# Graph Report - biotech_skilling (2026-09-20) ## Corpus Check - 213 files · ~523,464 words - Verdict: corpus is large enough that graph structure adds value. - Unclassified: 8 file(s) not represented in the graph (top: .csv 3, .css 3, (none) 1) ## Summary - 2030 nodes · 2798 edges · 222 communities (215 shown, 7 thin omitted) - Extraction: 100% EXTRACTED · 0% INFERRED · 0% AMBIGUOUS · INFERRED: 13 edges (avg confidence: 0.85) - Token cost: 0 input · 0 output ## Graph Freshness - Built from commit: `cc0ba87b` - Run `git rev-parse HEAD` and compare to check if the graph is stale. - Run `graphify update .` after code changes (no API cost). ## Community Hubs (Navigation) - README.md - consult.py - Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4 - LABLOOP · Master Plan v6 — The Cartographer's Path: from program manager to published AI scientist for biotech - Original v5 execution checklist snapshot - ACT VIII · Peer review and the crossroads (weeks 36-40) - PART 6 · Weeks 0-20, block by block - Week 00 — cockpit and positioning - Week 01 — fermentation simulator - Week 02 — indpensim data and baseline - Week 03 — statistical batch monitoring - Week 04 — batchlens first release - Week 05 — fermlit corpus and schema - Week 06 — human gold standard - Week 07 — measured extraction 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 draft - Week 15 — paper 1 review and revision - Week 16 — paper 1 preprint gate - Week 17 — paper 2 complete experiments - Week 18 — paper 2 full draft - Week 19 — recruiter portfolio and review - Week 20 — paper 2 gate and halfway review - Week 21 — protein study and partner scope - Week 22 — protein validation and baselines - Week 23 — extremophile candidate ranking - Week 24 — coauthor and validation gate - Week 25 — trialkit field module - Week 26 — trialkit plate module - Week 27 — loop audit offer and pipeline - Week 28 — first invoice gate - Week 29 — audit delivery or sales recovery - Week 30 — audit readout and validation results - Week 31 — paper 3 coauthor draft - Week 32 — paper 3 gate and career refresh - Week 33 — labdocs ingestion and traceability - Week 34 — labdocs retrieval evaluation - Week 35 — labdocs release and local benchmark - Week 36 — journal and joss submissions - Week 37 — pilot or job process - Week 38 — scientific talk and proof - Week 39 — fund portfolio offer - Week 40 — final retrospective and career decision - app.js - Week 04 — Materials: what to read, what to watch - Week 13 review and handoff - Week 14 review and handoff - Week 15 review and handoff - Week 16 review and handoff - Week 17 review and handoff - Week 18 review and handoff - Week 24 review and handoff - Week 28 review and handoff - Week 31 review and handoff - Week 33 review and handoff - Week 35 review and handoff - Week 36 review and handoff - Week 37 review and handoff - LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech - ACT IV · Becoming an author (weeks 14-20) - ACT VI · The first client (weeks 25-32) - Instructions for any model preparing or executing this plan - Sources and resource verification - Week 01 — Materials: what to read, what to watch - doc_view - Week 03 — Materials: what to read, what to watch - PART 9 · Branding, connection ladder, endorsement - ACT I · The apprentice learns the tank (weeks 0-4) - ACT III · From sample to census (weeks 9-13) - Week 00 commitment - Week 00 review and handoff - Week 01 review and handoff - Week 02 — Materials: what to read, what to watch - Week 03 review and handoff - mitocondria-model.test.cjs - mitocondria-game.js - Week 05 commitment - Week 05 review and handoff - Week 06 commitment - Week 06 review and handoff - Week 07 commitment - Week 07 review and handoff - Week 08 commitment - Week 08 review and handoff - Week 09 commitment - Week 09 review and handoff - Week 10 commitment - Week 10 review and handoff - Week 11 commitment - Week 11 review and handoff - Week 12 commitment - Week 12 review and handoff - Week 13 commitment - Week 14 commitment - Week 15 commitment - Week 16 commitment - Week 17 commitment - Week 18 commitment - Week 19 commitment - Week 19 review and handoff - Week 20 commitment - Week 20 review and handoff - Week 21 commitment - Week 21 review and handoff - Week 22 commitment - Week 22 review and handoff - Week 23 commitment - Week 23 review and handoff - Week 24 commitment - Week 25 commitment - Week 25 review and handoff - Week 26 commitment - Week 26 review and handoff - Week 27 commitment - Week 27 review and handoff - Week 28 commitment - Week 29 commitment - Week 29 review and handoff - Week 30 commitment - Week 30 review and handoff - Week 31 commitment - Week 32 commitment - Week 32 review and handoff - Week 33 commitment - Week 34 commitment - Week 34 review and handoff - Week 35 commitment - Week 36 commitment - Week 37 commitment - Week 38 commitment - Week 38 review and handoff - Week 39 commitment - Week 39 review and handoff - Week 40 commitment - Week 40 review and handoff - PART 0 · How to use this document (read this every Monday for the first month) - PART 4 · Curriculum from zero (four tracks, all free, exact units) - PART 5 · Repos and materials to prepare (day 0 to week 2) - ACT II · The reading robot (weeks 5-8) - ACT V · The protein detective finds a partner (weeks 21-24) - Talent and commercial asset requirements - Commands for App - LABLOOP: week-by-week execution - environment-checklist.md - Branding pack - Environment checklist - Week 09 evidence register - Founder paper - Opportunity actions - Positioning - Study notes - Week 04 review and handoff - Week 01 evidence register - app.py - Week 00 evidence register - Week 03 commitment - Week 03 evidence register - Week 27 evidence register - Week 06 evidence register - Week 07 evidence register - Week 08 evidence register - cards.py - _materials_cards - Week 11 evidence register - Week 12 evidence register - Week 02 review and handoff - Week 20 evidence register - post - Week 22 evidence register - Week 23 evidence register - Week 25 evidence register - Week 05 evidence register - index - git_sync - Week 30 evidence register - doc_rel - Week 33 evidence register - Week 38 evidence register - Week 39 evidence register - Week 13 evidence register - ACT VII · The lab's memory (weeks 33-35) - ARTIFACT-MAP.md - Source reconciliation and feasibility decisions - PARKING.md - PART 3 · The scientific thesis (explained twice: like a kid, then like a reviewer) - CLAUDE.md - VALIDATION.md - Week 35 evidence register - md - Week 02 commitment - Week 16 evidence register - Week 14 evidence register - Week 15 evidence register - Micromundo · Misión ATP - Week 17 evidence register - Week 18 evidence register - Week 24 evidence register - chatrunner.py - Week 31 evidence register - Week 02 evidence register - Week 26 evidence register - Week 36 evidence register - Week 37 evidence register - asset - Week 40 evidence register - qs - Week 28 evidence register - Week 32 evidence register - Week 34 evidence register - Week 10 evidence register - Week 29 evidence register - Week 04 commitment - Week 04 evidence register - Week 19 evidence register ## God Nodes (most connected - your core abstractions) 1. `PART 6 · Weeks 0-20, block by block` - 22 edges 2. `Original v5 execution checklist snapshot` - 22 edges 3. `Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4` - 17 edges 4. `LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech` - 17 edges 5. `ACT VIII · Peer review and the crossroads (weeks 36-40)` - 17 edges 6. `build()` - 15 edges 7. `Week 00 — cockpit and positioning` - 14 edges 8. `Week 01 — fermentation simulator` - 14 edges 9. `Week 02 — indpensim data and baseline` - 14 edges 10. `Week 03 — statistical batch monitoring` - 14 edges ## Surprising Connections (you probably didn't know these) - `chat_ask()` --calls--> `build_prompt()` [EXTRACTED] execution-plan/app/app.py → execution-plan/app/consult.py - `week_page()` --calls--> `index()` [EXTRACTED] execution-plan/app/app.py → execution-plan/app/cards.py - `chat_ask()` --calls--> `build_context()` [EXTRACTED] execution-plan/app/app.py → execution-plan/app/consult.py - `week_chapters()` --calls--> `chapters()` [EXTRACTED] execution-plan/app/consult.py → execution-plan/app/cards.py - `matching_cards()` --calls--> `index()` [EXTRACTED] execution-plan/app/consult.py → execution-plan/app/cards.py ## Import Cycles - None detected. ## Communities (222 total, 7 thin omitted) ### Community 0 - "README.md" Cohesion: 0.06 Nodes (3): Block log, Learning questions, Weekly folder index ### Community 1 - "consult.py" Cohesion: 0.11 Nodes (27): build_context(), build_prompt(), expand(), graph_hits(), matching_cards(), passages(), The plan consultant: find the parts of the programme a question touches, then…, graphify's view: which files and which named nodes this question lands on. (+19 more) ### Community 2 - "Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4" Cohesion: 0.04 Nodes (45): 0. Read this first (what changed and why), 10. Hardware, software and budget, 11. Metrics and gates, 12. Ignore for now, 13. Execution protocol, 14. The one thing to remember, 1. Thesis, 2. Strategy: how the dots connect (+37 more) ### Community 3 - "LABLOOP · Master Plan v6 — The Cartographer's Path: from program manager to published AI scientist for biotech" Cohesion: 0.06 Nodes (35): 0.1 The honest answer to your question, 0.2 The cockpit: five files, nothing else, 0.3 The rituals (this is the ADHD armor), 0.4 Weekly shape (never changes for 40 weeks), 3.1 Like a kid, 3.2 Like a reviewer, 4.1 Track B · Biology from zero (Tuesdays, ~30 h in Half 1), 4.2 Track M · AI science from the basics (Thursdays, ~30 h in Half 1) (+27 more) ### Community 4 - "Original v5 execution checklist snapshot" Cohesion: 0.08 Nodes (26): Original v5 execution checklist snapshot, PART 7 · Weeks 21-40, week by week (Half 2: depth, co-author, money), Programme progress, Sunday scorecard, Week 0 · Cockpit and positioning, Week 10 · Inter-annotator agreement and the first real analysis, Week 11 · Dataset engineering and the reporting finding, Week 12 · Endorsement route opens; hybrid model v0 (+18 more) ### Community 5 - "ACT VIII · Peer review and the crossroads (weeks 36-40)" Cohesion: 0.09 Nodes (23): 9.1 Profiles (week 0, updated at each gate), 9.2 Content pillars and cadence (same as v4, re-pointed), 9.3 The connection ladder (founders and scientists), 9.4 Connection ladder (established companies, funds, scientific-data companies), 9.5 arXiv endorsement: three parallel routes (start week 12), 9.6 Templates (reuse v4 section 9 for build log, gap note, video, targeted message, audit one-pager), ACT VIII · Peer review and the crossroads (weeks 36-40), APPENDIX V6-A · The NotebookLM calendar at a glance (+15 more) ### Community 6 - "PART 6 · Weeks 0-20, block by block" Cohesion: 0.09 Nodes (22): PART 6 · Weeks 0-20, block by block, Week 0 · Cockpit