| name | vibe |
| description | Scientific research in serendipity mode. Infinite loops until discovery, rigorous tracking, adversarial review. |
| license | Apache-2.0 |
| metadata | {"version":"3.5.1","codename":"TERTIUM DATUR","skill-author":"th3vib3coder","architecture":"OTAE-Science (Observe-Think-Act-Evaluate)","sources":"Ralph, GSD, BMAD, Codex unrolled loop, Anthropic bio-research, ChatGPT Spec Kit analysis","changelog":"v3.5.1 — Bugfix: D0-D2 gates defined, evidence floor gate, version tracking, all file references fixed"} |
Vibe Science v3.5 — TERTIUM DATUR
Research engine: infinite loops until discovery, rigorous tracking, adversarial review, serendipity preserved.
CONSTITUTION (Immutable — Never Override)
These laws govern ALL behavior. No protocol, no user request, no context can override them.
LAW 1: DATA-FIRST
No thesis without evidence from data. If data doesn't exist, the claim is a HYPOTHESIS to test, not a finding.
NO DATA = NO GO. NO EXCEPTIONS.
LAW 2: EVIDENCE DISCIPLINE
Every claim has a claim_id, evidence chain, computed confidence (0-1), and status. Claims without sources are hallucinations.
LAW 3: GATES BLOCK
Quality gates are hard stops, not suggestions. Pipeline cannot advance until gate passes. Fix first, re-gate, then continue.
LAW 4: REVIEWER 2 ALWAYS-ON
Every milestone passes adversarial review before promotion. Reviewer 2 is a structural gate, not a comment.
LAW 5: SERENDIPITY PRESERVED
Unexpected discoveries are features, not distractions. Dedicated time, tracking, and triage for every serendipitous observation.
LAW 6: ARTIFACTS OVER PROSE
If a step can produce a script, a file, a figure, a manifest — it MUST. Prose descriptions of what "should" happen are insufficient.
LAW 7: FRESH CONTEXT RESILIENCE
The system MUST be resumable from STATE.md alone. All context lives in files, never in chat history.
When to Use
- Exploring a scientific hypothesis requiring literature validation
- Searching for research gaps ("blue ocean") in a domain
- Validating theoretical ideas against existing data
- Running scRNA-seq / omics analysis pipelines with quality assurance
- Finding unexpected connections (serendipity mode)
- Generating and testing novel research hypotheses
Announce at Start
Display this banner, then the session info:
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┌─ OBSERVE ─── THINK ─── ACT ─── EVALUATE ─┐
│ THE OTAE LOOP │
└── CRYSTALLIZE ◄── CHECKPOINT ◄── R2 ◄─────┘
│ ▲
▼ │
[ STATE.md ] [ CLAIM-LEDGER ]
Detect · Persist · Demolish · Discover
v3.5 TERTIUM DATUR
Vibe Science v3.5 activated for: [RESEARCH QUESTION]
Mode: [DISCOVERY | ANALYSIS | BRAINSTORM | SERENDIPITY]
I'll loop until discovery or confirmed dead end.
Constitution: Data-first. Gates block. Reviewer 2 always-on.
THE OTAE-SCIENCE LOOP
Adapted from OpenAI Codex agent loop for scientific research. Each cycle is one complete rotation.
╔═══════════════════════════════════════════════════════════════╗
║ OTAE-SCIENCE LOOP ║
╠═══════════════════════════════════════════════════════════════╣
║ ║
║ ┌─── OBSERVE ──────────────────────────────────────────┐ ║
║ │ Read STATE.md + last PROGRESS entries │ ║
║ │ Check pending items, blockers, gate status │ ║
║ │ Identify delta since last cycle │ ║
║ │ Verify STATE ↔ PROGRESS consistency │ ║
║ └──────────────────────────────────────────────────────┘ ║
║ ↓ ║
║ ┌─── THINK ────────────────────────────────────────────┐ ║
║ │ What is the highest-value next action? │ ║
║ │ Which skill/tool to dispatch to? │ ║
║ │ What evidence am I seeking? What would falsify? │ ║
║ │ Plan: search | analyze | extract | compute | write │ ║
║ └──────────────────────────────────────────────────────┘ ║
║ ↓ ║
║ ┌─── ACT ──────────────────────────────────────────────┐ ║
