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v3-1-reintegration-discovery

v3.1 reintegration: discovery + panel fixes → workgraph_google_application_FINAL_v3_1.md

Metadata

Statusabandoned
Assignedagent-144
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-05-01T22:57:28.049024665+00:00
Started2026-05-01T23:09:29.072975727+00:00
Tagsgrant,urgent,v3,reintegration, eval-scheduled

Description

Description

The four discovery tasks (D1-D4) have produced concrete material to address the panel's raised issues. This task integrates everything into a new workgraph_google_application_FINAL_v3_1.md that addresses MUST FIX items M1, M2 (M3 handled separately as landing-page task; M4 requires Erik) and HIGH VALUE items H1, H2, H3, H6 from the panel synthesis, AND folds in discovery findings to give v3.1 specific named science deliverables.

Goal: v3.1 is the strongest version that has been produced. v2 and v3 stay as fallbacks. Erik picks at submission time.

What to read

  1. workgraph_google_application_FINAL_v3.md (commit 70c8e7f on worktree branch wg/agent-77/v3-assemble-stitch). Use git show 70c8e7f:workgraph_google_application_FINAL_v3.md.
  2. ~/poietic.life/notes/v3-review-synthesis-20260501.md — the panel synthesis with M1-M4, H1-H7, O1-O5
  3. ~/poietic.life/notes/v3-discovery-d1-pangenome-ecosystem-20260501.md
  4. ~/poietic.life/notes/v3-discovery-d2-phr-research-arc-20260501.md
  5. ~/poietic.life/notes/v3-discovery-d3-cnv-methods-20260501.md
  6. ~/poietic.life/notes/v3-discovery-d4-luca-highrisk-arc-20260501.md
  7. workgraph_google_application_FINAL_v2.md — for fallback reference if v3.1 hits a snag
  8. CLAUDE.md 'Word Limits'

What to do

Mechanical fixes from panel synthesis

  • M1: §36 'MIT, 93+ commits' → 'MIT, 2,000+ commits' or drop the count
  • M2: §26 reword vg / PGGB / citations packaging per synthesis recommendation
  • H1: §29 add adoption metric numbers (target: 10+ adopter labs by month 18, 50+ by month 36)
  • H2: §17a 'in production today' → 'in daily use across the founders' labs'
  • H3: §28 append architectural divergence sentence on Liverpool
  • H6: §19c soften 'BioBench established as the open standard' → 'BioBench actively used as a public benchmark by ≥3 external groups'

Discovery integration (this is the big lift)

Use the discovery outputs to replace v3's vague claims with named, verifiable deliverables:

  • §17 / §19 (approach + impact): weave in the substrate framing — WorkGraph as the substrate for Garrison lab's pangenome work (HPRC contributions, PHR research, CNV-aware methods development) AND for Luca's high-risk research arc systematically considered. Word caps ARE strict — you may need to compress existing content to make room.
  • §43-§46 (milestones): replace vague milestones with named deliverables from D1, D2, D3. At least one named software release, one named paper / preprint, one named consortium contribution by month 18 or 36. Keep timeline structure from v2.
  • §28 (related work): optionally reference ongoing pangenome group / vgteam ecosystem as 'WorkGraph deployed across' for context. Liverpool ack stays.
  • High-risk research arc: insert per D4's recommended placement (likely §17 or §19), 200-300 words framed as 'systematically considered research direction.' Watch Luca's COI on generative DNA.

Style sweep

  • No em-dashes
  • No 'PI' / 'lead PI'
  • Founder order Erik / Luca / Vaughn
  • No specific effort percentages
  • No v1 terms (KRAS, MRTX1133, pancreatic, Boltz, RFdiffusion, DiffDock)
  • No 'wrote this proposal with WorkGraph' recursion claim
  • CRISPRme/Casgevy: 'independently identified', no implied direct collaboration
  • DNA-Diffusion: track record only, not funded scope (COI)

Word cap recount

Every section. CLAUDE.md 'Word Limits' is the source of truth. If a section is over after integration, tighten.

Hard checks

  • Budget sums to $1,500,000
  • Liverpool ack present and now argued (H3 applied)
  • §30 'reviewers want science deliverable' risk preserved
  • v2 and v3 untouched (do NOT overwrite them)

Output

  1. workgraph_google_application_FINAL_v3_1.md at project root.
  2. ~/poietic.life/notes/v3-1-integration-summary-20260501.md (under 800 words):
    • Section-by-section word counts (final)
    • Which panel fixes applied (M1, M2, H1, H2, H3, H6) with before/after
    • Which discovery items integrated, into which sections
    • High-risk arc placement and final wording
    • Any TODOs left for Erik (M3 is separate; M4 is GitHub admin)
    • One paragraph 'how to choose v2 vs v3 vs v3.1' for Erik

wg log a one-paragraph summary on this task.

Constraints

  • HARD: every word cap respected. Recount every section.
  • HARD: do NOT overwrite v2 or v3.
  • HARD: COI rules (DNA-Diffusion outside funded scope; CRISPRme framing precise).
  • HARD: no em-dashes, no PI, no v1 terms, no recursion claim.
  • SOFT: prefer concrete named deliverables over abstract claims wherever the discovery provides them.

Validation

  • All discovery outputs read
  • M1, M2, H1, H2, H3, H6 applied
  • At least 3 named deliverables from D1/D2/D3 integrated into milestones
  • D4 high-risk arc paragraph integrated
  • Every word cap respected
  • Budget sums to $1.5M
  • v2 and v3 untouched
  • No em-dashes, no PI, no v1, no recursion claim
  • CRISPRme / DNA-Diffusion framing precise
  • workgraph_google_application_FINAL_v3_1.md exists at project root
  • Integration summary at ~/poietic.life/notes/v3-1-integration-summary-YYYYMMDD.md
  • Committed on worktree branch (not pushed)

Depends on

Required by

Log