and positioning, Week 10 · Inter-annotator agreement and the first real analysis, Week 11 · Dataset engineering and the reporting finding, Week 12 · Endorsement route opens; hybrid model v0, Week 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined, Week 14 · Write Paper 1, Week 15 · Review, revise, human read (+14 more) ### Community 7 - "Week 00 — cockpit and positioning" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 8 - "Week 01 — fermentation simulator" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 9 - "Week 02 — indpensim data and baseline" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 10 - "Week 03 — statistical batch monitoring" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 11 - "Week 04 — batchlens first release" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 12 - "Week 05 — fermlit corpus and schema" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 13 - "Week 06 — human gold standard" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 14 - "Week 07 — measured extraction agent" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 15 - "Week 08 — technical report gate" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 16 - "Week 09 — fermlit scale up" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 17 - "Week 10 — annotation agreement and analysis" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 18 - "Week 11 — fermlit dataset engineering" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 19 - "Week 12 — endorsement and hybrid model" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 20 - "Week 13 — fermlit release and paper outline" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 21 - "Week 14 — paper 1 full draft" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 22 - "Week 15 — paper 1 review and revision" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 23 - "Week 16 — paper 1 preprint gate" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 24 - "Week 17 — paper 2 complete experiments" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 25 - "Week 18 — paper 2 full draft" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 26 - "Week 19 — recruiter portfolio and review" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 27 - "Week 20 — paper 2 gate and halfway review" Cohesion: 0.11 Nodes (18): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+10 more) ### Community 28 - "Week 21 — protein study and partner scope" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 29 - "Week 22 — protein validation and baselines" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 30 - "Week 23 — extremophile candidate ranking" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 31 - "Week 24 — coauthor and validation gate" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 32 - "Week 25 — trialkit field module" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 33 - "Week 26 — trialkit plate module" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 34 - "Week 27 — loop audit offer and pipeline" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 35 - "Week 28 — first invoice gate" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 36 - "Week 29 — audit delivery or sales recovery" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 37 - "Week 30 — audit readout and validation results" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 38 - "Week 31 — paper 3 coauthor draft" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 39 - "Week 32 — paper 3 gate and career refresh" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 40 - "Week 33 — labdocs ingestion and traceability" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 41 - "Week 34 — labdocs retrieval evaluation" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 42 - "Week 35 — labdocs release and local benchmark" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 43 - "Week 36 — journal and joss submissions" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 44 - "Week 37 — pilot or job process" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 45 - "Week 38 — scientific talk and proof" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 46 - "Week 39 — fund portfolio offer" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 47 - "Week 40 — final retrospective and career decision" Cohesion: 0.12 Nodes (17): AI/scientific-method unit, Artifact contracts, Biology/domain unit, Branding and opportunity execution brief, Completion and gate review, Deeper walkthrough (v6), Founder/scientist paper, Handoff to the next model (+9 more) ### Community 48 - "app.js" Cohesion: 0.22 Nodes (8): account(), book(), embed(), folderPicker(), openEditor(), renderLists(), renderTimer(), ytId() ### Community 49 - "Week 04 — Materials: what to read, what to watch" Cohesion: 0.29 Nodes (7): Deeper — Saturday sandbox only, and only after the release is out, Link check log — 2026-09-15, NotebookLM kit sources for `LABLOOP-W04`, Read, Watch (YouTube), Week 04 — Materials: what to read, what to watch, Where this fits in the week ### Community 50 - "Week 13 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 13 review and handoff, What was actually completed? ### Community 51 - "Week 14 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 14 review and handoff, What was actually completed? ### Community 52 - "Week 15 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 15 review and handoff, What was actually