@diottodev/runic 1.0.0 → 1.1.0

package/research/grants/commands/cs-grants.md

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+---
+name: "cs-grants"
+description: "/cs:grants <research-idea> — NIH funding intelligence. 6-Q grill-me intake (idea + career stage + prelim + environment + posture + institutes) → 5-facet Consensus positioning + RePORTER POST institute mapping + NOSI fetches → 9-section .docx with mandatory program officer recommendation."
+---
+
+# /cs:grants — NIH Funding Intelligence
+
+**Command:** `/cs:grants <research-idea>`
+
+The `cs-grants` persona produces a strategic NIH funding overview as an editable `.docx` for clinical researchers.
+
+## When to Run
+
+- Scoping NIH funding for a new research idea
+- Preparing for an R01 / R21 / K-award submission
+- Identifying institute targets + study sections
+- Generating draft Significance/Innovation language
+
+## NIH-Only Scope
+
+Non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are **out of scope** — surfaced and flagged at intake. Use a different skill or manual search for those.
+
+## Forcing Intake (6 Questions, One at a Time)
+
+| Q | Asks | Notes |
+|---|---|---|
+| Q1 | Research idea (2-3 sentences) | refuses vague; "AI for healthcare" gets pushed back |
+| Q2 | Career stage: pre-doc / postdoc / early career / independent / senior | forcing choice |
+| Q3 | Preliminary data: none / pilot / strong / validated | forcing choice |
+| Q4 | Environment: R01-eligible / mid-tier / resource-constrained / industry-collab | forcing choice |
+| Q5 | Submission posture: new / resubmission / exploring | forcing choice |
+| Q6 | Known institute targets, or "no preference — find the right ones" | accept either |
+
+Stop condition: after Q6, commit and start Phase 2A. Never re-open intake.
+
+## What You Get
+
+After all 6 Qs + Phase 2A (Consensus) + Phase 2B (RePORTER) + NOSI discovery + Phase 3 DOCX:
+
+```
+grants_<topic-slug>_<YYYY-MM-DD>.docx
+
+9 sections:
+1. Executive Summary (career stage, environment, 3-4 key findings)
+2. Research Positioning (3-5 gap quotes + draft Significance/Innovation)
+3. Target Institutes (ranking table + interpretation)
+4. Grant Opportunities (NOSI callout if any + top-3 FOAs)
+5. Funded Overlap (top-5 projects + differentiation)
+6. Study Sections (ranking + best-match)
+7. Strategic Recommendations & Next Steps (3-4 recs + program officer + timeline)
+8. References (numbered, hyperlinked to Consensus)
+9. Audit Log (Consensus + RePORTER + NOSI tables + counts + plan tier)
+```
+
+## Critical Tool Constraints
+
+- **Consensus**: 1 q/sec sequential. Plan-tier detected from "Found N, showing top M" patterns.
+- **RePORTER**: **POST-only**. Use `bash_tool` + `curl`. NEVER `web_fetch` (GET-only — will fail silently).
+- **NOSI fetch**: `web_fetch` for `NOT-*` URLs. If fetch fails, log `[NOSI {number} — fetch failed]` and continue.
+
+## Discipline (Research-Pack Convention)
+
+- **One intake Q per turn.** Never bundle.
+- **Sequential Consensus.** 1 q/sec.
+- **RePORTER POST.** `bash_tool` + `curl`. Not `web_fetch`.
+- **Source discipline.** Cite only session results.
+- **Three-count tracking.** Sent / shown / cited (Consensus) + projects / cited (RePORTER).
+- **Plan-tier detect at first Consensus call.** Surface in audit.
+- **Dynamic FY window.** Compute at runtime; never hardcode years.
+- **Scope-aware mechanisms.** Career stage + scope + prelim, not stage alone.
+- **Mandatory program officer rec.** Single most valuable advice.
