Graph Report - biotech_skilling (2026-09-20)

01

Corpus Check

212 files · ~522,974 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)

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02

Summary

2026 nodes · 2795 edges · 219 communities (212 shown, 7 thin omitted)
Extraction: 100% EXTRACTED · 0% INFERRED · 0% AMBIGUOUS · INFERRED: 13 edges (avg confidence: 0.85)
Token cost: 0 input · 0 output

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03

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).

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04

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-batchlens-first-release/materials.md
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 01 commitment
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
Week 21 evidence register
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

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05

God Nodes (most connected - your core abstractions)

PART 6 · Weeks 0-20, block by block - 22 edges
Original v5 execution checklist snapshot - 22 edges
Applied AI for Biotech R&D and Biomanufacturing — Upskilling Plan v4 - 17 edges
LABLOOP · Master Plan v5 — From program manager to published AI scientist for biotech - 17 edges
ACT VIII · Peer review and the crossroads (weeks 36-40) - 17 edges
build() - 15 edges
Week 00 — cockpit and positioning - 14 edges
Week 01 — fermentation simulator - 14 edges
Week 02 — indpensim data and baseline - 14 edges
Week 03 — statistical batch monitoring - 14 edges

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06

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

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07

Import Cycles

None detected.

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08

Communities (219 total, 7 thin omitted)

Community 0 - "README.md"

Cohesion: 0.07 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)