completed? ### Community 53 - "Week 16 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 16 review and handoff, What was actually completed? ### Community 54 - "Week 17 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 17 review and handoff, What was actually completed? ### Community 55 - "Week 18 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 18 review and handoff, What was actually completed? ### Community 56 - "Week 24 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 24 review and handoff, What was actually completed? ### Community 57 - "Week 28 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 28 review and handoff, What was actually completed? ### Community 58 - "Week 31 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 31 review and handoff, What was actually completed? ### Community 59 - "Week 33 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 33 review and handoff, What was actually completed? ### Community 60 - "Week 35 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 35 review and handoff, What was actually completed? ### Community 61 - "Week 36 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 36 review and handoff, What was actually completed? ### Community 62 - "Week 37 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 37 review and handoff, What was actually completed? ### Community 63 - "LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech" Cohesion: 0.18 Nodes (11): LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech, PART 10 · Money (unchanged in substance from v4, moved to Half 2), PART 11 · Rescue protocols (for the days the plan meets your brain), PART 12 · Gates and metrics (the only numbers you track), PART 13 · Ignore for 40 weeks, PART 14 · Day 0 (tomorrow), minute by minute, PART 15 · The one thing to remember, PART 1 · The strategy in one picture (+3 more) ### Community 64 - "ACT IV · Becoming an author (weeks 14-20)" Cohesion: 0.22 Nodes (9): ACT IV · Becoming an author (weeks 14-20), PART 7 · Weeks 21-40 as chapters (depth, co-author, money), Week 14 · Write Paper 1, Week 15 · Review, revise, human read, Week 16 · GATE 16: Paper 1 on bioRxiv (L3), Week 17 · Paper 2 experiments, complete, Week 18 · Write Paper 2, Week 19 · Endorsement closed; review; site (+1 more) ### Community 65 - "ACT VI · The first client (weeks 25-32)" Cohesion: 0.22 Nodes (9): ACT VI · The first client (weeks 25-32), Week 25 · Instrument 2 trialkit (field module), Week 26 · Instrument 2 (plate module), Week 27 · Loop Audit offer, built on papers, Week 28 · GATE 28: first Loop Audit sold, Week 29 · Audit delivery 1, Week 30 · Audit delivery 2; Paper 3 results, Week 31 · Write Paper 3 (+1 more) ### Community 66 - "Instructions for any model preparing or executing this plan" Cohesion: 0.25 Nodes (8): Capacity and block shape, Commercial and career evidence, Completion and recovery, Default request: prepare one week, Instructions for any model preparing or executing this plan, Ownership and authority, Scientific evidence contract, Scope and source hierarchy ### Community 67 - "Sources and resource verification" Cohesion: 0.29 Nodes (7): Checks performed on 2026-09-12, Curriculum locator catalog, Known unverified on 2026-09-15, carried with a (verify) mark, Links confirmed through search on 2026-09-15, Local source register, Sources and resource verification, Weeks 00–04 reading and viewing lists (added 2026-09-15) ### Community 68 - "Week 01 — Materials: what to read, what to watch" Cohesion: 0.29 Nodes (7): Deeper — Saturday sandbox only, Link check log — 2026-09-15, NotebookLM kit sources for `LABLOOP-W01`, Read, Watch (YouTube), Week 01 — Materials: what to read, what to watch, Where this fits in the week (600-minute cap respected) ### Community 69 - "doc_view" Cohesion: 0.19 Nodes (16): doc_page(), doc_parts(), doc_path(), doc_save(), doc_task(), doc_view(), mark_tasks(), Resolve a library path, refusing anything outside ROOT, non-Markdown or inside… (+8 more) ### Community 70 - "Week 03 — Materials: what to read, what to watch" Cohesion: 0.29 Nodes (7): Deeper — Saturday sandbox only, Link check log — 2026-09-15, NotebookLM kit sources for `LABLOOP-W03`, Read, Watch (YouTube), Week 03 — Materials: what to read, what to watch, Where this fits in the week ### Community 71 - "PART 9 · Branding, connection ladder, endorsement" Cohesion: 0.29 Nodes (7): 9.1 Profiles (week 0, updated at each gate), 9.2 Content pillars and cadence (same as v4, re-pointed), 9.3 The connection ladder (founders and scientists), 9.4 Connection ladder (established companies, funds, scientific-data companies), 9.5 arXiv endorsement: three parallel routes (start week 12), 9.6 Templates (reuse v4 section 9 for build log, gap note, video, targeted message, audit one-pager), PART 9 · Branding, connection ladder, endorsement ### Community 72 - "ACT I · The apprentice learns the tank (weeks 0-4)" Cohesion: 0.33 Nodes (6): ACT I · The apprentice learns the tank (weeks 0-4), Week 0 · Cockpit and positioning, Week 1 · A tank in 80 lines, Week 2 · One hundred real batches, Week 3 · Golden batch, with statistics, Week 4 · L1: public and reproducible ### Community 73 - "ACT III · From sample to census (weeks 9-13)" Cohesion: 0.33 Nodes (6): ACT III · From sample to census (weeks 9-13), Week 10 · Inter-annotator agreement and the first real analysis, Week 11 · Dataset engineering and the reporting finding, Week 12 · Endorsement route opens; hybrid model