+
+## Mechanism Reference (Embedded)
+
+| Mechanism | Career stage | Scope | Prelim needed | Budget (typical) |
+|---|---|---|---|---|
+| F31, F32 | Trainee | Solo training | None–pilot | $40-50k/yr × 2-3 yr |
+| T32 | Inst. training grants | Pre-doc/postdoc | Institutional | Varies |
+| R03 | Independent | Small/pilot | None–pilot | $50k/yr × 2 yr |
+| R21 | Independent | Pilot/exploratory | None–pilot | $275k DC × 2 yr |
+| K-series | Early career | Career dev. | Pilot | $100-180k × 5 yr |
+| K99/R00 | Postdoc → ind. | Transition | Strong | $90k + $250k × 3 yr |
+| R01 | Independent | Hypothesis-driven | Strong | $250-499k × 4-5 yr |
+| R35 | Senior PI | Program | Validated | $750k × 5-8 yr |
+| U01 | Multi-site | Cooperative | Strong–validated | Varies; usually >$500k |
+| P01/P30 | Senior | Program | Validated | Multi-PI; >$1M/yr |
+
+## Submission Timeline (Embedded)
+
+| Mechanism | Standard receipt dates |
+|---|---|
+| R01, R21, R03 | Feb 5, Jun 5, Oct 5 |
+| K awards (K01, K08, K23, K99) | Feb 12, Jun 12, Oct 12 |
+| R34, R61/R33 | Feb 16, Jun 16, Oct 16 |
+| F31, F32 | Apr 8, Aug 8, Dec 8 |
+
+## Trigger Phrases
+
+- "grants for [topic]"
+- "find grants for my research idea"
+- "what grants match my research"
+- "help me find NIH funding"
+- "grant opportunities for my research"
+- "NIH funding for [topic]"
+
+## Anti-Patterns Rejected
+
+- Parallelizing Consensus calls
+- Using `web_fetch` for RePORTER (POST-only)
+- Hardcoded fiscal year values
+- Mechanism recommendations on career stage alone
+- Silently filling thin facets with training knowledge
+- Skipping audit log
+- Skipping program officer recommendation
+- Conflating "found" / "shown" / "cited"
+- Fabricating NOSI details when fetch fails
+
+## Related
+
+- Agent: [`cs-grants`](../agents/cs-grants.md)
+- Skill: [`grants`](../skills/grants/SKILL.md)
+- Source spec: [`megaprompts/08-grants-megaprompt.md`](../../../megaprompts/08-grants-megaprompt.md)
+- Sibling: `/cs:litreview` (academic literature, no RePORTER)
+
+---
+
+**Version:** 1.0.0
+**Source:** Path-B direct conversion of `megaprompts/08-grants-megaprompt.md`

package/research/grants/skills/grants/SKILL.md

@@ -0,0 +1,286 @@
+---
+name: grants
+description: "NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-facet Consensus positioning analysis (with draft Significance/Innovation language), maps the research to the right NIH institutes and study sections via RePORTER, finds NOSIs and funded overlap, and produces an editable Word document (.docx) with budget/scope-aware mechanism recommendations, submission timelines, and a mandatory program officer recommendation. Triggers: 'grants for [topic]', 'find grants for my research idea', 'what grants match my research', 'help me find NIH funding', 'grant opportunities for my research', or any grant-related request. NIH-only scope — non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are out of scope and flagged at intake."
+license: MIT
+metadata:
+  source_spec: "megaprompts/08-grants-megaprompt.md"
+  build_pattern: "Path B (direct conversion)"
+  research_pack_convention: "Agent Integrity Rules verbatim per PR #657 audit"
+  version: 1.0.0
+---
+
+# Grants — NIH Funding Intelligence
+
+> **Portability:** Requires `bash_tool` (for RePORTER POST via curl), Node.js with `docx` package, and a Consensus MCP connection. Works in Claude Code CLI natively. In Claude.ai with Code Execution + Consensus MCP, the workflow is supported but slower.
+
+> **Scope: NIH-only.** Non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are out of scope and flagged at intake.
+
+For a clinical researcher with a research idea, produce a strategic NIH funding overview as an editable `.docx`. Output covers research positioning analysis, institute mapping, targeted grant discovery, and strategic recommendations the researcher can edit, copy from, and share with their mentor.
+
+## Agent Integrity Rules (Research-Pack Convention)
+
+Inherited; locked verbatim per PR #657 audit.
+
+- **Execution discipline.** A step isn't complete until result is confirmed received. Consensus calls **sequential with 1+ sec pause**. RePORTER calls sequential.
+- **Data sourcing.** Count only what tool calls returned this session. Never supplement with training knowledge. Training knowledge labeled `[Not from Consensus/RePORTER — reference information]` and excluded from counts.
+- **Counts & attribution.** Queries sent / results shown / results cited — three separate numbers, never conflate. Every cited paper has retrievable URL from this session.
