# Week 26 — trialkit plate module

[**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 7 with retained v4 details. Deeper walkthrough: [v6 · Week 26 · Instrument 2 (plate module)](../../../LABLOOP-Master-Plan-v6.md#week-26--instrument-2-plate-module). Active project/repository: trialkit.

[Programme](../../README.md) · [Model instructions](../../specs.md) · [Decisions](../../DECISIONS.md) · [Resources](../../SOURCES.md) · [**v6 walkthrough**](../../../LABLOOP-Master-Plan-v6.md#week-26--instrument-2-plate-module) · [Previous week review](../week-25-trialkit-field-module/review.md) · [Next week](../week-27-loop-audit-offer-and-pipeline/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: Specify plate layout and metadata mapping for 96/384-well exports with blanks, controls and replicate IDs.
- Public/profile priority: Draft a plate-analysis post describing one QC failure and why it changes the decision.
- Career/relationship/commercial priority: Ask an assay scientist for feedback and prepare an interview explanation connecting measurements, QC and decision quality.

## Deeper walkthrough (v6)

Read [v6 · Week 26 · Instrument 2 (plate module)](../../../LABLOOP-Master-Plan-v6.md#week-26--instrument-2-plate-module) 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](../../../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 VI · Threads: B, M, $, R · Next gate: 28**

**Where this week sits.**
- ← **From:** week 1 (growth phases), week 7 (Michaelis-Menten), week 16 (intervals), week 25 (trialkit schema and report).
- → **Feeds:** week 27 (offer covers archetype C, lab assays), weeks 28-30 (partner's validation data analysis), Loop Audits for assay-heavy startups.
- ⟳ **Returns in:** Paper 3 Results (enzyme activity curves).

**Goals.**
- 🎯 **This week:** `trialkit/plate`: parse plate-reader exports, growth curves, 4PL dose-response, Michaelis-Menten, Z′ QC, with intervals.
- 🏁 **Next milestone:** Gate 28.
- 🌟 **Final:** the same statistical care applied to the partner's validation data.

**The plan (from v5 Part 7, expanded; gate and output unchanged).**
> *v5 row:* 26 | Instrument 2 (plate module) | Assay statistics (4PL, growth curves, Z′) | `trialkit/plate` (v4 week 11) | L-Sun
- **Goal:** a plate export in, a QC'd, fitted, interval-bearing report out.
- **Tue (study):** assay statistics: 4PL, logistic/Gompertz growth models, Z′-factor.
- **Build:** [ ] Mon: parser for 96/384 layouts (plate map + readings) into the trial schema. Done when two different vendor export formats load. [ ] Wed: growth-curve fits (logistic, Gompertz; growth rate, lag, carrying capacity) and 4PL dose-response with bootstrap intervals. Done when a published dataset's parameters are reproduced. [ ] Fri: Z′ per plate and Michaelis-Menten module; plate report. Done when a bad plate is flagged automatically.
- **Sun:** L-Sun "The Z′ factor: the one number that says whether your assay deserves your conclusions".
- **Only one thing:** growth-curve fits with intervals.

**Mentor check.** *"I can look at a plate report and say whether the assay is trustworthy before I talk about the result."*

## Required inputs and dependency check

- [Week 25](../week-25-trialkit-field-module/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 26 · Instrument 2 (plate module)](../../../LABLOOP-Master-Plan-v6.md#week-26--instrument-2-plate-module), 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 | Specify plate layout and metadata mapping for 96/384-well exports with blanks, controls and replicate IDs. Stop when: Generate one plate report with correct control handling, replicate identities and explicit fit/QC failures. |
| Tuesday | 90 min | Read the original Z-prime assay-QC paper and an open dose-response methods source; derive control means/SDs and fit a small 4PL example. Produce: One concise applied note, a worked decision/example and unresolved questions. |
| Wednesday | 90 min | Fit dose-response/growth/kinetics examples with model diagnostics, parameter bounds and explicit failure reports. Stop when: At least one verified public example per implemented model has identifiable fits and uncertainty. Reserve the last 10 minutes for the optional Wednesday note. |
| Thursday | 90 min | Review residuals, curve identifiability and technical versus biological replicate reporting. Last 30 minutes: founder assay paper. Apply the Half 2 one-formal-study-block rule. |
| Friday | 90 min | Add Z-prime/control QC and a report with data provenance; scope MIC to validated rules if applicable. Stop when: Bad controls, insufficient points and failed fits appear in the output. |
| 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. |

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.

## Learning specification

### Biology/domain unit

Material: Read the original Z-prime assay-QC paper and an open dose-response methods source; derive control means/SDs and fit a small 4PL example.

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: Review residuals, curve identifiability and technical versus biological replicate reporting. Last 30 minutes: founder assay 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](../../../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 |
|---|---|---|
| `plate-schema.md` | Specify plate layout and metadata mapping for 96/384-well exports with blanks, controls and replicate IDs. Acceptance: Generate one plate report with correct control handling, replicate identities and explicit fit/QC failures. | Model assists; Peter checks and owns the outcome |
| `plate-fit-report.md` | Fit dose-response/growth/kinetics examples with model diagnostics, parameter bounds and explicit failure reports. Acceptance: At least one verified public example per implemented model has identifiable fits and uncertainty. | Model assists; Peter checks and owns the outcome |
| `plate-qc-checklist.md` | Add Z-prime/control QC and a report with data provenance; scope MIC to validated rules if applicable. Acceptance: Bad controls, insufficient points and failed fits appear in the output. | 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 plate-analysis post describing one QC failure and why it changes the decision.

Opportunity action: Ask an assay scientist for feedback and prepare an interview explanation connecting measurements, QC and decision quality.

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 implement every assay family in one block without reliable validation. Start with one complete path; no biological replicate inflation or unsupported potency claims.

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

- [ ] Monday artifact satisfies: Generate one plate report with correct control handling, replicate identities and explicit fit/QC failures.
- [ ] Wednesday artifact satisfies: At least one verified public example per implemented model has identifiable fits and uncertainty.
- [ ] Friday artifact satisfies: Bad controls, insufficient points and failed fits appear in the output.
- [ ] 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

Expanded minimum derived from the source goal: Generate one plate report with correct control handling, replicate identities and explicit fit/QC failures.

Operational first step if stalled: open `plate-schema.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 26 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-26-trialkit-plate-module/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 26 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 expands this row into a full brief, with the gate and output unchanged, inside [v6 · Week 26 · Instrument 2 (plate module)](../../../LABLOOP-Master-Plan-v6.md#week-26--instrument-2-plate-module).
The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.

| Week | Goal | Study (Tue) | Build (Mon/Wed/Fri) | Output |
|---|---|---|---|---|
| 26 | Instrument 2 (plate module) | Assay statistics (4PL, growth curves, Z′) | `trialkit/plate` (v4 week 11) | L-Sun |