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概要と使いどころ
Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
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NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. Optimize reactant and product geometries, run CI-NEB path search, optimize the transition state with a Hessian, verify with IRC (one imaginary mode, endpoints matching reactant/product, single NEB maximum), and report the electronic and Gibbs barriers. Use when you need a transition state, reaction barrier, activation energy, minimum energy path, or intrinsic reaction coordinate. Covers reactant/product atom-ordering pitfalls, feasibility sizing for single-core runs, and thermochemistry corrections. Renders an IRC energy-profile plot and an animated TS imaginary-mode HTML viewer. For 2D reaction scheme drawing use rdkit-chemdraw-cdxml.
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Query and download NCI Imaging Data Commons (IDC) cancer radiology and pathology datasets via the idc-index Python client. No authentication required: the parquet index ships inside the pip wheel, SQL runs locally via DuckDB, and DICOM downloads stream from public S3/GCS buckets through s5cmd. Use sql_query() for DuckDB cohort selection, get_collections/get_patients/get_dicom_studies/get_dicom_series for hierarchical browsing, download_from_selection() for downloads, and get_viewer_URL() for OHIF/Slim links. Use pydicom-medical-imaging for local DICOM reading; histolab for whole-slide pathology preprocessing.
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Computational pathology toolkit for whole-slide images (WSIs): load slides, extract tiles, stain normalization, nuclear segmentation, feature extraction, and ML training. Supports H&E and multiplex. For end-to-end pipelines from raw WSIs to quantitative outputs.
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WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep, tile-based DL, slide QC. Use pathml for multiplexed imaging.
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Analyze construction schedule critical path. Identify critical activities, calculate float, simulate schedule impacts, and optimize project duration.
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Analyze project critical path from schedule data. Identify critical activities, calculate float, and assess schedule risk.
日本語の概要は準備中です。原文の説明を表示しています。
Pre-implementation gate covering think-first, simplicity, surgical edits, and verifiable goals. Use when starting implementation to verify the approach.
日本語の概要は準備中です。原文の説明を表示しています。
自然言語メモリファイル（CLAUDE.md, todos, 設定）を原始人形式に圧縮し入力トークン削減。 技術内容・コード・URL・構造は完全保持。圧縮版が原ファイルを上書き、人間可読版は FILE.original.md として保存。「/genshijin-compress <filepath>」「メモリファイル圧縮」で起動。
This skill should be used when the user asks to "write a branching story", "interactive fiction", "choose your own adventure", "plan the branches", "choice graph", "add a choice", "gamebook", "Twine", "Ink", "draft a branch", "where the branches rejoin", "add an ending", "unreachable chapter", "path continuity", "state-differs-by-path", or wants to plan, draft, or revise a story project whose chapters carry `choices`. NOT for turning a finished linear book into an interactive edition in Ink or Twine (use adaptation).
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Applies the mental models and frameworks of Andrej Karpathy (deep learning, former Director of AI at Tesla, founding member of OpenAI, Eureka Labs). Use this skill whenever you are helping the user build neural networks from scratch, debug deep learning pipelines, evaluate AI agent workflows, design LLM apps, or navigate the transition to Software 3.0 (vibe coding). It is highly relevant for pedagogy (untangling complex knowledge), assessing AI capabilities vs. limitations (jagged intelligence, tokenization limits), and architectural decisions (end-to-end optimization vs. complex pipelines). Reach for this whenever discussing LLM training, autonomous systems, or AI-assisted coding.
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Fix iOS AVPlayer "CoreMediaErrorDomain error -12939 - byte range length mismatch" or similar video streaming failures when a proxy/edge/CDN service sits between the client and object storage (GCS, S3, R2). Use when: (1) iOS video fails with -12939 "byte range length mismatch - should be length 2 is length N", (2) curl with Range: bytes=0-1 returns full file instead of 2 bytes, (3) one URL path works with Range but another path to the same storage doesn't, (4) proxy advertises Accept-Ranges: bytes but returns 200 with full file for range requests. The root cause is typically a proxy handler that constructs a new request to the backend without forwarding the client's Range header.