+- **Error handling.** On failure → wait 3s → retry once → log. After 3 consecutive failures across tools: stop, alert researcher, explain what's missing. Never silently skip.
+- **Transparency.** Audit Log section in the DOCX. Same standards in chat summary as in document.
+
+See [`references/reporter_post_patterns.md`](references/reporter_post_patterns.md) for the RePORTER POST canon + plan-tier detection.
+
+## Phase 1: Grill-Me Intake (6 forcing questions, one at a time)
+
+### Q1 (root) — Research idea
+
+> **Describe the research idea in 2–3 sentences. What's the question, what's new, and what's the clinical relevance? Vague answers ("AI for healthcare", "biomarkers for disease X") will be rejected — push for specificity.**
+>
+> *Why I'm asking:* Five Consensus searches (established / stakes / current approaches / adjacent methods / gaps) depend on a precise research idea. Vague ideas produce vague gap quotes and useless positioning narrative.
+
+Refuse mush. Re-ask once with examples if user is too broad.
+
+### Q2 (depends on Q1) — Career stage
+
+> **Career stage — pick one:**
+>
+> 1. Pre-doctoral (PhD student, T32 trainee)
+> 2. Postdoctoral fellow (F32, K99 candidate)
+> 3. Early career (K-award candidate, first R01)
+> 4. Independent investigator (multiple R01s, established lab)
+> 5. Senior PI (R35, P-series, U01 leadership)
+>
+> *Why I'm asking:* Career stage filters mechanism recommendations. F-series for trainees, K-series for early career, R-series for independent. Picking the wrong stage produces unfundable mechanism suggestions.
+
+Forcing choice.
+
+### Q3 (depends on Q2) — Preliminary data status
+
+> **Preliminary data — pick one:**
+>
+> 1. None (de novo project, no pilot data yet)
+> 2. Pilot data (early findings, single-site)
+> 3. Strong preliminary (multi-experiment, ready for R01-scale)
+> 4. Validated and ready (multi-site, publication-ready)
+>
+> *Why I'm asking:* Prelim data status drives mechanism budget. No data → R03 / R21 pilot scope. Strong prelim → R01 / U01 multi-site scale. Mismatch produces uncompetitive applications.
+
+### Q4 (depends on Q2) — Environment
+
+> **Research environment — pick one:**
+>
+> 1. R01-eligible (research-intensive institution with NIH base funding)
+> 2. Mid-tier (regional academic medical center, modest NIH portfolio)
+> 3. Resource-constrained (smaller institution, minimal NIH base)
+> 4. Industry-collaborative (academic + industry partnership)
+>
+> *Why I'm asking:* Environment affects scope realism (multi-site U01 requires R01-eligible) and which mechanism categories are competitive (R15 specifically targets resource-constrained).
+
+### Q5 (depends on Q1) — Submission posture
+
+> **Submission posture — pick one:**
+>
+> 1. New application (first submission, no prior reviews)
+> 2. Resubmission (A1 with reviewer responses needed)
+> 3. Exploring (haven't decided yet whether to submit)
+>
+> *Why I'm asking:* Resubmissions need reviewer-response guidance in the DOCX (Section 7). New applications skip that. Exploring shifts emphasis to landscape over strategy.
+
+### Q6 (depends on Q1) — Known institute targets
+
+> **Are you already considering specific NIH institutes? List names (NCI / NHLBI / NIMH / NINDS / NIDDK / etc.) or say "no preference — find the right ones".**
+>
+> *Why I'm asking:* If you have an institute hypothesis, I'll validate it against RePORTER data. If not, I'll surface the top-3 institutes funding adjacent work from the institute-tally.
+
+Accept "no preference" as the common case.
+
+**Stop condition:** After Q6, commit and start Phase 2A. Never re-open intake after Phase 2A begins.
+
+## Phase 2A: Research Positioning (5 Consensus searches)
+
+Run sequentially at 1 q/sec. Each search corresponds to one positioning facet:
+
+1. **Established** — `"<research idea>" established evidence` — what's known
+2. **Stakes** — `"<topic>" mortality OR burden OR cost OR prevalence` — why it matters
+3. **Current Approaches** — `"<topic>" current treatment OR standard of care OR approach` — state of the art
+4. **Adjacent Methods** — `"<related technique>" applied to <topic>` — methodological possibilities
+5. **Gaps** — `"<topic>" limitations OR unanswered OR future directions OR challenge` — gap signals
+
+Use `scripts/citation_tracker.py --action record_consensus_search` for each. Plan-tier detected from first response.
