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概要と使いどころ
Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug mechanism/indication data.
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Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts. Includes composition, icon sourcing, color for biological entities, and accessibility. Use when creating illustrative (not data-driven) scientific figures.
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Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriptions, assay summaries, and download SDF/PNG. For local cheminformatics use rdkit; for bioactivity-centric workflows use chembl-database-bioactivity.
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Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs. Affinities (pKi/pIC50/pKd), action (Agonist/Antagonist/etc.), species, structures (SMILES/InChI). No auth. Always resolve targets via geneSymbol/accession; most metadata lives in sub-resources (/databaseLinks, /structure, /synonyms).
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Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mouse. Use liana for pure-Python.
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Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.
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Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem. Use OpenCV for real-time video; CellPose for DL cell segmentation; napari for visualization.
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Benchling R&D Python SDK: CRUD on registry entities (DNA, RNA, proteins, custom), inventory, ELN, workflow automation. Needs Benchling account and API key. Use biopython for local sequence analysis; pubchem for chemical DBs.
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Register, segment, filter, resample 3D medical images (MRI, CT, microscopy) via SimpleITK Python; DICOM, NIfTI, multi-modal. Rigid/affine/deformable registration, threshold/region-growing segmentation, Gaussian/morph filtering, label stats, format conversion. Use to align volumes across timepoints/modalities, segment fluorescence, or convert DICOM→NIfTI.
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Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. Pipeline: sequence → MFE → partition function and pair-probability matrix → dot-bracket → duplex. Use for siRNA/sgRNA targeting, ribozyme design, RNA accessibility. Use RNAfold CLI for batch use without Python.
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Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
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Reviews code for security vulnerabilities and guides secure implementation using OWASP Top 10:2025, ASVS 5.0, the OWASP Top 10 for LLM Applications (2026), and the OWASP Top 10 for Agentic Applications (2026). Use when reviewing code or a diff for security issues, implementing authentication, authorization, sessions, or cryptography, handling untrusted input, files, or URLs, hardening config, dependencies, or CI, or building LLM and AI agent features.
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Get option chain data from Interactive Brokers for equities, ETFs, and futures (FOP), including calls and puts with strikes, bids, asks, volume, implied volatility, and model Greeks. Use when user asks about options using IBKR data, futures options (NQ/ES/CL/GC...), or needs real-time option quotes from their broker. Requires TWS or IB Gateway running locally.
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Security hardening and best practices for robotic systems, covering SROS2 DDS security, network segmentation, secrets management, secure boot, and the physical-cyber safety intersection. Use this skill when securing ROS2 communications, configuring DDS encryption and access control, hardening robot onboard computers, managing certificates and credentials, setting up network segmentation for robot fleets, or addressing the unique security challenges where cyber vulnerabilities become physical safety risks. Trigger whenever the user mentions SROS2, DDS security, robot security, robot hardening, ROS2 encryption, ROS2 access control, robot network security, secure robot deployment, robot certificates, keystore generation, robot firewall, e-stop security, safety controller isolation, or IEC 62443 for robotics.
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Provides comprehensive Tailwind CSS utility-first styling patterns including responsive design, layout utilities, flexbox, grid, spacing, typography, colors, and modern CSS best practices. Use when styling React/Vue/Svelte components, building responsive layouts, implementing design systems, or optimizing CSS workflow.
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Generates complete CRUD modules for NestJS applications with Drizzle ORM. Use when building server-side features in NestJS that require database operations, including creating new entities with full CRUD endpoints, services with Drizzle queries, Zod-validated DTOs, and unit tests. Triggered by requests like "generate a user module", "create a product CRUD", "add a new entity with endpoints", or when setting up database-backed features in NestJS.
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Enables interaction with Google NotebookLM for advanced RAG (Retrieval-Augmented Generation) capabilities via the notebooklm-mcp-cli tool. Use when querying project documentation stored in NotebookLM, managing research notebooks and sources, retrieving AI-synthesized information, generating audio podcasts or reports from notebooks, or performing contextual queries against curated knowledge bases. Triggers on "notebooklm", "nlm", "notebook query", "research notebook", "query documentation in notebooklm".
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Creates reusable Zod v4 schemas, validates API payloads, forms, and configuration input, transforms and coerces data safely, and handles validation errors with strong type inference for TypeScript applications. Use when designing validation layers, parsing `z.string()`, `z.object()`, or `z.email()` schemas, or implementing runtime type-safe data validation.
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Provides implementation patterns for Clean Architecture, Domain-Driven Design (DDD), and Hexagonal Architecture (Ports & Adapters) in NestJS/TypeScript applications. Use when structuring complex backend systems, designing domain layers with entities/value objects/aggregates, implementing ports and adapters, creating use cases, or refactoring from anemic models to rich domain models with dependency inversion.
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Provides implementation patterns for Clean Architecture, Hexagonal Architecture (Ports & Adapters), and Domain-Driven Design in Python applications with FastAPI or Flask. Use when designing maintainable backends with separation of concerns, implementing repository patterns, creating entities/value objects/aggregates, or structuring domain logic independent of frameworks for testability.
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Provides implementation patterns for Clean Architecture, Hexagonal Architecture (Ports & Adapters), and Domain-Driven Design in PHP 8.3+ with Symfony 7.x. Use when architecting enterprise PHP applications with entities/value objects/aggregates, refactoring legacy code to modern patterns, implementing domain-driven design with Symfony, or creating testable backends with clear separation of concerns.
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Provides LangChain4j patterns for implementing MCP (Model Context Protocol) servers, creating Java AI tools, exposing tool calling capabilities, and integrating MCP clients with AI services. Use when building a Java MCP server, implementing tool calling in Java, connecting LangChain4j to external MCP servers, or securing tool exposure for agent workflows.
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Provides Retrieval-Augmented Generation (RAG) implementation patterns with LangChain4j for Java. Generates document ingestion pipelines, embedding stores, vector search, and semantic search capabilities. Use when building chat-with-documents systems, document Q&A over PDFs or text files, AI assistants with knowledge bases, semantic search over document repositories, or knowledge-enhanced AI applications with source attribution.
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Provides Spring Data Neo4j integration patterns for Spring Boot applications. Use when you need to work with a graph database, Neo4j nodes and relationships, Cypher queries, or Spring Data Neo4j. Creates node entities with @Node annotation, defines relationships with @Relationship, writes Cypher queries using @Query, configures imperative and reactive Neo4j repositories, implements graph traversal patterns, and sets up testing with embedded databases.
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。