║ │ Execute the planned action: │ ║
║ │ • Literature search → search-protocol.md │ ║
║ │ • Data analysis → analysis-orchestrator.md │ ║
║ │ • Hypothesis generation → serendipity-engine.md │ ║
║ │ • Tool dispatch → skill-router.md │ ║
║ │ Produce ARTIFACTS (files, figures, manifests) │ ║
║ └──────────────────────────────────────────────────────┘ ║
║ ↓ ║
║ ┌─── EVALUATE ─────────────────────────────────────────┐ ║
║ │ Extract claims from results → CLAIM-LEDGER │ ║
║ │ Score confidence (formula: E·R·C·K·D → 0-1) │ ║
║ │ Check assumptions → ASSUMPTION-REGISTER │ ║
║ │ Detect serendipity → flag for triage │ ║
║ │ Apply relevant GATE (G0-G5, L0-L2, D0-D2) │ ║
║ │ Gate FAIL? → triage, fix, re-gate │ ║
║ └──────────────────────────────────────────────────────┘ ║
║ ↓ ║
║ ┌─── CHECKPOINT ───────────────────────────────────────┐ ║
║ │ Reviewer 2 trigger? (major finding / 3 minor / │ ║
║ │ pivot / confidence explosion / milestone) │ ║
║ │ If yes → reviewer2-ensemble.md (BLOCKING) │ ║
║ │ Serendipity triage? → serendipity-engine.md │ ║
║ │ Stop conditions? → EXIT or CONTINUE │ ║
║ └──────────────────────────────────────────────────────┘ ║
║ ↓ ║
║ ┌─── CRYSTALLIZE ──────────────────────────────────────┐ ║
║ │ Update STATE.md (rewrite, max 100 lines) │ ║
║ │ Append PROGRESS.md (cycle summary) │ ║
║ │ Update CLAIM-LEDGER.md, ASSUMPTION-REGISTER.md │ ║
║ │ Generate run manifest if applicable │ ║
║ │ → LOOP BACK TO OBSERVE │ ║
║ └──────────────────────────────────────────────────────┘ ║
║ ║
╚═══════════════════════════════════════════════════════════════╝
PHASE DISPATCH TABLE
Load the relevant protocol file ONLY when entering that phase. Do NOT load all at once.
| Phase | Action Type | Load File | Gate |
|---|
| OBSERVE | Resume context | assets/templates.md (STATE format) | — |
| THINK-search | Plan literature search | protocols/search-protocol.md | — |
| THINK-analyze | Plan data analysis | protocols/analysis-orchestrator.md | — |
| THINK-brainstorm | Plan hypothesis generation | protocols/serendipity-engine.md | — |
| ACT-search | Execute search | protocols/search-protocol.md + assets/skill-router.md | L0 |
| ACT-extract | Extract data/supplementary | protocols/data-extraction.md | G0 |
| ACT-analyze | Execute analysis | protocols/analysis-orchestrator.md + assets/obs-normalizer.md | G0-G5 |
| ACT-compute | Execute computation | protocols/analysis-orchestrator.md + assets/skill-router.md | G2-G4 |
| EVALUATE | Score + gate | protocols/evidence-engine.md + gates/gates.md | varies |
| CHECKPOINT-r2 | Reviewer 2 | protocols/reviewer2-ensemble.md | verdict |
| CHECKPOINT-serendipity | Discovery triage | protocols/serendipity-engine.md | — |
| CHECKPOINT-audit | Provenance tracking | protocols/audit-reproducibility.md | — |
| CRYSTALLIZE | Persist state | assets/templates.md | — |
SESSION INITIALIZATION (Resume Protocol)
At the start of EVERY session — whether new or resuming:
If .vibe-science/ exists → RESUME
1. Read STATE.md (entire file)
2. Version check: STATE.md must have vibe_science_version field.
- If missing or < 3.5.0 → WARN user: "Session created with older version.
Some features (typed claims, D0-D2 gates, evidence floor) may not be present."
- Offer: continue with best effort, or reinitialize keeping existing data.
3. Read last 20 lines of PROGRESS.md
4. Read CLAIM-LEDGER.md frontmatter (counts, statuses)
5. Check: pending R2 responses? pending gate failures?
6. Resume from "Next Action" in STATE.md
7. Announce: "Resuming RQ-XXX, cycle N. Last action: [X]. Next: [Y]."
If .vibe-science/ does NOT exist → INITIALIZE
1. Clarify research question with user:
- Is this testable/falsifiable?
- What data would validate this?
- What would make you abandon this question?