+
+**Synthesis:** for each facet, extract 2-3 quotable findings (becomes Section 2 gap quotes). Draft Significance/Innovation language using "the field has established X (refs), but Y remains unanswered (refs)" pattern.
+
+## Phase 2B: Institute Mapping + Grant Discovery (RePORTER POST)
+
+RePORTER is **POST-only**. Use `bash_tool` + `curl` — never `web_fetch`.
+
+### Dynamic fiscal year window
+
+Compute at runtime via `scripts/fiscal_year_calculator.py`. Default: current FY + 3 prior. Federal FY starts Oct 1, so:
+
+```bash
+python ../scripts/fiscal_year_calculator.py --output json
+# Returns: {"current_fy": 2026, "window": [2023, 2024, 2025, 2026]}
+```
+
+### Narrow (AND) search — finds direct overlap
+
+```bash
+curl -X POST 'https://api.reporter.nih.gov/v2/projects/search' \
+  -H 'Content-Type: application/json' \
+  -d '{
+    "criteria": {
+      "fiscal_years": [2023, 2024, 2025, 2026],
+      "include_active_projects": true,
+      "advanced_text_search": {
+        "operator": "AND",
+        "search_field": "all",
+        "search_text": "<key term 1> <key term 2>"
+      }
+    },
+    "limit": 50,
+    "include_fields": ["project_num", "project_title", "agency_ic_admin", "study_section", "fiscal_year", "principal_investigators", "abstract_text"]
+  }'
+```
+
+### Broad (OR) search — finds adjacent work
+
+```bash
+curl -X POST 'https://api.reporter.nih.gov/v2/projects/search' \
+  -H 'Content-Type: application/json' \
+  -d '{
+    "criteria": {
+      "fiscal_years": [2023, 2024, 2025, 2026],
+      "advanced_text_search": {
+        "operator": "OR",
+        "search_field": "all",
+        "search_text": "<term> <synonym> <related concept>"
+      }
+    },
+    "limit": 50
+  }'
+```
+
+### Institute tally + study section ranking
+
+After RePORTER responses:
+- Tally `agency_ic_admin` (institute code: NCI, NHLBI, NIMH, etc.) → top-3 funding institutes
+- Tally `study_section` → top-2 study sections (where applications go for review)
+
+### NOSI discovery
+
+Parse RePORTER responses for `NOT-*` opportunity numbers. For each:
+
+```bash
+# NOSIs live at predictable URLs:
+# https://grants.nih.gov/grants/guide/notice-files/NOT-<INSTITUTE>-<YEAR>-<NUMBER>.html
+web_fetch <url>
+```
+
+If fetch fails: log `[NOSI {number} — fetch failed, not included]`, continue.
+
+## Mechanism Matching (Scope-Aware)
+
+NOT career stage alone. Career stage **+** project scope **+** prelim data drive recommendation.
+
+Use `scripts/mechanism_matcher.py`:
+
+```bash
+python ../scripts/mechanism_matcher.py \
+  --career-stage "early_career" \
+  --prelim-data "pilot" \
+  --environment "r01_eligible" \
+  --scope "single_site" \
+  --output json
+# Returns mechanism shortlist with rationale
+```
+
+See [`references/nih_mechanism_matching.md`](references/nih_mechanism_matching.md) for the full matrix.
+
+## Phase 3: DOCX Generation
+
+9 sections via Node.js + `docx` library. See [`references/docx_9_sections.md`](references/docx_9_sections.md) for full spec.
