Results for “toc”

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

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Use this skill when the user asks about driver ergonomics — back/neck/shoulder injury prevention, seat adjustment + lumbar support, entering and exiting cab safely, load handling techniques, vibration reduction, stretching protocols, and how ergonomics affects workers compensation costs in trucking. Reference OSHA + ATA ergonomics research.

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Use this skill when the user asks about buying or selling a trucking company — valuation drivers (revenue, fleet age, CSA scores, customer concentration), asset purchase vs stock purchase, FMCSA authority transfer, due diligence checklist, common deal structures (cash, earnout, seller-financed), and what changes operationally after acquisition. Reference 49 CFR 365.401 (authority transfer).

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Use this skill when the user asks about the agricultural exemption from Hours of Service (HOS) rules under 49 CFR 395.1(k) — what qualifies as agricultural commodity, the 150-air-mile radius rule, state-declared planting/harvest seasons, livestock hauling specifics, and how to document operations under the exemption. Cite 49 CFR 395.1(k) and 49 USC 5117.

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Rigorous benchmarking of multi-agent coordination systems: experiment design, statistical analysis, human evaluation protocols, and reproducible reporting. NOT FOR ML model evaluation (use llm-evaluation-harness), A/B testing for web products, survey design, or general data science.

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Interpret and design bounded FIPA communicative-act exchanges using XC00037H semantics while keeping delivery, authority, and external effects separate. NOT for proving delivery, task authorization, or external effect completion.

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Building resilient distributed systems with circuit breakers, retries with full-jitter exponential backoff, retry budgets (per-request 3-attempt + per-client 10% ratio per Google SRE), deadline propagation, and the cascading-failure math (4 layers × 3 retries = 64x amplification). Grounded in Resilience4j, Microsoft Cloud Patterns, AWS Architecture Blog (Marc Brooker), and Google SRE Book. NOT for server-side rate limiting, bulkhead isolation, backpressure protocols, or database-specific retry.

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Architecture-level decisions for putting a CDN in front of a web app's static assets, API responses, and file/media delivery: provider selection (hyperscaler vs. specialist $/GB), signed-URL / tokenized access for gating private content at the edge, cache invalidation strategy (versioned URLs vs. purge APIs), origin shield / tiered caching for high-miss-rate content, and CDN-layer geo-restriction. Use when deciding which CDN to put in front of a new or growing service, when private/paywalled files need edge delivery without an origin round-trip per request, or when purge/invalidation behavior is being designed rather than debugged. NOT for HTTP cache-control header syntax, Vary, stale-while-revalidate, or surrogate-key purge mechanics (see `cdn-cache-control-headers`); NOT for Cloudflare-specific product configuration once Cloudflare is already chosen (see `cloudflare`); NOT for video-specific transcoding, adaptive bitrate ladders, or streaming-protocol packaging (see `managed-video-streaming-pipeline`).

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Expert in cluttering -- the lesser-known fluency disorder characterized by rapid/irregular speech rate, excessive disfluencies, and frequent ADHD comorbidity. Covers differential diagnosis from stuttering, assessment protocols, therapy approaches (rate control, self-monitoring, pragmatic awareness), technology-assisted intervention, and AI tools for people who clutter. Activate on 'cluttering', 'rapid speech disorder', 'speech rate too fast', 'speech disfluency not stuttering', 'disorganized speech', 'ADHD speech problems', 'cluttering vs stuttering', 'speech intelligibility', 'mazed speech', 'telescoping words'. NOT for stuttering-only treatment (overlap is common but they are distinct), hearing disorders, or voice disorders (pitch, resonance).

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Declare an agentic application's interaction disclosure, state, context, capabilities, and effect-control boundaries. Use for a reviewable design specification and static consistency audit before implementation. NOT for proving that controls are deployed or enforced, exposing private chain-of-thought, selecting a model/router, or designing a multi-agent protocol.

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Audit a compliance-ladder design (C0-C6) and transcript-fidelity ladder (T0-T5) plus their adapter conformance fixtures — Codex, Claude Code, Cloudflare, Ollama/LM Studio, custom stdio/HTTP agents — for the two failure modes that make a C-badge or T-fidelity label a lie: the ladder disagreeing with itself across doc/schema/ui/probe surfaces, and a level being reachable by self-report because no daemon-witnessed negative probe actually tries to forge it. Use when designing or freezing a compliance ladder, wiring an adapter conformance probe suite, deciding whether a numeric C-badge or T-label is safe to ship, or investigating a self-attestation or observed-to-controlled bypass risk. NOT for auditing a cryptographic protocol or whitepaper for adversarial soundness (`redteam-review`), writing TLA+/formal invariants for a daemon monitor (`runtime-verification-for-agents`), or agent identity, successor linkage, and reputation across restarts (`agent-identity-continuity-reputation`).

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Technical SEO audit across 9 categories: crawlability, indexability, security, URL structure, mobile, Core Web Vitals, structured data, JavaScript rendering, and IndexNow protocol. Use when user says "technical SEO", "crawl issues", "robots.txt", "Core Web Vitals", "site speed", or "security headers".

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Trial protocol for teaching AI Matrx an expert's knowledge until the platform breaks, fixing it. Use when asked to run an expertise trial, distil a person/creator/recent video into a Masterwork, or test the capture product. NOT for a known-missing feature (use build-sub-feature).

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No-loss protocol for changing an existing mandate's output contract. Use when changing what an agent or mandate emits or how it is typed: binding a kind, declaring output_kind, kind-backfill batches, provision reconciliation, or any make-this-contract-honest sweep. NOT for creating a new agent (use create-agent).

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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テスト可能なSwiftコードのためのプロトコルベースの依存性注入 — 焦点を絞ったプロトコルとSwift Testingを使用してファイルシステム、ネットワーク、外部APIをモック化。

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Law-driven abstraction protocol: evidence first, seam test, minimal algebra, executable law check.

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Agent-to-Agent (A2A) executor implementation patterns for task handling, execution management, and agent coordination. Use when building A2A executors, implementing task handlers, creating agent execution flows, or when user mentions A2A protocol, task execution, agent executors, task handlers, or agent coordination.

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Agent-to-Agent (A2A) server configuration patterns for HTTP, STDIO, SSE, and WebSocket transports. Use when building A2A servers, configuring MCP transports, setting up server endpoints, or when user mentions A2A configuration, server transport, MCP server setup, or agent communication protocols.

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Generate A2UI 0.8 protocol compliant UI code. Use when building agent-driven interfaces, generating JSONL messages for surfaceUpdate/dataModelUpdate/beginRendering, creating forms, lists, cards, or any UI components that render across web/mobile/desktop platforms.

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[52] EXECUTE. Three-stage refactoring workflow: (1) iterative research of refactor/modularization options, (2) plan + risk/edge-case analysis + Scope150 validation, then implement with tests after user confirmation, and (3) apply Scout105 cleanup protocol. Use when asked to refactor, modularize, or restructure code safely.

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