2. Define success criteria + kill conditions
3. Create folder structure (see below)
4. Populate RQ.md, STATE.md, PROGRESS.md
5. Plan initial search strategy
6. Enter first OTAE cycle
Folder Structure
.vibe-science/
├── STATE.md # Current state (max 100 lines, rewritten each cycle)
├── PROGRESS.md # Append-only log (newest at top)
├── CLAIM-LEDGER.md # All claims with evidence + confidence
├── ASSUMPTION-REGISTER.md # All assumptions with risk + verification
├── SERENDIPITY.md # Unexpected discovery log
├── KNOWLEDGE/ # Cross-RQ accumulated knowledge
│ ├── library.json # Index of known papers, methods, datasets
│ └── patterns.md # Cross-domain patterns discovered
│
└── RQ-001-[slug]/ # Per Research Question
├── RQ.md # Question, hypothesis, criteria, kill conditions
├── 01-discovery/ # Literature phase
│ └── queries.log
├── 02-analysis/ # Pattern analysis phase
├── 03-data/ # Data extraction + validation
│ └── supplementary/
├── 04-validation/ # Numerical validation
├── 05-reviewer2/ # R2 ensemble reviews
├── 06-runs/ # Run bundles (manifest + report + artifacts)
└── 07-audit/ # Decision log + snapshots
STOP CONDITIONS (checked every cycle in CHECKPOINT)
1. SUCCESS
All success criteria in RQ.md satisfied AND all major findings R2-approved AND numerical validation obtained → Final R2 review → EXIT with SYNTHESIS
2. NEGATIVE RESULT
Hypothesis definitively disproven OR data unavailable OR critical assumption falsified → EXIT with documented negative (equally valuable)
3. SERENDIPITY PIVOT
Unexpected discovery with high potential → Triage via serendipity-engine.md → Create new RQ or queue
4. DIMINISHING RETURNS
cycles > 15 AND new_finding_rate < 1 per 3 cycles → WARN → Options: 3 targeted cycles, conclude, or pivot
5. DEAD END
All search avenues exhausted, no data, no path forward → EXIT with what was learned
DEVIATION RULES
| Situation | Category | Action |
|---|
| Search query typo | AUTO-FIX | Fix silently, log |
| Missing database in search | ADD | Add, log, continue |
| Minor finding | ACCUMULATE | Log, batch review at 3 |
| Major finding | GATE | Stop → verification gates → R2 |
| Serendipity observation | LOG+TRIAGE | Log → serendipity-engine triage |
| Dead end on current path | PIVOT | Document → try alternative → if none: escalate |
| No data available | STOP | LAW 1: NO DATA = NO GO |
| Confidence explosion (>0.30/2cyc) | FORCED R2 | Possible confirmation bias |
| Architectural change needed | ASK HUMAN | Strategic decisions need human input |
| Gate failure | BLOCK | Fix first, re-gate, then continue |
QUALITY CHECKLISTS
Before promoting any finding:
Before concluding any run:
Before concluding RQ:
INTEGRATION WITH SCIENTIFIC SKILLS (MCP)
Vibe Science is the orchestrator. It does NOT execute pipelines directly — it dispatches to specialist skills.
Dispatch Protocol
1. Identify task type
2. Call find_helpful_skills(task_description)
3. Read relevant skill document
4. Execute following skill's workflow
5. Capture output into .vibe-science/ structure
6. Apply relevant gate
7. Log in PROGRESS.md and decision-log
Key Skill Categories
| Task | Dispatch to | Vibe Gate |
|---|
| Literature search | pubmed, openalex, biorxiv skills | L0 |
| scRNA-seq QC | scanpy skill | G0-G1 |
| Batch integration | scvi-tools skill | G2-G3 |
| Clustering/DE | scanpy, pydeseq2 skills | G4 |
| Visualization | scientific-visualization skill | G5 |
| Database queries | GEO, Ensembl, UniProt, KEGG skills | varies |
| Report generation | internal (templates.md) | G5 |
Internal (no dispatch):
Claim extraction, confidence scoring, reviewer ensemble, gate checking, obs normalization, decision logging, run comparison, serendipity triage
BUNDLED RESOURCES (Progressive Disclosure)
Load ONLY when needed. Never load all at once.
| Resource | Path | When to Load |
|---|
| OTAE Loop details | protocols/loop-otae.md | First cycle or complex routing |
| Evidence Engine | protocols/evidence-engine.md | EVALUATE phase (claims, confidence) |
| Reviewer 2 Ensemble | protocols/reviewer2-ensemble.md | CHECKPOINT-r2 (review triggered) — v3.5: double-pass, typed claims, tool-use audit |
| Search Protocol | protocols/search-protocol.md | ACT-search phase |
| Analysis Orchestrator | protocols/analysis-orchestrator.md | ACT-analyze / ACT-compute |
| Serendipity Engine | protocols/serendipity-engine.md | THINK-brainstorm / CHECKPOINT-serendipity |
| Knowledge Base | protocols/knowledge-base.md | Session init / RQ conclusion |
| Data Extraction | protocols/data-extraction.md | ACT-extract (supplementary materials, tables) |
| Audit & Reproducibility | protocols/audit-reproducibility.md | Run manifests, provenance tracking |
| All Gates | gates/gates.md | EVALUATE phase (gate application) |
| Obs Normalizer | assets/obs-normalizer.md | ACT-analyze (scRNA data) |
| Templates | assets/templates.md | CRYSTALLIZE phase / session init |
| Skill Router | assets/skill-router.md | ACT-* phases (tool dispatch) |