+
+1. **Executive Summary** — title + career stage + environment + 3-4 key findings bullets
+2. **Research Positioning** — 3-5 gap quotes (italicized, inline Consensus citations) + 2-3 paragraph positioning narrative + supporting evidence table
+3. **Target Institutes** — ranking table (institute, project count in window, % match to your idea) + 2-3 sentence interpretation
+4. **Grant Opportunities** — bold NOSI callout if any. Top-3 grants table with hyperlinked FOAs + per-grant scope/budget fit paragraph
+5. **Funded Overlap** — top-5 projects table (PI, project_num, IC, year, hyperlinked to RePORTER) + differentiation paragraph
+6. **Study Sections** — ranking table + best-match interpretation
+7. **Strategic Recommendations & Next Steps** — 3-4 numbered recs + **mandatory program officer rec** + submission timeline note + (if resubmission Q5=2) reviewer-response guidance + closing paragraph
+8. **References** — numbered bibliography, hyperlinked to Consensus
+9. **Audit Log** — Consensus searches table, plan-tier note, RePORTER searches table, NOSI fetches table, summary stats, tool constraints note, failed steps
+
+### Styling
+
+Arial 12pt body, navy headings (#1a3a5c), light blue table headers (#e8f0f8), amber NOSI callout. `ExternalHyperlink` patterns:
+- Paper citations: `https://consensus.app/papers/...`
+- FOA links: `https://grants.nih.gov/grants/guide/...`
+- RePORTER projects: `https://reporter.nih.gov/project-details/<id>`
+
+## Mandatory Program Officer Recommendation
+
+Always include in Section 7:
+
+> **Recommended next step: contact program officer at {top institute}.** Find their staff page at https://www.nih.gov/institutes-nih/list-nih-institutes-centers-offices → {institute} → Program Officers. Prepare: 1-page specific aims + your CV + 3 specific questions about fit. Email subject: "Pre-application inquiry: <topic>".
+
+This is the single most valuable advice for any applicant. Never skip.
+
+## Submission Timeline (Embedded in DOCX Section 7)
+
+| Mechanism | Standard receipt dates |
+|---|---|
+| R01, R21, R03 | Feb 5, Jun 5, Oct 5 |
+| K awards (K01, K08, K23, K99) | Feb 12, Jun 12, Oct 12 |
+| R34, R61/R33 | Feb 16, Jun 16, Oct 16 |
+| F31, F32 | Apr 8, Aug 8, Dec 8 |
+
+## Phase 4: Deliver
+
+- Save DOCX to `<output-dir>/grants_<topic-slug>_<YYYY-MM-DD>.docx`
+- Chat summary: file path + audit counts + plan tier + verdict on institute targets
+- Validate: `python scripts/office/validate.py <docx>`
+
+## Tooling
+
+| Script | Role |
+|---|---|
+| `scripts/citation_tracker.py` | Three-count audit (Consensus sent/shown/cited + RePORTER projects/cited) at `~/.grants_sessions/<session>.json` |
+| `scripts/fiscal_year_calculator.py` | Current FY + 3-prior window. Computed at runtime, never hardcoded. |
+| `scripts/mechanism_matcher.py` | Career stage × scope × prelim → mechanism recommendation shortlist |
+
+## References
+
+- [`references/nih_mechanism_matching.md`](references/nih_mechanism_matching.md) — career stage × scope × prelim → mechanism canon (7+ sources)
+- [`references/reporter_post_patterns.md`](references/reporter_post_patterns.md) — RePORTER curl POST templates + plan-tier detection (7+ sources)
+- [`references/docx_9_sections.md`](references/docx_9_sections.md) — 9-section .docx spec + technical requirements (7+ sources)
+
+## Error Handling
+
+| Failure | Behavior |
+|---|---|
+| Consensus rate-limit hit | Wait 3s, retry once, log; if still failing, alert researcher |
+| Consensus returns 0 for a facet | Surface explicitly; never fill with training knowledge |
+| Consensus plan-tier cap detected | Log tier, note in audit, surface to researcher |
+| RePORTER POST returns error | Retry once after 3s; if still failing, log and continue |
+| RePORTER returns <5 on narrow | Document; broad OR should compensate; surface low count |
+| NOSI fetch fails | Log `[NOSI {n} — fetch failed]`, continue |
+| 3 consecutive tool failures | Stop, alert researcher with what's missing |
+| DOCX generation fails | Save raw data as JSON fallback so researcher doesn't lose work |
+
+## Anti-Patterns To Reject
+
+- Parallelizing Consensus calls (will hit rate limit)
+- Using `web_fetch` for RePORTER (POST-only — `web_fetch` is GET)
+- Hardcoded fiscal year values
+- Mechanism recommendations based on career stage alone (must consider scope too)
+- Silently filling thin facet results with training knowledge
+- Skipping the audit log
+- Skipping the program officer recommendation
+- Conflating "papers found" with "papers shown" with "papers cited"
+- Fabricating NOSI details when fetch fails
+
+---
+
+**Version:** 1.0.0
+**Source spec:** [`megaprompts/08-grants-megaprompt.md`](../../../../megaprompts/08-grants-megaprompt.md)
+**Build pattern:** Path B (direct conversion). Research-pack sibling of pulse + litreview.