WEEK 13 · Mon 14 Dec → Sun 20 Dec 2026
UNDERSTAND · PRACTICE · KEEP EVIDENCE
Read the week in plain language, refresh the foundations, follow each challenge step by step, and check what evidence to keep. Includes worked examples, answer keys and prompts for visual study resources.
Use this within your existing weekly blocks. Your learning completion and research evidence remain in your current tracker and week files.
START HERE · 2 MINUTES
STATUS
| Deliverable | Acceptance | State |
|---|---|---|
dataset-release-checklist.mdBuild create ＋ |
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. | |
paper-1-outline.mdBuild create ＋ |
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. | |
paper-1-claims-audit.mdBuild create ＋ |
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. | |
study-notes.mdLearning create ＋ |
Selected exact free resources; bounded lesson/exercise; separate solution; quiz and grading rubric; Peter's answers and gaps when executed | |
founder-paper.mdFounder papers create ＋ |
Verified source and P11 digest; authentic question and connection sentence; access limitations | |
branding-pack.mdBranding create ＋ |
Wednesday note, Sunday build log, X adaptation, figure/caption/alt text and the week's special asset; each claim linked to real proof | |
opportunity-actions.mdOpportunities create ＋ |
Qualified target/role, source/date, ladder stage, next action, message/interview/proposal draft and actual status | |
evidence.mdEvidence & review open & edit ↗ |
Actual paths/URLs, versions, checks/metrics, preparation versus execution state and external receipts when applicable | |
review.mdEvidence & review open & edit ↗ |
Checklist, learning assessment, gate status, shortfalls, next actions and carryover |
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.
600 MINUTES MAXIMUM
Target. 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.
Do these in this order — the plan's own sequence:
Target. *Modern Statistics for Modern Biology* (Holmes & Huber) ch. 1-2 — huber.embl.de/msmb Produce: Two exercises redone in Python
Do these in this order — the plan's own sequence:
Target. 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.
No material for Wednesday — this is a pure build day. Need something to study instead? →
Target. 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.
Do these in this order — the plan's own sequence:
Target. 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.
No material for Friday — this is a pure build day. Need something to study instead? →
Target. 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.
Optional, only if the day went well:
Target. 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.
No material for Sunday — this is a pure build day. Need something to study instead? →
Spare pockets, repo exercises and anything the plan lists without a day. Take them in this order when a day finishes early.
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.
The source lists more material than necessarily fits. Select exact excerpts for the learning objective and park the remainder; no full-course completion requirement.
WHAT TO WATCH, READ AND RUN
A census office's proudest day is not when the counting ends; it is when the tables go public and a journalist, a mayor and a researcher all use them for different purposes. Today FermLit goes public: dataset on Hugging Face with its card, Zenodo DOI, v0.5 release. Then you do something that feels premature and is actually the professional move: you build the skeleton of Paper 1 before writing a single paragraph of …
0 of 13 finished · give me one to start now → · open in the deck →
In the plan's running order: each card says which block it belongs to and what has to come before it. The seven-day plan lists the same cards under the day that owns them.
Monday build block · Read it inside Monday's build block
Build-block reading · Mensh & Kording (2017), "Ten simple rules for structuring papers", PLoS Computational Biology 13(9):e1005619
In: LABLOOP-W13 Notebook
Holmes & Huber, Modern Statistics for Modern Biology, ch. 1 (generative models for discrete data) and ch. 2 (statistical modeling) — search "Modern Statistics for Modern Biology Holmes Huber" (free online book
In: LABLOOP-W13 Notebook
Tuesday · after Holmes & Huber, Modern Statistics for Modern Biology, ch. 1 (generative models for discrete data…
EMBL link may move) (75 min)
In: LABLOOP-W13 Notebook
von Stosch et al. (2014), "Hybrid semi-parametric modeling in process systems engineering: past, present and future", Computers & Chemical Engineering 60:86-101 (sections 1-3)
In: LABLOOP-W13 Notebook
Thursday · after von Stosch et al. (2014), "Hybrid semi-parametric modeling in process systems engineering: past,…
Chen et al. (2018), "Neural Ordinary Differential Equations", arXiv:1806.07366 (abstract + figure 1)
In: LABLOOP-W13 Notebook
Saturday sandbox
Steve Brunton "Neural ODEs" (YouTube)
In: LABLOOP-W13 Notebook
Saturday sandbox · after Steve Brunton "Neural ODEs"
Coursera Writing in the Sciences (Stanford, Kristin Sainani), module 1 "Principles of effective writing" — preview for week 14
In: LABLOOP-W13 Notebook
Saturday sandbox · after Coursera Writing in the Sciences (Stanford, Kristin Sainani), module 1 "Principles of effective…
Karniadakis et al. (2021), "Physics-informed machine learning", Nature Reviews Physics 3:422-440 (figures 1-2)
In: LABLOOP-W13 Notebook
Saturday sandbox · after Karniadakis et al. (2021), "Physics-informed machine learning"
Stanford CS197 (cs197.stanford.edu), lecture on "vertical paper structure" (verify lecture title)
In: LABLOOP-W13 Notebook
examples/ode_demo.py: learn a spiral's dynamics; read how a neural network replaces the right-hand side of an ODE
In: LABLOOP-W13 Notebook
Optional JAX alternative with excellent docs on neural ODEs
In: LABLOOP-W13 Notebook
Put the Paper 1 skeleton into a Quarto manuscript; make paper builds a PDF with placeholder figures
In: LABLOOP-W13 Notebook
Browse the datasets examples for pushing a dataset with a card from code
In: LABLOOP-W13 Notebook
READ FIRST
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.