v0, Week 13 · GATE 13: FermLit v0.5 public, Paper 1 outlined, Week 9 · FermLit at scale ### Community 74 - "Week 00 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 00 commitment ### Community 75 - "Week 00 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 00 review and handoff, What was actually completed? ### Community 76 - "Week 01 review and handoff" Cohesion: 0.18 Nodes (9): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 01 commitment, Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 01 review and handoff (+1 more) ### Community 77 - "Week 02 — Materials: what to read, what to watch" Cohesion: 0.29 Nodes (7): Deeper — Saturday sandbox only, Link check log — 2026-09-15, NotebookLM kit sources for `LABLOOP-W02`, Read, Watch (YouTube), Week 02 — Materials: what to read, what to watch, Where this fits in the week ### Community 78 - "Week 03 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 03 review and handoff, What was actually completed? ### Community 79 - "mitocondria-model.test.cjs" Cohesion: 0.10 Nodes (21): advance(), applyAction(), challengeComplete(), initialState(), restoreState(), unavailable(), assert, { chromium } (+13 more) ### Community 80 - "mitocondria-game.js" Cohesion: 0.20 Nodes (22): act(), animateAction(), animateNode(), answer(), clearFeedback(), finishAnimations(), next(), openInfo() (+14 more) ### Community 81 - "Week 05 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 05 commitment ### Community 82 - "Week 05 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 05 review and handoff, What was actually completed? ### Community 83 - "Week 06 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 06 commitment ### Community 84 - "Week 06 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 06 review and handoff, What was actually completed? ### Community 85 - "Week 07 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 07 commitment ### Community 86 - "Week 07 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 07 review and handoff, What was actually completed? ### Community 87 - "Week 08 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 08 commitment ### Community 88 - "Week 08 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 08 review and handoff, What was actually completed? ### Community 89 - "Week 09 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 09 commitment ### Community 90 - "Week 09 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 09 review and handoff, What was actually completed? ### Community 91 - "Week 10 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 10 commitment ### Community 92 - "Week 10 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 10 review and handoff, What was actually completed? ### Community 93 - "Week 11 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 11 commitment ### Community 94 - "Week 11 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 11 review and handoff, What was actually completed? ### Community 95 - "Week 12 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 12 commitment ### Community 96 - "Week 12 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 12 review and handoff, What was actually completed? ### Community 97 - "Week 13 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 13 commitment ### Community 98 - "Week 14 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 14 commitment ### Community 99 - "Week 15 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 15 commitment ### Community 100 - "Week 16 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 16 commitment ### Community 101 - "Week 17 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 17 commitment ### Community 102 - "Week 18 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 18 commitment ### Community 103 - "Week 19 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 19 commitment ### Community 104 - "Week 19 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 19 review and handoff, What was actually completed? ### Community 105 - "Week 20 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 20 commitment ### Community 106 - "Week 20 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 20 review and handoff, What was actually completed? ### Community 107 - "Week 21 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 21 commitment ### Community 108 - "Week 21 review and handoff" Cohesion: 0.18 Nodes (9): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 21 evidence register, Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 21 review and handoff (+1 more) ### Community 109 - "Week 22 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 22 commitment ### Community 110 - "Week 22 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 22 review and handoff, What was actually completed? ### Community 111 - "Week 23 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 23 commitment ### Community 112 - "Week 23 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 23 review and handoff, What was actually completed? ### Community 113 - "Week 24 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 24 commitment ### Community 114 - "Week 25 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 25 commitment ### Community 115 - "Week 25 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 25 review and handoff, What was actually completed? ### Community 116 - "Week 26 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 26 commitment ### Community 117 - "Week 26 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 26 review and handoff, What was actually completed? ### Community 118 - "Week 27 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 27 commitment ### Community 119 - "Week 27 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 27 review and handoff, What was actually completed? ### Community 120 - "Week 28 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 28 commitment ### Community 121 - "Week 29 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 29 commitment ### Community 122 - "Week 29 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 29 review and handoff, What was actually completed? ### Community 123 - "Week 30 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 30 commitment ### Community 124 - "Week 30 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 30 review and handoff, What was actually completed? ### Community 125 - "Week 31 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 31 commitment ### Community 126 - "Week 32 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 32 commitment ### Community 127 - "Week 32 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 32 review and handoff, What was actually completed? ### Community 128 - "Week 33 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 33 commitment ### Community 129 - "Week 34 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 34 commitment ### Community 130 - "Week 34 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 34 review and handoff, What was actually completed? ### Community 131 - "Week 35 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 35 commitment ### Community 132 - "Week 36 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 36 commitment ### Community 133 - "Week 37 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 37 commitment ### Community 134 - "Week 38 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 38 commitment ### Community 135 - "Week 38 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 38 review and handoff, What was actually completed? ### Community 136 - "Week 39 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 39 commitment ### Community 137 - "Week 39 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 39 review and handoff, What was actually completed? ### Community 138 - "Week 40 commitment" Cohesion: 0.40 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 40 commitment ### Community 139 - "Week 40 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 40 review and handoff, What was actually completed? ### Community 140 - "PART 0 · How to use this document (read this every Monday for the first month)" Cohesion: 0.40 Nodes (5): 0.1 The honest answer to your question, 0.2 The cockpit: five files, nothing else, 0.3 The rituals (this is the ADHD armor), 0.4 Weekly shape (never changes for 40 weeks), PART 0 · How to use this document (read this every Monday for the first month) ### Community 141 - "PART 4 · Curriculum from zero (four tracks, all free, exact units)" Cohesion: 0.40 Nodes (5): 4.1 Track B · Biology from zero (Tuesdays, ~30 h in Half 1), 4.2 Track M · AI science from the basics (Thursdays, ~30 h in Half 1), 4.3 Track D · Domain and craft (inside build blocks, no separate hours), 4.4 Track F · Founder papers (Thursday, last 30 minutes), PART 4 · Curriculum from zero (four tracks, all free, exact units) ### Community 142 - "PART 5 · Repos and materials to prepare (day 0 to week 2)" Cohesion: 0.40 Nodes (5): 5.1 Repositories, 5.2 README skeleton (same for every instrument repo), 5.3 Local environment (day 0, one block), 5.4 Annotation kit for FermLit (week 6), PART 5 · Repos and materials to prepare (day 0 to week 2) ### Community 143 - "ACT II · The reading robot (weeks 5-8)" Cohesion: 0.40 Nodes (5): ACT II · The reading robot (weeks 5-8), Week 5 · FermLit begins: the corpus, Week 6 · The gold set (the most important week of Half 1), Week 7 · The extraction agent, measured, Week 8 · GATE 8: technical report and L2 ### Community 144 - "ACT V · The protein detective finds a partner (weeks 21-24)" Cohesion: 0.40 Nodes (5): ACT V · The protein detective finds a partner (weeks 21-24), Week 21 · Paper 3 scoped with a partner, Week 22 · Baselines beaten honestly, Week 23 · Extremophile focus, Week 24 · GATE 24: co-authorship agreed ### Community 145 - "Talent and commercial asset requirements" Cohesion: 0.50 Nodes (4): Asset contracts, Required asset milestones, Talent and commercial asset requirements, Two hiring narratives to prepare ### Community 146 - "Commands for App" Cohesion: 0.50 Nodes (3): Commands for App, Next actions, Notes ### Community 147 - "LABLOOP: week-by-week execution" Cohesion: 0.50 Nodes (4): Governing documents, How to use it, LABLOOP: week-by-week execution, Weekly map ### Community 148 - "environment-checklist.md" Cohesion: 0.50 Nodes (3): environment-checklist.md, Next actions, Notes ### Community 149 - "Branding pack" Cohesion: 0.50 Nodes (3): Branding pack, Next actions, Notes ### Community 150 - "Environment checklist" Cohesion: 0.50 Nodes (3): Environment checklist, Next actions, Notes ### Community 151 - "Week 09 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 09 evidence register ### Community 152 - "Founder paper" Cohesion: 0.50 Nodes (3): Founder paper, Next actions, Notes ### Community 153 - "Opportunity actions" Cohesion: 0.50 Nodes (3): Next actions, Notes, Opportunity actions ### Community 154 - "Positioning" Cohesion: 0.50 Nodes (3): Next actions, Notes, Positioning ### Community 155 - "Study notes" Cohesion: 0.50 Nodes (3): Next actions, Notes, Study notes ### Community 156 - "Week 04 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 04 review and handoff, What was actually completed? ### Community 157 - "Week 01 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 01 evidence register ### Community 158 - "app.py" Cohesion: 0.15 Nodes (20): dashboard(), date(), focus_between(), folder_of(), folders(), LABLOOP study cockpit. Run `python app.py`, then open http://127.0.0.1:5000, Measured minutes inside one programme week (its Monday through its Sunday)., slug() (+12 more) ### Community 159 - "Week 00 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 00 evidence register ### Community 160 - "Week 03 commitment" Cohesion: 0.50 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 03 commitment ### Community 161 - "Week 03 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 03 evidence register ### Community 162 - "Week 27 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 27 evidence register ### Community 163 - "Week 06 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 06 evidence register ### Community 164 - "Week 07 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 07 evidence register ### Community 165 - "Week 08 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 08 evidence register ### Community 166 - "cards.py" Cohesion: 0.11 Nodes (26): blocks(), build(), chapters(), _fold(), Resource library: turns the v6 master plan and the weekly materials files into…, {week number: chapter text} from the v6 master plan., The bold labels v6 uses inside every chapter ('Welcome.', 'Learn it.', …) ->…, Every card in the programme, plus the per-week context /now needs. (+18 more) ### Community 167 - "_materials_cards" Cohesion: 0.13 Nodes (23): _bullets(), _clean(), _day(), _kind(), _learn_cards(), _materials_cards(), _mins(), Where this fits in the week' -> {ref: which day, which slot, which position in… (+15 more) ### Community 168 - "Week 11 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 11 evidence register ### Community 169 - "Week 12 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 12 evidence register ### Community 170 - "Week 02 review and handoff" Cohesion: 0.40 Nodes (5): Decision and next-model handoff, Gate and capacity, Learning and outcome, Week 02 review and handoff, What was actually completed? ### Community 171 - "Week 20 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 20 evidence register ### Community 172 - "post" Cohesion: 0.13 Nodes (25): context_processor, card_action(), chat_ask(), chat_job(), chat_log(), doc_move(), doc_pin(), focus_action() (+17 more) ### Community 173 - "Week 22 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 22 evidence register ### Community 174 - "Week 23 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 23 evidence register ### Community 175 - "Week 25 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 25 evidence register ### Community 176 - "Week 05 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 05 evidence register ### Community 177 - "index" Cohesion: 0.22 Nodes (12): card_view(), chat_page(), current_week(), files(), learn_page(), now_page(), pick(), One card for the next block: unfinished, inside the time budget, nearest to… (+4 more) ### Community 178 - "git_sync" Cohesion: 0.31 Nodes (11): after_request, count_interaction(), git(), git_sync(), pending(), {interactions, pushed: {commit: push time}}; `update(state)` mutates it under a…, Commit every change and push. The counter resets once the commit is in., sync_page() (+3 more) ### Community 179 - "Week 30 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 30 evidence register ### Community 180 - "doc_rel" Cohesion: 0.28 Nodes (9): doc_folders(), doc_list(), doc_new(), doc_rel(), doc_title(), library(), place(), Every folder a document can live in, as paths relative to ROOT ('' is the… (+1 more) ### Community 181 - "Week 33 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 33 evidence register ### Community 182 - "Week 38 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 38 evidence register ### Community 183 - "Week 39 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 39 evidence register ### Community 184 - "Week 13 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 13 evidence register ### Community 185 - "ACT VII · The lab's memory (weeks 33-35)" Cohesion: 0.50 Nodes (4): ACT VII · The lab's memory (weeks 33-35), Week 33 · Instrument 3 labdocs, part 1, Week 34 · labdocs, part 2, Week 35 · labdocs, part 3 ### Community 187 - "Source reconciliation and feasibility decisions" Cohesion: 0.67 Nodes (3): Assumptions left visible, Capacity decisions to make during execution, Source reconciliation and feasibility decisions ### Community 189 - "PART 3 · The scientific thesis (explained twice: like a kid, then like a reviewer)" Cohesion: 0.67 Nodes (3): 3.1 Like a kid, 3.2 Like a reviewer, PART 3 · The scientific thesis (explained twice: like a kid, then like a reviewer) ### Community 195 - "Week 35 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 35 evidence register ### Community 196 - "md" Cohesion: 0.25 Nodes (8): heading_ids(), href(), link_mentions(), one(), md(), Relative Markdown link -> app URL. Markdown goes to the reader/editor, anything…, Backticked `file.md` mentions -> open/edit link. A weekly deliverable that is…, GitHub-compatible anchors on headings, so `file.md#some-heading` links land in… ### Community 197 - "Week 02 commitment" Cohesion: 0.50 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 02 commitment ### Community 198 - "Week 16 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 16 evidence register ### Community 199 - "Week 14 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 14 evidence register ### Community 200 - "Week 15 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 15 evidence register ### Community 201 - "Micromundo · Misión ATP" Cohesion: 0.50 Nodes (3): Archivos, Comprobaciones, Micromundo · Misión ATP ### Community 202 - "Week 17 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 17 evidence register ### Community 203 - "Week 18 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 18 evidence register ### Community 204 - "Week 24 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 24 evidence register ### Community 205 - "chatrunner.py" Cohesion: 0.22 Nodes (9): datetime, finish(), main(), Runs one consultant question through opencode and writes the answer to its job…, json, pathlib, re, subprocess (+1 more) ### Community 206 - "Week 31 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 31 evidence register ### Community 207 - "Week 02 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 02 evidence register ### Community 208 - "Week 26 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 26 evidence register ### Community 209 - "Week 36 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 36 evidence register ### Community 210 - "Week 37 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 37 evidence register ### Community 211 - "asset" Cohesion: 0.67 Nodes (3): asset(), Static URL stamped with the file's mtime, so an edited stylesheet or script is…, template_global ### Community 212 - "Week 40 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 40 evidence register ### Community 213 - "qs" Cohesion: 0.67 Nodes (3): qs(), Filter chips rebuild the current query string with one key changed., template_filter ### Community 214 - "Week 28 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 28 evidence register ### Community 215 - "Week 32 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 32 evidence register ### Community 216 - "Week 34 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 34 evidence register ### Community 217 - "Week 10 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 10 evidence register ### Community 218 - "Week 29 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 29 evidence register ### Community 219 - "Week 04 commitment" Cohesion: 0.50 Nodes (4): Deliverables to commit, Dependency and capacity check, Proposed calendar, Week 04 commitment ### Community 220 - "Week 04 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 04 evidence register ### Community 221 - "Week 19 evidence register" Cohesion: 0.50 Nodes (4): Actual learning and decisions, External events, when authorized and actually performed, Reproduction and scientific measurements, Week 19 evidence register ## Knowledge Gaps - **1300 isolated node(s):** `{ chromium }`, `assert`, `{ pathToFileURL }`, `path`, `test` (+1295 more) These have ≤1 connection - possible missing edges or undocumented components. (Counts symbols only; 1399 node(s) total have ≤1 connection when file, concept and rationale nodes are included.) - **7 thin communities (<3 nodes) omitted from report** — run `graphify query` to explore isolated nodes. ## Suggested Questions _Questions this graph is uniquely positioned to answer:_ - **Why does `LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech` connect `LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech` to `README.md`, `PART 6 · Weeks 0-20, block by block`, `PART 9 · Branding, connection ladder, endorsement`, `PART 0 · How to use this document (read this every Monday for the first month)`, `PART 4 · Curriculum from zero (four tracks, all free, exact units)`, `PART 5 · Repos and materials to prepare (day 0 to week 2)`, `PART 3 · The scientific thesis (explained twice: like a kid, then like a reviewer)`?** _High betweenness centrality (0.046) - this node is a cross-community bridge._ - **Why does `ACT VIII · Peer review and the crossroads (weeks 36-40)` connect `ACT VIII · Peer review and the crossroads (weeks 36-40)` to `README.md`?** _High betweenness centrality (0.034) - this node is a cross-community bridge._ - **Why does `Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4` connect `Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4` to `README.md`?** _High betweenness centrality (0.033) - this node is a cross-community bridge._ - **What connects `{ chromium }`, `assert`, `{ pathToFileURL }` to the rest of the system?** _1300 weakly-connected nodes found - possible documentation gaps or missing edges._ - **Should `README.md` be split into smaller, more focused modules?** _Cohesion score 0.06371406371406371 - nodes in this community are weakly interconnected._ - **Should `consult.py` be split into smaller, more focused modules?** _Cohesion score 0.11375661375661375 - nodes in this community are weakly interconnected._ - **Should `Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4` be split into smaller, more focused modules?** _Cohesion score 0.044444444444444446 - nodes in this community are weakly interconnected._