched partner candidates and R&D discovery requests to established companies; continue live applications.

Read v6 · Week 21 · Paper 3 scoped with a partner 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 V · Threads: B, EL, R · Next gate: 24

Where this week sits. - ← From: week 16-17 (ESM-2, Meltome baseline), week 18 (extremophile founder digests), Part 9.3 ladder (rungs 1-4 with those founders). - → Feeds: week 22 (honest baselines), week 23 (partner-specific candidates), week 24 (co-author agreement), weeks 30-32 (Paper 3). - ⟳ Returns in: Paper 3 Introduction and Methods.

Goals. - 🎯 This week: enzymelens repo; embeddings cached; baseline table for three heads; partner call booked. - 🏁 Next milestone: Gate 24 (written co-author agreement; pre-registered validation plan). - 🌟 Final: Paper 3 with a founder co-author and wet-lab validation (wk 32).

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

v5 row: 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 - Goal: Paper 3 has a candidate partner, a dataset on disk and a baseline table. - Tue (study): FLIP thermostability task and Meltome atlas, deep read; for each of the 3 candidate partners, list the enzyme families (EC classes) and organisms they publish on. - Build: Mon: enzymelens skeleton (same README template as Part 5.2); download Meltome splits; start overnight embedding job with checkpointing. Done when the job resumes after an interruption. Wed: ridge, LightGBM and a 2-layer MLP on cached embeddings; Spearman ρ with bootstrap intervals. Done when the baseline table regenerates with make baselines. Fri: partner email (P13, co-authorship variant) sent to the most engaged founder, with both preprints and one figure relevant to their enzyme class. Done when the call is booked or a follow-up date is logged. - Sun: L-Sun "What a protein language model sees in 30,000 melting curves" with the baseline table. - Only one thing: the partner call booked.

Mentor check. "I can explain what my baseline predicts, how well, and why the partner's lab is the only way to know if it matters."

• Week 17: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 18: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 20: 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 21 · Paper 3 scoped with a partner, 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.

Biology/domain unit

Material: Meltome/FLIP task definitions and partner enzyme papers; read label-generation methods and split design. Produce a target/context comparison and five biological questions.

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: Revisit the ESM model card and implement a bounded embedding smoke test; compare sequence length, pooling and actual VRAM. Last 30 minutes: verified partner paper digest.

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.

Branding: Draft a protein-ML transition post linking the new question to earlier evaluation work.

Opportunity action: Prepare a call with one of three researched partner candidates and R&D discovery requests to established companies; continue live applications.

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.

An overnight embedding job is unattended compute, not extra working hours. Thermal proteome measurements are not automatically purified-enzyme stability measurements.

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: 24. Complete the acceptance checklist below; do not promote reputation from a draft.

• Monday artifact satisfies: Write paper-3-protocol.md with one testable target, one dataset/split and a concrete partner-call request; run one verified baseline if data are ready.
• Wednesday artifact satisfies: Actual memory/runtime fit is measured before a full run; failed sequences are retained.
• Friday artifact satisfies: A baseline table and concrete request for scientific input exist.
• 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: Write paper-3-protocol.md with one testable target, one dataset/split and a concrete partner-call request; run one verified baseline if data are ready.

Operational first step if stalled: open paper-3-protocol.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 21 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-21-protein-study-and-partner-scope/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 21 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 21 · Paper 3 scoped with a partner. The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.