READ FIRST
Read v6 · Week 13 · GATE 13: FermLit v0.5 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, 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 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."
OPEN WHEN NEEDED
READ FIRST
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.
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: 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.
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.
OPEN WHEN NEEDED
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. 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.
OPEN WHEN NEEDED
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.
READ FIRST
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.
READ FIRST
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: 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.
OPEN WHEN NEEDED
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.
OPEN WHEN NEEDED
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.
OPEN WHEN NEEDED
v6 reproduces this brief unchanged inside v6 · Week 13 · GATE 13: FermLit v0.5 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.
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.WEEK FILES
State: UNCONFIRMED. Owner: Peter Ciancaglini. Specification
Start date: not set. End date: not set. Available hours: confirm (planned ceiling 10). Primary outcome: fermlit release and paper outline. Minimum that keeps the next gate alive: the HF dataset.
dataset-release-checklist.md: Card, version, actual N, quality metrics and allowed distribution are verified before release.paper-1-outline.md: All six figures have source data/commands; missing results remain visibly unresolved.paper-1-claims-audit.md: No unsupported claim is promoted into a headline; endorsement conversation status is dated.| Day | Minutes | Physical action / outcome | Actual slot | Done |
|---|---|---|---|---|
| Mon | 90 | Prepare FermLit v0.5 dataset card, permitted export, data/code citation metadata and HF/Zenodo release package. | Not set | ☐ |
| Tue | 90 | Two exercises redone in Python | Not set | ☐ |
| Wed | 90 | Assemble Paper 1 skeleton with six figures, contribution claims, methods and availability statements. Last ten minutes: optional note. | Not set | ☐ |
| Thu | 90 | Hybrid model v0: Monod + GBM residual Include relevant founder-paper work within this block. | Not set | ☐ |
| Fri | 90 | Review the skeleton as a skeptical scientist and link each unsupported claim to a correction owner and deadline. | Not set | ☐ |
| Sat | 90 | Resolve critical spillover; long-form draft if due; sandbox only if done. | Not set | ☐ |
| Sun | 60 | Build log, evidence, gap review, next actions. | Not set | ☐ |
Peter's commitment / adjustments: pending. Reviewing model and date: pending.
Execution state: NOT_STARTED. Specification This file is a blank register with planned artifact names; none of the rows prove completion.
| Item | Path / URL / version | State | Verification / actual result | Verified by / date |
|---|---|---|---|---|
| dataset-release-checklist.md | Not created | NOT_STARTED | Pending: Card, version, actual N, quality metrics and allowed distribution are verified before release. | — |
| paper-1-outline.md | Not created | NOT_STARTED | Pending: All six figures have source data/commands; missing results remain visibly unresolved. | — |
| paper-1-claims-audit.md | Not created | NOT_STARTED | Pending: No unsupported claim is promoted into a headline; endorsement conversation status is dated. | — |
| Learning exercise / Peter's quiz | Not created | NOT_STARTED | Peter's actual answers required | — |
| Founder paper digest | Not created | NOT_STARTED | Source/content and access checked | — |
| Branding pack | Not created | NOT_STARTED | Claims audited; drafted/public status distinct | — |
| Opportunity actions | Not created | NOT_STARTED | Drafted/sent/replied/booked/held distinct | — |
| Gate 13 | No evidence | NOT_STARTED | FermLit v0.5 public with dataset card and DOI; Paper 1 skeleton with all figures; at least one dated live endorsement conversation. | — |
| Question / metric | Dataset, N and unit | Split / seed / config | Command or verification method | Output path and measured value | Uncertainty / limitation |
|---|---|---|---|---|---|
| Date | Action / counterpart | Receipt or private reference | State | Next action / date |
|---|---|---|---|---|
Peter's teach-back / quiz score: not assessed. Scientific assumptions and deviations: none recorded yet. Budget allocated / spent: not assessed / no spend recorded. Missing evidence and responsible owner: pending inspection.
Do not put API keys, source full texts with restricted rights, client data or invoice personal details in a public version of this register. Keep private evidence references private.
Review status: NOT_REVIEWED. Specification · Evidence
What Peter can explain or reproduce now: not assessed. Quiz / teach-back gaps: not assessed. Measured result and limitations: pending. Best evidence link for a scientist/recruiter/buyer: pending. What failed or changed, and why: pending.
Gate requirement: FermLit v0.5 public with dataset card and DOI; Paper 1 skeleton with all figures; at least one dated live endorsement conversation. Gate status: NOT_STARTED. Original target week: 13. Actual completion date / forecast: not set. Missing external evidence: pending inspection. Blocks completed / 7: not recorded. Days with commits / 7: not recorded. Sunday build log / optional Wednesday note: not recorded. Founder conversations cumulative: not recorded. Earned evidence level and proof: not assessed. Consecutive lost weeks: not assessed.
Week-specific risk to revisit: 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.
Continue / recover / blocked: not decided. Retain as the minimum: the HF dataset. Skipped permanently with reason: none recorded. Carryover with owner, dependency and target week: none recorded. Canonical repository paths and versions: pending. Data permissions, split definitions or assumptions to preserve: pending. External action authorization that still applies: not assessed. Next physical action, exact file/function/paragraph: pending. Updates to root PROGRESS / LOG / TODAY completed: ☐
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