/orchestrate

name: orchestrate
description: Use when the user describes a research goal without naming a skill, or the task spans several skills. Classifies the request, plans the order and routes to the right medsci-skills skill(s) instead of producing their output itself.
metadata:
  triggers: "orchestrate, research help, what should I do next, where do I start, help me with my paper, run the pipeline, which skill, end-to-end, e2e"

Orchestrate Skill

Route research requests in the **medsci-skills** bundle to the right skill, or chain several skills in the correct order. You classify, plan and delegate: never produce a routed skill's output yourself — invoke the skill that owns it.

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Available Skills

| Skill | Domain | When to Route | |-------|--------|---------------| | **search-lit** | Literature | Find papers, verify citations, build reference lists, check if a topic has been studied | | **design-study** | Methodology | Review study design, identify leakage/bias, pick reporting guideline, validate analysis plan | | **intake-project** | Project setup | New or messy project folder, "what is this project?", classify and scaffold | | **manage-project** | Project mgmt | Scaffold directories, track progress, generate checklists and timelines | | **analyze-stats** | Statistics | Generate R/Python code for diagnostic accuracy, demographics, meta-analysis stats, agreement, regression (logistic/linear), propensity score, repeated measures | | **make-figures** | Visualization | ROC curves, forest plots, flow diagrams (PRISMA/CONSORT/STARD), Kaplan-Meier, Bland-Altman, visual/graphical abstracts | | **meta-analysis** | Systematic review | Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA | | **write-paper** | Writing | IMRAD manuscript drafting (8-phase pipeline), any section writing | | **self-review** | Quality | Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional `--panel` for a high-stakes final QC pass | | **check-reporting** | Compliance | Audit against 49 reporting guidelines and risk-of-bias tools | | **revise** | Revision | Parse reviewer comments, generate point-by-point response, track changes | | **grant-builder** | Funding | Structure grant proposals: significance, innovation, approach, milestones | | **present-paper** | Presentation | Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep | | **publish-skill** | Packaging | Convert a personal skill into an open-source distributable package | | **calc-sample-size** | Statistics | Sample size calculation (17 tests including Cox EPV), power analysis, IRB justification text | | **find-journal** | Submission | Journal recommendation based on abstract/scope matching, post-rejection re-targeting | | **add-journal** | Journal DB | Add a new journal to the profile database; extracts metadata from author guidelines | | **fulltext-retrieval** | Literature | Batch download open-access PDFs by DOI using Unpaywall, PMC, OpenAlex APIs | | **deidentify** | Data safety | De-identify clinical data containing PHI before any LLM processing. Standalone Python CLI (no LLM). | | **clean-data** | Data | Data profiling, missing value flagging, outlier detection, cleaning code generation | | **generate-codebook** | Data | Generate a citable data dictionary/codebook from a dataset; flags coded variables as [NEEDS DICTIONARY]; feeds /define-variables | | **version-dataset** | Data | Content-hash manifest of a dataset; verify drift (schema/rows/values) and diff versions; reproducibility lock | | **write-protocol** | Protocol | IRB/ethics protocol drafting, 4 core sections + 6 skeleton sections with TODO markers | | **define-variables** | Operationalization | Literature-grounded variable definitions, cutoffs, DB-variable mappings; runs between `/search-lit` and `/write-protocol` for observational studies | | **verify-refs** | Reference audit | Read-only PubMed/CrossRef audit of manuscript references; first-author cross-check; sole writer of `qc/reference_audit.json`. Never modifies refs | | **manage-refs** | Reference lifecycle | Citekey validation, journal-CSL pandoc rendering, manuscript ↔ DOCX cross-reference QC, [N] ↔ [@key] marker conversion, Zotero CWYW field-code injection. Sole writer of `manuscript_final.docx`, `qc/xref_audit.json` | | **lit-sync** | Reference sync | Zotero collection ↔ Better BibTeX `manuscript/_src/refs.bib` ↔ Obsidian literature notes. Sole writer of refs.bib (auto-export); upstream of `manage-refs` | | **obsidian-paper-vault** | Vault build | A folder of PDFs → templated Obsidian literature notes + atomic concept notes synthesized across them. Enters the same vault folders as `lit-sync` from the PDF side | | **humanize** | Quality | AI-pattern density sweep (<2.0/1000 words target); rewrites flagged passages while preserving technical accuracy. Phase 7.5 of write-paper | | **academic-aio** | Visibility | AI-search-engine optimization for medical AI papers (Perplexity, ChatGPT web, Elicit, Consensus, SciSpace, RAG tools). Opt-in checklist; never auto-applies edits | | **render-pdf-doc** | Document layout | Non-bibliography academic markdown → PDF (proposal, briefing, anchor doc, IRB cover, reference table), CJK-aware. Boundary opposite of `manage-refs scripts/render_pandoc.sh` | | **fill-protocol** | Form filling | Institutional Word form filling (.doc/.docx) for IRB/ethics/grant templates; renders `write-protocol` content into the institutional template | | **fill-icmje-coi** | Form filling | Batch ICMJE COI Disclosure Form generation per author from a synthetic seed | | **sync-submission** | Submission | SSOT-to-submission drift audit; journal-specific submission manifest creation from canonical manuscript artifacts | | **peer-review** | Review | External manuscript peer review draft generation (journal-specific formatting). Use ONLY for reviewing other authors' work, never for self-review | | **review-paper** | Writing |