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How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Infers genetic super-population ancestry from a 23andMe/AncestryDNA file and computes ancestry-stratified odds ratios with an exploratory Ancestry Elevation Score (AES) showing where ancestry-specific GWAS effect sizes diverge from European reference estimates.

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This skill recommends that a multidisciplinary team, including an experienced endocrinologist, incorporates patient values and preferences while providing education about treatment options for Cushing’s syndrome. Use when planning treatment for a CS patient requiring coordinated care; triggers include persistent hypercortisolism after transsphenoidal surgery, consideration of bilateral adrenalectomy, radiotherapy, or medical therapy, and need for shared decision‑making.

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Recommends antihypertensive therapy including mineralocorticoid receptor antagonists (MRAs) for patients with a positive primary aldosteronism (PA) screening test who decline confirmatory testing. Triggers include when a patient has positive screening but refuses additional tests and asks "What should I treat with?" or initiates empiric therapy, with preference for MRAs in typical PA presentations (e.g., spontaneous hypokalemia, resistant hypertension, adrenal tumor on CT).

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Recommends correcting serum potassium to the laboratory reference range and repeating aldosterone-to-renin ratio (ARR) screening when the initial screen is negative in a hypertensive patient with hypokalemia. Use when a clinician encounters a negative PA screen in a hypertensive patient with hypokalemia and wonders whether to repeat testing after potassium repletion.

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Complete bedside prescribing reference for Mirago (mirabegron, beta-3 adrenoceptor agonist) for overactive bladder — covering contraindications, safety screening, drug interactions, dose selection in special populations, titration, and administration. Use when a clinician asks how to start mirabegron, what dose to use in renal or hepatic impairment, is mirabegron safe in this patient, mirabegron drug interactions, or Mirago for OAB.

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Bedside prescribing reference for Bemdec (bempedoic acid / NEXLETOL) — indication check, dose, statin co-prescribing safety caps, monitoring plan, warnings for hyperuricemia and tendon rupture, and special population guidance. Use when a clinician asks "can I start bempedoic acid", "Bemdec indication", "is bempedoic acid safe with my statin", "patient on Nexletol has joint pain or high uric acid", "bempedoic acid in CKD or liver disease or pregnancy", or any prescribing or monitoring question about bempedoic acid.

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Suggests using longer-acting glucocorticoids when standard hydrocortisone regimens are impractical due to nonavailability, poor adherence, or need for once-daily dosing. Triggers include glucocorticoid replacement therapy decisions where patients report difficulty with multiple daily doses, lack of access to hydrocortisone, or preference for simplified regimens.

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Diagnose monogenic and syndromic obesity in children and adolescents using a structured step-by-step algorithm. Use this skill whenever a clinician suspects a genetic cause of obesity, asks about leptin deficiency, MC4R mutation, POMC deficiency, PCSK1 deficiency, leptin receptor deficiency, Bardet-Biedl syndrome, Prader-Willi syndrome, Alström syndrome, or any case of early-onset severe obesity with hyperphagia. Also trigger for questions about targeted pharmacotherapy including setmelanotide or metreleptin, or when to order a genomic obesity panel. Cross-references the NHS Genomic Test Finder skill to surface the relevant R-code once a diagnosis is reached.

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Recommends measurement of plasma ACTH to establish primary adrenal insufficiency (PAI) diagnosis in patients with confirmed cortisol deficiency; a plasma ACTH concentration ≥2-fold the upper limit of the reference range supports PAI. Use when evaluating plasma ACTH in a patient with low morning cortisol or abnormal corticotropin stimulation test.

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Decompose an MVP vision into a sprint manifest — a prioritized feature list where every feature carries explicit done-criteria (a done-record reference, named edge tests, and a wiring test). Produces the sprint manifest that `sprint-oracle` checks for completeness. Use when planning a sprint of parallel work (Slice A of the sprint-mode epic). Not a workflow phase; the manifest it writes is the completeness contract a sprint is held to.

