# Week 13 — fermlit release and paper outline [**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 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined](../../../LABLOOP-Master-Plan-v6.md#week-13--gate-13-fermlit-v05-public-paper-1-outlined). 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-13--gate-13-fermlit-v05-public-paper-1-outlined) · [Previous week review](../week-12-endorsement-and-hybrid-model/review.md) · [Next week](../week-14-paper-1-full-draft/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: Prepare FermLit v0.5 dataset card, permitted export, data/code citation metadata and HF/Zenodo release package. - Public/profile priority: Prepare Medium deep dive 3, dataset release post and recruiter-facing one-paragraph evidence summary. - Career/relationship/commercial priority: Follow up on a live endorsement route and prepare feedback requests focused on the dataset's reuse value. ## Deeper walkthrough (v6) Read [v6 · Week 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined](../../../LABLOOP-Master-Plan-v6.md#week-13--gate-13-fermlit-v05-public-paper-1-outlined) 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 III (finale) · Threads: B, M, FL, R · GATE 13** **Where this week sits.** - ← **From:** Act III weeks 9-12. - → **Feeds:** weeks 14-16 (write, review, submit Paper 1), week 16 (founders and funds receive a real link), week 19 (personal site), week 36 (journal version). - ⟳ **Returns in:** L6 "used" when someone cites FermLit. **Goals.** - 🎯 **This week:** HF dataset + card + Zenodo DOI; Paper 1 skeleton with every figure; P10 list of unsupported claims. - 🏁 **This gate (13):** dataset public, skeleton complete, one endorsement conversation alive. - 🌟 **Final:** Paper 1 and a dataset with a life beyond you. **Mentor check.** *"FermLit has a DOI and a card, and I can pitch Paper 1 in three sentences with three numbers."* ## Required inputs and dependency check - [Week 10](../week-10-annotation-agreement-and-analysis/specs.md): inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins. - [Week 11](../week-11-fermlit-dataset-engineering/specs.md): inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins. - [Week 12](../week-12-endorsement-and-hybrid-model/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 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined](../../../LABLOOP-Master-Plan-v6.md#week-13--gate-13-fermlit-v05-public-paper-1-outlined), 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 | Prepare FermLit v0.5 dataset card, permitted export, data/code citation metadata and HF/Zenodo release package. Stop when: Card, version, actual N, quality metrics and allowed distribution are verified before release. | | Tuesday | 90 min | *Modern Statistics for Modern Biology* (Holmes & Huber) ch. 1-2 — huber.embl.de/msmb Produce: Two exercises redone in Python | | Wednesday | 90 min | Assemble Paper 1 skeleton with six figures, contribution claims, methods and availability statements. Stop when: All six figures have source data/commands; missing results remain visibly unresolved. Reserve the last 10 minutes for the optional Wednesday note. | | Thursday | 90 min | von Stosch et al. 2014, "Hybrid semi-parametric modeling in process systems engineering: past, present and future"; Chen et al. 2018, "Neural Ordinary Differential Equations" (abstract + fig. 1 only) Select material/exercise that fits 60 minutes; use the last 30 for the founder paper. | | Friday | 90 min | Review the skeleton as a skeptical scientist and link each unsupported claim to a correction owner and deadline. Stop when: No unsupported claim is promoted into a headline; endorsement conversation status is dated. | | 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: B13 · Statistics for biologists I Material: *Modern Statistics for Modern Biology* (Holmes & Huber) ch. 1-2 — huber.embl.de/msmb Produce: Two exercises redone in Python Understanding check: You know why biologists distrust p-values from n=3 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: M13 · Hybrid and scientific ML Material: von Stosch et al. 2014, "Hybrid semi-parametric modeling in process systems engineering: past, present and future"; Chen et al. 2018, "Neural Ordinary Differential Equations" (abstract + fig. 1 only) Produce: Hybrid model v0: Monod + GBM residual Understanding check: You can draw the hybrid architecture 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 | |---|---|---| | `dataset-release-checklist.md` | Prepare FermLit v0.5 dataset card, permitted export, data/code citation metadata and HF/Zenodo release package. Acceptance: Card, version, actual N, quality metrics and allowed distribution are verified before release. | Model assists; Peter checks and owns the outcome | | `paper-1-outline.md` | Assemble Paper 1 skeleton with six figures, contribution claims, methods and availability statements. Acceptance: All six figures have source data/commands; missing results remain visibly unresolved. | Model assists; Peter checks and owns the outcome | | `paper-1-claims-audit.md` | Review the skeleton as a skeptical scientist and link each unsupported claim to a correction owner and deadline. Acceptance: No unsupported claim is promoted into a headline; endorsement conversation status is dated. | 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: Prepare Medium deep dive 3, dataset release post and recruiter-facing one-paragraph evidence summary. Opportunity action: Follow up on a live endorsement route and prepare feedback requests focused on the dataset's reuse value. 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 Public dataset plus DOI and outline are the gate, not a particular dataset size. Record any scope deviation against the 2,000-paper target; a proposed CC BY license is not blanket permission to relicense source text. 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 Gate 13: **Dataset release**. Required proof: FermLit v0.5 public with dataset card and DOI; Paper 1 skeleton with all figures; at least one dated live endorsement conversation. Reputation interpretation: L2. Record target, forecast, actual date and evidence link. The original gate stays incomplete until the required external proof exists. - [ ] Monday artifact satisfies: Card, version, actual N, quality metrics and allowed distribution are verified before release. - [ ] Wednesday artifact satisfies: All six figures have source data/commands; missing results remain visibly unresolved. - [ ] Friday artifact satisfies: No unsupported claim is promoted into a headline; endorsement conversation status is dated. - [ ] 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: the HF dataset. Operational first step if stalled: open `dataset-release-checklist.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 13 of this LABLOOP execution plan. Read execution-plan/specs.md, execution-plan/DECISIONS.md, execution-plan/GATES.md and execution-plan/weeks/week-13-fermlit-release-and-paper-outline/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 13 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 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined](../../../LABLOOP-Master-Plan-v6.md#week-13--gate-13-fermlit-v05-public-paper-1-outlined). The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md. ### 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.