What do you
need right now?

No resource card mentions that.

• LABLOOP W06 — human gold standard: full learning notebook
  Those are useful findings about the task. **Your systems, software and AI connection.** Annotation resembles writing a specification with concrete examples and edge cases. Your quality-engineering habits help, but biological ambiguity requires reading context and documenting un execution-plan/weeks/week-06-human-gold-standard18×
• LABLOOP W10 — annotation agreement and analysis: full learning notebook
  # LABLOOP W10 — annotation agreement and analysis: full learning notebook Prepared 2026-09-23 for Peter Ciancaglini. This is a study and execution guide; it does not record that you completed the work. Kee execution-plan/weeks/week-10-annotation-agreement-and-analysis14×
• LABLOOP · Master Plan v6 — The Cartographer's Path: from program manager to published AI scientist for biotech
  tebooks stay at ≤ 15 sources. Protocol in Prologue 4; calendar in Appendix V6-A. ### 5.4 Annotation kit for FermLit (week 6) - `annotate/GUIDELINES.md` written with Prompt P7: one page per field, with positive and negative examples. - `annotate/gold/` : 50 papers, each a JSON w root12×
• Week 10 — annotation agreement and analysis
  # Week 10 — annotation agreement and analysis [**Full learning notebook: explanations, step-by-step challenges, stashes and evidence**](./learning-notebook.md) · [NotebookLM export](./notebooklm.txt) execution-plan/weeks/week-10-annotation-agreement-and-analysis6×
• LABLOOP W14 — paper 1 full draft: full learning notebook
  ic conclusion about reporting quality. An LLM’s confident answer is not source evidence. Annotation guidelines make interpretation rules explicit. Independent annotators apply the rules separately; agreement is measured before **adjudication**, the later process of resolving dif execution-plan/weeks/week-14-paper-1-full-draft6×
• LABLOOP W05 — fermlit corpus and schema: full learning notebook
  s); your v3/Vara experience with LLM pipelines. - → **Feeds:** week 6 (the schema becomes annotation guidelines), week 7 (the agent fills the schema), week 9 (corpus scales to 2,000), week 14 (`RELATED.md` becomes Paper 1's related work). - ⟳ **Returns in:** Paper 1 Methods: "Cor execution-plan/weeks/week-05-fermlit-corpus-and-schema5×
• Week 06 — human gold standard
  e first 15 papers while timing the first three. - Public/profile priority: Draft a manual-annotation build log using actual completed counts and one observed ambiguity. - Career/relationship/commercial priority: Prepare an independent annotator request with bounded workload, due execution-plan/weeks/week-06-human-gold-standard5×
• LABLOOP W13 — fermlit release and paper outline: full learning notebook
  re starting: locate inputs and repair only the needed foundations - [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. 1. Open the existing commitment and p execution-plan/weeks/week-13-fermlit-release-and-paper-outline5×
• Graph Report - biotech_skilling (2026-09-29)
  traction agent - Week 08 — technical report gate - Week 09 — fermlit scale up - Week 10 — annotation agreement and analysis - Week 11 — fermlit dataset engineering - Week 12 — endorsement and hybrid model - Week 13 — fermlit release and paper outline - Week 14 — paper 1 full draf graphify-out5×
• Graph Report - biotech_skilling (2026-09-19)
  traction agent - Week 08 — technical report gate - Week 09 — fermlit scale up - Week 10 — annotation agreement and analysis - Week 11 — fermlit dataset engineering - Week 12 — endorsement and hybrid model - Week 13 — fermlit release and paper outline - Week 14 — paper 1 full draf graphify-out/2026-09-195×
• Graph Report - biotech_skilling (2026-09-29)
  traction agent - Week 08 — technical report gate - Week 09 — fermlit scale up - Week 10 — annotation agreement and analysis - Week 11 — fermlit dataset engineering - Week 12 — endorsement and hybrid model - Week 13 — fermlit release and paper outline - Week 14 — paper 1 full draf graphify-out/2026-09-295×
• LABLOOP W07 — measured extraction agent: full learning notebook
  ic conclusion about reporting quality. An LLM’s confident answer is not source evidence. Annotation guidelines make interpretation rules explicit. Independent annotators apply the rules separately; agreement is measured before **adjudication**, the later process of resolving dif execution-plan/weeks/week-07-measured-extraction-agent4×
• LABLOOP W09 — fermlit scale up: full learning notebook
  book](../week-08-technical-report-gate/learning-notebook.md) · [Next notebook](../week-10-annotation-agreement-and-analysis/learning-notebook.md) ## 1. The week in plain language: what, why and where it leads Scaling FermLit means processing more papers without losing track of execution-plan/weeks/week-09-fermlit-scale-up4×
• LABLOOP W23 — extremophile candidate ranking: full learning notebook