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Fix "content disappears after publishing" bugs caused by REST API indexing lag. Use when: (1) User publishes content but it doesn't appear in their feed/profile, (2) REST API returns stale data immediately after write operations, (3) Async indexing backends (ClickHouse, Elasticsearch, etc.) haven't processed new events, (4) Content shows briefly then vanishes on refresh. Applies to any system with separate write path (WebSocket/direct DB) and read path (REST API with async indexing).
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Debug 404 errors for API endpoints in microservice architectures where code exists but routing sends requests to wrong service. Use when: (1) API endpoint returns 404 despite code being deployed, (2) Multiple services share same hostname via HTTPRoute/Ingress, (3) Service logs show "Health server" but you expected API endpoints, (4) Monorepo deploys multiple images and endpoint might be in different service than expected. Covers: verifying which service handles which paths, HTTPRoute path precedence, testing endpoints directly from inside cluster, matching image tags across services.
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Instruments authentication, authorization, and input-handling code paths to monitor security-relevant events and states at runtime. Use this skill when developers need to add security monitoring and logging to their code, including tracking authentication attempts (login/logout), authorization decisions (access control checks), input validation failures, session management events, and other security-critical operations. Supports Python, JavaScript/TypeScript, and Java with structured logging patterns. Triggers when users ask to add security instrumentation, monitor security events, log authentication/authorization, track security-sensitive operations, or add security observability to their codebase.
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Performs abstract interpretation to produce summarized execution traces and high-level program behavior representations. Highlights key control flow paths, variable relationships, loop invariants, function summaries, and potential runtime states using abstract domains (intervals, signs, nullness, etc.). Use when analyzing program behavior, understanding execution paths, computing loop invariants, tracking variable ranges, detecting potential runtime errors, or generating program summaries without concrete execution.
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Implements API versioning using URL paths, headers, or query parameters with backward compatibility and deprecation strategies. Use when managing multiple API versions, planning breaking changes, or designing migration paths.
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Think and work like an expert Civil Engineer. Use when a task calls for Civil Engineer judgment. Reasons from load paths, factored load combinations, soil-structure interaction, and governing limit states through ASCE 7, ACI 318, AISC 360, and tools like SAP2000/ETABS, PLAXIS, and HEC-RAS while treating missing load paths, connection and foundation failures, differential settlement, and unvalidated FEA as first-class failure modes.
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Think and work like an expert Acoustics Physicist. Use when a task calls for Acoustics Physicist judgment. Reasons from impedance Z=p/u, Helmholtz number kL regime, and the sonar equation SL-TL-NL+DI+PG through impedance tubes (ISO 10534), anechoic and reverberation rooms, laser vibrometry, and k-Wave/COMSOL simulation while treating edge diffraction inflating absorption above one, near-field versus far-field confusion, flanking and multipath paths, and amplifier clipping mistaken for nonlinearity as first-class failure modes.
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Think and work like an expert Acoustical Engineer. Use when a task calls for Acoustical Engineer judgment. Reasons from source-path-receiver control, logarithmic decibel levels, and mass-law transmission loss through IEC 61672 Class 1 metering, ISO 9613-2 propagation, SEA/FEM/BEM simulation, and ISO 9612 occupational surveys while treating flanking paths, coincidence dips, tonality penalties, and background-correction errors as first-class failure modes.
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Build production realtime voice agents with Hume's Empathic Voice Interface (EVI): speech-to-speech sessions, empathic/prosodic response design, EVI 3 versus EVI 4-mini selection, WebSocket and SDK integration, tools/function calling, interruption/barge-in, turn-taking, transcripts/audio artifacts, pricing/limits, privacy, safety, consent, and QA.
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Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.
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Workflow for outbreak-style pathogen genomics, surveillance, lineage assignment, and transmission-oriented comparative analysis.
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Discover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics, multi-omics, pathway, metagenomics, database queries, visualization, workflows): search the index, locate the best-matching skill, fetch its SKILL.md, and follow it.
日本語の概要は準備中です。原文の説明を表示しています。