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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Message queues, pub/sub, event sourcing with Kafka, RabbitMQ, Redis Streams. Activate on: event-driven, message queue, pub/sub, Kafka, RabbitMQ, event bus, async messaging, dead letter queue. NOT for: CQRS projections (use cqrs-event-sourcing-architect), real-time WebSocket (use websocket-realtime-expert), observability (use observability-apm-expert).

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Environment configuration manager for 12-factor config, feature flags, and multi-environment management. Activate on: environment variables, ConfigMap, feature flags, 12-factor config, dotenv management, config per environment, runtime config. NOT for: secret storage (use secret-management-expert), IaC provisioning (use terraform-module-builder), CI/CD variables (use github-actions-pipeline-builder).

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S3, multipart uploads, CDN integration, and presigned URLs for file storage. Activate on: file upload, S3, presigned URL, multipart upload, CDN, blob storage, image upload, media storage. NOT for: data warehouse storage (use lakehouse-architect), database design (use dimensional-modeler).

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Use when running analytical SQL over Parquet/CSV/JSON without a warehouse, replacing pandas for data wrangling, joining S3 data in-place, building local data marts, or embedding OLAP into an app. Triggers: read_parquet/read_csv setup, partitioned dataset queries, hive partitioning, glob patterns for S3, COPY TO export, attach Postgres/MySQL, UDFs in Python/R, MotherDuck cloud sync, columnar performance vs row stores. NOT for OLTP workloads (concurrent writes), distributed analytics at petabyte scale (use Spark/Trino), or vector search (use pgvector/Lance).

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Implementing distributed tracing with W3C Trace Context — the byte-precise `traceparent` and `tracestate` header formats, OpenTelemetry's W3CTraceContextPropagator as the modern default (replacing X-B3-* and X-Datadog-*), head vs tail sampling, and HTTP→SQL trace propagation via sqlcommenter. Grounded in the W3C REC and OpenTelemetry specs. NOT for OTel metrics/logs pipelines, vendor backend setup (Datadog/Honeycomb/Jaeger/Tempo), or browser RUM tracing.

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Expert data engineer for ETL/ELT pipelines, streaming, data warehousing. Activate on: data pipeline, ETL, ELT, data warehouse, Spark, Kafka, Airflow, dbt, data modeling, star schema, streaming data, batch processing, data quality. NOT for: API design (use api-architect), ML training (use ML skills), dashboards (use design skills).

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Generate, fill, and assemble PDF documents at scale. Handles legal forms, contracts, invoices, certificates. Supports form filling (pdf-lib), template rendering (Puppeteer, LaTeX), digital signatures (DocuSign), and document assembly. Use for legal tech, HR automation, invoice generation. Activate on "PDF generation", "form filling", "document automation", "digital signatures". NOT for simple PDF viewing, basic file conversion, or OCR text extraction.

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Warehouse cost reduction, auto-scaling, query optimization, and lifecycle policies for data infrastructure. Activate on: data cost, warehouse credits, cost reduction, auto-scaling, lifecycle policy, cold storage, cost monitoring, resource optimization. NOT for: query performance tuning (use data-warehouse-optimizer), batch job optimization (use batch-processing-optimizer).

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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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Build production computer vision pipelines for object detection, tracking, and video analysis. Handles drone footage, wildlife monitoring, and real-time detection. Supports YOLO, Detectron2, TensorFlow, PyTorch. Use for archaeological surveys, conservation, security. Activate on "object detection", "video analysis", "YOLO", "tracking", "drone footage". NOT for simple image filters, photo editing, or face recognition APIs.

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Practical incident-response runbook for a suspected or confirmed ComfyUI / GPU-daemon compromise. Triage, scope, contain, forensic collection, weight-integrity verification, rebuild from clean snapshot, postmortem. NOT for hygiene scans on a healthy box (use supply-chain-defense-for-ml-extensions), and NOT for runtime hardening of a fresh deployment (use gpu-hosted-asset-hardening).