  in order.** 1. Agree or provisionally define the enzyme family, organism scope, required annotations and assay-compatible inclusion criteria. 2. Query versioned UniProt records and save accessions, sequence versions, evidence qualifiers, source URLs and retrieval date. 3. Distin execution-plan/weeks/week-23-extremophile-candidate-ranking4×
• LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech
  NotebookLM: three notebooks, "Bio", "ML", "Thesis", each with at most 8 sources. ### 5.4 Annotation kit for FermLit (week 6) - `annotate/GUIDELINES.md` written with Prompt P7: one page per field, with positive and negative examples. - `annotate/gold/` : 50 papers, each a JSON w root3×
• Source reconciliation and feasibility decisions
  | Freeze paper-level development/held-out partitions; report the distinction. Independent annotation remains human. | | Kappa requested for all schema fields | Categorical kappa where meaningful; numeric tolerance/error agreement for continuous values. Retain pre-adjudication lab execution-plan3×
• LABLOOP — full weekly learning notebooks
  lm.txt) | [W09 stash](http://127.0.0.1:5000/learn?stash=LABLOOP-W09%20Notebook) | | 10 | [annotation agreement and analysis](./weeks/week-10-annotation-agreement-and-analysis/learning-notebook.md) | [TXT](./weeks/week-10-annotation-agreement-and-analysis/notebooklm.txt) | [W10 st execution-plan3×
• Graph Report - biotech_skilling (2026-09-20)
  traction agent - Week 08 — technical report gate - Week 09 — fermlit scale up - Week 10 — annotation agreement and analysis - Week 11 — fermlit dataset engineering - Week 12 — endorsement and hybrid model - Week 13 — fermlit release and paper outline - Week 14 — paper 1 full draf graphify-out/2026-09-203×
• Graph Report - biotech_skilling (2026-09-20)
  traction agent - Week 08 — technical report gate - Week 09 — fermlit scale up - Week 10 — annotation agreement and analysis - Week 11 — fermlit dataset engineering - Week 12 — endorsement and hybrid model - Week 13 — fermlit release and paper outline - Week 14 — paper 1 full draf graphify-out/2026-09-233×
• Talent and commercial asset requirements
  ion, reproducible models, evaluation and uncertainty in biotech/pharma contexts | FermLit annotation/evaluation, batchlens grouped validation, protein generalization, reproducible papers | | Scientific AI lead / research engineering lead | Executive and engineering experience tra execution-plan2×
• Programme progress
  ermlit scale up](./weeks/week-09-fermlit-scale-up/specs.md) — NOT_STARTED - [ ] Week 10: [annotation agreement and analysis](./weeks/week-10-annotation-agreement-and-analysis/specs.md) — NOT_STARTED - [ ] Week 11: [fermlit dataset engineering](./weeks/week-11-fermlit-dataset-engi execution-plan2×
• LABLOOP: week-by-week execution
  port | | 09 | [fermlit scale up](./weeks/week-09-fermlit-scale-up/specs.md) | — | | 10 | [annotation agreement and analysis](./weeks/week-10-annotation-agreement-and-analysis/specs.md) | — | | 11 | [fermlit dataset engineering](./weeks/week-11-fermlit-dataset-engineering/specs.md execution-plan2×
• Week 05 — fermlit corpus and schema
  s); your v3/Vara experience with LLM pipelines. - → **Feeds:** week 6 (the schema becomes annotation guidelines), week 7 (the agent fills the schema), week 9 (corpus scales to 2,000), week 14 (`RELATED.md` becomes Paper 1's related work). - ⟳ **Returns in:** Paper 1 Methods: "Cor execution-plan/weeks/week-05-fermlit-corpus-and-schema2×
• Week 06 commitment
  Minimum that keeps the next gate alive: 50 gold JSONs. ## Deliverables to commit - [ ] `annotation-guidelines.md`: Each annotated value has a source sentence and document locator. - [ ] `annotation-progress.csv`: Completed and incomplete records are counted, with no model label execution-plan/weeks/week-06-human-gold-standard2×
• Week 06 evidence register
  ion | State | Verification / actual result | Verified by / date | |---|---|---|---|---| | annotation-guidelines.md | Not created | NOT_STARTED | Pending: Each annotated value has a source sentence and document locator. | — | | annotation-progress.csv | Not created | NOT_STARTED | execution-plan/weeks/week-06-human-gold-standard2×
• Week 10 commitment
  t set. End date: not set. Available hours: confirm (planned ceiling 10). Primary outcome: annotation agreement and analysis. Minimum that keeps the next gate alive: kappa. ## Deliverables to commit - [ ] `agreement-report.md`: Pre-adjudication labels are retained and agreement execution-plan/weeks/week-10-annotation-agreement-and-analysis2×
• LABLOOP W11 — fermlit dataset engineering: full learning notebook
  OTEBOOKS.md) · [NotebookLM upload text](./notebooklm.txt) [Previous notebook](../week-10-annotation-agreement-and-analysis/learning-notebook.md) · [Next notebook](../week-12-endorsement-and-hybrid-model/learning-notebook.md) ## 1. The week in plain language: what, why and where execution-plan/weeks/week-11-fermlit-dataset-engineering2×