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The primary tool for code-navigation questions in ANY language (frontend or backend) — walk the structural graph from an entry point (page, route, handler, command, `main`) down through imports to the IO boundary (network call, query, file read). Use this skill, in preference to the Explore agent or global grep, whenever the user asks "where does X come from?", "what API/data populates Y?", "what renders or wraps the Z panel?", "which file for feature F?", "how is this wired up?", or any code-navigation question mapping a UI element, route, or feature concept to source files. Also reverse queries ("what uses /api/foo?", "who consumes this service?"). Keyword search routinely picks up unrelated flows sharing a domain word and produces wrong answers; the walk follows the actual graph. The JS/TS `walk.mjs`/`discover.mjs` are an optional accelerator, not required — the walk is language-agnostic.

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The sprint completeness oracle — a mechanical, exit-code-driven check that every feature in a sprint manifest is provably complete across three dimensions (a done-record reference, resolvable edge tests, and a resolvable wiring test). Fails loud with a per-feature gap list naming the missing dimension. Read-only. Use to gate a sprint before it is called done (Slice A of the sprint-mode epic), or any time you want a completeness reading.

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Draft or revise English prose for any brief — documentation body, intake problem statements, spec context, RCA summaries, marketing copy, README sections, PR descriptions. Mandatorily invokes `Skill(humanizer)` as the final pass on every draft. Conditionally invokes `copywriting` for persuasive register, `documentation` for reference docs, `technical-tutorials` for tutorials. Used when any phase needs human-readable prose written or rewritten. Composition only — research and register-picking happen in the caller's context.

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Drift check between the baseline implementation on disk and the claims in `docs/init/seed.md` + cross-references in CLAUDE.md, README.md, and the rendered docs site. Verifies hook/agent/skill/command names + counts, settings.json wiring, project.json key presence, .mcp.json servers, vendored license files, and helper script presence. Exit 0 PASS / 1 FAIL — suitable for CI. Read-only; safe to invoke any time.

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Workflow Phase 10 — orchestrator for documentation work. Surveys the diff, routes any page on a documentation surface through `technical-writer`, standalone technical reference through the `documentation` skill, tutorials through `technical-tutorials`, and all other prose body work (inline docs, README updates, user-facing copy) through the `prose` skill (which mandates `humanizer` and conditionally `copywriting`). Verifies completeness and marks phase done.

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Use RoutIR — call a running endpoint with the client, stand up a local server that mixes locally-hosted services with services proxied from a remote master server, and extend RoutIR with new bi-encoders, rerankers, and document collections by writing a small config (and optionally one Python file referenced via `file_imports`). No checkout of the routir source is required.

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Use when a request needs external sources, current facts, listings, a supplied URL, papers, or library and API documentation. When using Firecrawl for the request, use firecrawl_search to find sources and firecrawl_scrape to read a supplied or discovered URL. Firecrawl also retrieves documents, collects structured data, and tracks website changes. Respect explicit source and tool preferences.

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Generate production-ready manga pages, chapter pages, covers, and panel sequences with strict recurring-character consistency. Use this when the user asks for a manga page, manga scene, chapter page, comic page, storyboard page, or character-consistent page generation. Before generating any page, inspect `img-memory`, create missing character sprites/reference sheets, make those images visible to image generation, then generate the final manga page.

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Understand audience demographics, preferences, behavior patterns, and engagement quality across Facebook, Instagram, YouTube, and TikTok.

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AI-powered presentation generation via the 2slides API — create slides from text, match a reference image style, summarize documents into decks, add AI voice narration, and export pages/audio. Use for any "make slides", "create a deck", or "slides from this document" request.

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Local-only regression / benchmark skill for ui-clone-skills maintainers. Drives the standard ui-reverse-engineering pipeline against the canonical reference site (https://realfood.gov) and records AE/SSIM, iteration count, gate fail counts, and outcome to benchmark/history.csv so prompt / sub-doc / model-version drift surfaces as a trend. Trigger phrases: "run benchmark" / "regression benchmark" / "benchmark clone". The Makefile no longer has a `benchmark` target — setup is inline bash in this skill (Step 1 below). Internal: NOT registered in `.claude-plugin/plugin.json` `skills`. Not part of the public 3-skill marketplace surface. Maintainer tooling only.

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Capture baseline evidence from a live website URL: screenshots, scroll states, hover/click behavior, parallax, timers, and transition recordings. Use when reference artifacts are needed before implementation or comparison; not to build or diagnose a clone.

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