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Use when wrangler deploys silently fail or produce wrong artifacts, secrets upload as empty strings, custom domain DNS is not resolving, route assignment broke after rename, observability/tail logs are needed, D1/KV/R2 bindings are missing, OAuth scope errors block a command, cookies on a redirect are not attaching, or the worker exceeds CPU time. Triggers: "Tenant or user not found", "Authentication error" on wrangler d1 push, secret length is 0 after upload, route returns origin not worker, "compatibility_date too old", 1101 errors, custom_domain assignment lost on script rename. NOT for AWS Lambda / Vercel Edge / Deno Deploy (different runtimes), Cloudflare Zero Trust, or R2-specific tuning.

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API gateway and reverse proxy configuration with Kong, Nginx, Traefik, routing, and auth middleware. Activate on: API gateway, reverse proxy, Kong, Nginx, Traefik, load balancer, ingress, auth middleware. NOT for: rate limiting algorithms (use api-rate-limiting-throttling-expert), service mesh (use service-mesh-microservices-expert).

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AWS CDK infrastructure builder using TypeScript with L2/L3 constructs and Well-Architected patterns. Activate on: AWS CDK, CDK construct, CDK stack, CDK pipeline, AWS infrastructure as code TypeScript, L2 construct, CDK patterns. NOT for: Terraform IaC (use terraform-module-builder), Kubernetes manifests (use kubernetes-manifest-generator), serverless framework (use devops-automator).

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Use when designing a background-job system, choosing between BullMQ / Sidekiq / RQ / Temporal / SQS, deciding queue-vs-workflow, sizing concurrency vs rate limits, building dead-letter queues, or making handlers idempotent. Triggers: jobs running twice on retry, lost jobs after worker crash, DLQ filling up, Redis OOM from job backlog, exactly-once requested, "do we need Temporal?", visibility timeout / lockDuration confusion, exponential backoff vs jitter, fan-out fan-in workflows. NOT for outbound webhook publishing (different concerns), receiver-side webhook handling (different concerns), event-streaming/Kafka topology, or in-process async (event loop only).

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Produces a narrow-interval quality signal for a WinDAGs skill that a third party can verify without inspecting model weights or method internals. The mechanism is attribution-kNN over a tamper-evident outcome log (task→skills→accept/reject store), combined with a conformal-prediction calibration certificate that provides a formal coverage guarantee. Thompson/Beta sampling is explicitly rejected as a category error: it produces a selection signal for stationary i.i.d. rewards, not an attestation signal for context-dependent LLM output quality. The resulting bundle — outcome-log Merkle root + conformal threshold + optional TEE guardrail signature — constitutes a "narrow-interval trust" credential: verifiable, bounded, and internals-opaque.

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Expert in background job processing with Bull/BullMQ (Redis), Celery, and cloud queues. Implements retries, scheduling, priority queues, and worker management. Use for async task processing, email campaigns, report generation, batch operations. Activate on "background job", "async task", "queue", "worker", "BullMQ", "Celery". NOT for real-time WebSocket communication, synchronous API calls, or simple setTimeout operations.

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Apache Airflow DAGs, operators, SLA monitoring, and workflow orchestration. Activate on: Airflow, DAG, operator, sensor, scheduler, task dependency, SLA, backfill, XCom. NOT for: dbt transformations (use dbt-analytics-engineer), streaming pipelines (use streaming-pipeline-architect).

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The TTS/STT/audio-playback system behind the one `speak()` entry point. Use when working on read-aloud, the Listen panel, voice/speed settings, transcription, mic capture, SpeakerButton, iOS playing silence, audio API routes, or files in features/audio/, features/tts/, hooks/tts/, app/api/audio/.

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Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with specialized knowledge, workflows, or tool integrations.

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Spring Bootアーキテクチャパターン、REST API設計、レイヤードサービス、データアクセス、キャッシング、非同期処理、ログ。Java Spring Bootバックエンド作業に使用。

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