• Week 11 — fermlit dataset engineering
  ek-11--dataset-engineering-and-the-reporting-finding) · [Previous week review](../week-10-annotation-agreement-and-analysis/review.md) · [Next week](../week-12-endorsement-and-hybrid-model/specs.md) ## Outcome and relevance This week delivers the three concrete artifacts below execution-plan/weeks/week-11-fermlit-dataset-engineering2×
• Week 14 — paper 1 full draft
  plied to a FermLit comparison | | Wednesday | 90 min | Write reproducible corpus, schema, annotation, extraction and evaluation methods with availability statement. Stop when: A reader can identify data versions, splits, prompts, annotators and scoring rules. Reserve the last 10 execution-plan/weeks/week-14-paper-1-full-draft2×
• Sources and resource verification
  or Paper 3 | | UniProt | https://www.uniprot.org/help | Accessions, evidence and sequence annotations | | NIST statistics handbook | https://www.itl.nist.gov/div898/handbook/ | Chapters 5 and 6 on design and process monitoring | | statsmodels | https://www.statsmodels.org/stable/ execution-plan1×
• Instructions for any model preparing or executing this plan
  , implement and review within the requested scope. Independent humans perform independent annotation and scientific review. Partner labs own wet-lab feasibility/execution. Co-authors approve their contribution and final manuscript. The current request authorizes local planning a execution-plan1×
• LABLOOP W00 — cockpit and positioning: full learning notebook
  scientific responsibility and external relationships; independent humans own their actual annotation/review contributions and partner laboratories own their laboratory execution. This notebook prepares the steps; it does not publish, contact, spend, submit or perform the programm execution-plan/weeks/week-00-cockpit-and-positioning1×
• LABLOOP W01 — fermentation simulator: full learning notebook
  scientific responsibility and external relationships; independent humans own their actual annotation/review contributions and partner laboratories own their laboratory execution. This notebook prepares the steps; it does not publish, contact, spend, submit or perform the programm execution-plan/weeks/week-01-fermentation-simulator1×
• LABLOOP W02 — indpensim data and baseline: full learning notebook
  scientific responsibility and external relationships; independent humans own their actual annotation/review contributions and partner laboratories own their laboratory execution. This notebook prepares the steps; it does not publish, contact, spend, submit or perform the programm execution-plan/weeks/week-02-indpensim-data-and-baseline1×
• LABLOOP W03 — statistical batch monitoring: full learning notebook
  scientific responsibility and external relationships; independent humans own their actual annotation/review contributions and partner laboratories own their laboratory execution. This notebook prepares the steps; it does not publish, contact, spend, submit or perform the programm execution-plan/weeks/week-03-statistical-batch-monitoring1×
• LABLOOP W04 — batchlens first release: full learning notebook
  scientific responsibility and external relationships; independent humans own their actual annotation/review contributions and partner laboratories own their laboratory execution. This notebook prepares the steps; it does not publish, contact, spend, submit or perform the programm execution-plan/weeks/week-04-batchlens-first-release1×
• Week 05 commitment
  ms and company gaps are hypotheses. Freeze paper-level development/test partitions before annotation or prompt tuning. - Existing session authorization for external actions or spending: not assessed; local planning only at scaffold creation. - Scope to cut first: optional polish/ execution-plan/weeks/week-05-fermlit-corpus-and-schema1×
• Week 05 review and handoff
  ms and company gaps are hypotheses. Freeze paper-level development/test partitions before annotation or prompt tuning. ## Decision and next-model handoff Continue / recover / blocked: not decided. Retain as the minimum: `RELATED.md`. If someone did it already, you must know now execution-plan/weeks/week-05-fermlit-corpus-and-schema1×
• LABLOOP W08 — technical report gate: full learning notebook
  scientific responsibility and external relationships; independent humans own their actual annotation/review contributions and partner laboratories own their laboratory execution. This notebook prepares the steps; it does not publish, contact, spend, submit or perform the programm execution-plan/weeks/week-08-technical-report-gate1×
• Week 09 review and handoff
  h: pending. Updates to root PROGRESS / LOG / TODAY completed: [ ] [Next week](../week-10-annotation-agreement-and-analysis/specs.md) execution-plan/weeks/week-09-fermlit-scale-up1×