pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
pymc-bayesian-modeling
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
pytorch-lightning
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
qiskit
Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.
qutip
Quantum mechanics simulations and analysis using QuTiP (Quantum Toolbox in Python). Use when working with quantum systems including: (1) quantum states (kets, bras, density matrices), (2) quantum operators and gates, (3) time evolution and dynamics (Schrödinger, master equations, Monte Carlo), (4) open quantum systems with dissipation, (5) quantum measurements and entanglement, (6) visualization (Bloch sphere, Wigner functions), (7) steady states and correlation functions, or (8) advanced methods (Floquet theory, HEOM, stochastic solvers). Handles both closed and open quantum systems across various domains including quantum optics, quantum computing, and condensed matter physics.
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
reportlab
PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
scholar-evaluation
Systematic framework for evaluating scholarly and research work based on the ScholarEval methodology. This skill should be used when assessing research papers, evaluating literature reviews, scoring research methodologies, analyzing scientific writing quality, or applying structured evaluation criteria to academic work. Provides comprehensive assessment across multiple dimensions including problem formulation, literature review, methodology, data collection, analysis, results interpretation, and scholarly writing quality.
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
add-uint-support
Add unsigned integer (uint) type support to PyTorch operators by updating AT_DISPATCH macros. Use when adding support for uint16, uint32, uint64 types to operators, kernels, or when user mentions enabling unsigned types, barebones unsigned types, or uint support.
Agent Development
This skill should be used when the user asks to "create an agent", "add an agent", "write a subagent", "agent frontmatter", "when to use description", "agent examples", "agent tools", "agent colors", "autonomous agent", or needs guidance on agent structure, system prompts, triggering conditions, or agent development best practices for Claude Code plugins.
AgentDB Advanced Features
Master advanced AgentDB features including QUIC synchronization, multi-database management, custom distance metrics, hybrid search, and distributed systems integration. Use when building distributed AI systems, multi-agent coordination, or advanced vector search applications.
AgentDB Learning Plugins
Create and train AI learning plugins with AgentDB's 9 reinforcement learning algorithms. Includes Decision Transformer, Q-Learning, SARSA, Actor-Critic, and more. Use when building self-learning agents, implementing RL, or optimizing agent behavior through experience.
AgentDB Memory Patterns
Implement persistent memory patterns for AI agents using AgentDB. Includes session memory, long-term storage, pattern learning, and context management. Use when building stateful agents, chat systems, or intelligent assistants.
AgentDB Performance Optimization
Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.
AgentDB Vector Search
Implement semantic vector search with AgentDB for intelligent document retrieval, similarity matching, and context-aware querying. Use when building RAG systems, semantic search engines, or intelligent knowledge bases.
agile-product-owner
Agile product ownership toolkit for Senior Product Owner including INVEST-compliant user story generation, sprint planning, backlog management, and velocity tracking. Use for story writing, sprint planning, stakeholder communication, and agile ceremonies.
ai-multimodal
Process and generate multimedia content using Google Gemini API. Capabilities include analyze audio files (transcription with timestamps, summarization, speech understanding, music/sound analysis up to 9.5 hours), understand images (captioning, object detection, OCR, visual Q&A, segmentation), process videos (scene detection, Q&A, temporal analysis, YouTube URLs, up to 6 hours), extract from documents (PDF tables, forms, charts, diagrams, multi-page), generate images (text-to-image, editing, composition, refinement). Use when working with audio/video files, analyzing images or screenshots, processing PDF documents, extracting structured data from media, creating images from text prompts, or implementing multimodal AI features. Supports multiple models (Gemini 2.5/2.0) with context windows up to 2M tokens.
andrew-kane-gem-writer
Write Ruby gems following Andrew Kane's proven patterns and philosophy. Use when creating new Ruby gems, refactoring existing gems, designing gem APIs, or when the user wants clean, minimal, production-ready Ruby library code. Triggers on requests like "create a gem", "write a Ruby library", "design a gem API", or mentions of Andrew Kane's style.
angular-migration
Migrate from AngularJS to Angular using hybrid mode, incremental component rewriting, and dependency injection updates. Use when upgrading AngularJS applications, planning framework migrations, or modernizing legacy Angular code.
api-design-principles
Master REST and GraphQL API design principles to build intuitive, scalable, and maintainable APIs that delight developers. Use when designing new APIs, reviewing API specifications, or establishing API design standards.
api-test-generator
Генерация полных Python pytest тестов для REST API эндпоинтов с валидацией схемы. Использовать при создании тестов для новых эндпоинтов, добавлении покрытия для CRUD операций или валидации соответствия API с OpenAPI схемами.
arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
architecture-patterns
Implement proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design. Use when architecting complex backend systems or refactoring existing applications for better maintainability.
archon
Interactive Archon integration for knowledge base and project management via REST API. On first use, asks for Archon host URL. Use when searching documentation, managing projects/tasks, or querying indexed knowledge. Provides RAG-powered semantic search, website crawling, document upload, hierarchical project/task management, and document versioning. Always try Archon first for external documentation and knowledge retrieval before using other sources.
artifacts-builder
Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.
arxiv-search
Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields
astropy
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
async-python-patterns
Master Python asyncio, concurrent programming, and async/await patterns for high-performance applications. Use when building async APIs, concurrent systems, or I/O-bound applications requiring non-blocking operations.
at-dispatch-v2
Convert PyTorch AT_DISPATCH macros to AT_DISPATCH_V2 format in ATen C++ code. Use when porting AT_DISPATCH_ALL_TYPES_AND*, AT_DISPATCH_FLOATING_TYPES*, or other dispatch macros to the new v2 API. For ATen kernel files, CUDA kernels, and native operator implementations.
auth-implementation-patterns
Master authentication and authorization patterns including JWT, OAuth2, session management, and RBAC to build secure, scalable access control systems. Use when implementing auth systems, securing APIs, or debugging security issues.
Awakening Stage Recognition
Recognize which awakening stage consciousness is navigating through. Use when diagnosing seeker development, identifying stage transitions, or recognizing readiness levels. Covers 7 stages from initial dissatisfaction through natural flow mastery.
aws-skills
Collection of AWS development skills covering CDK infrastructure as code, cost optimization, and serverless/event-driven architectures with integrated MCP servers.
aws-cdk-development
AWS Cloud Development Kit (CDK) expert for building cloud infrastructure with TypeScript/Python. Use when creating CDK stacks, defining CDK constructs, implementing infrastructure as code, or when the user mentions CDK, CloudFormation, IaC, cdk synth, cdk deploy, or wants to define AWS infrastructure programmatically. Covers CDK app structure, construct patterns, stack composition, and deployment workflows.
aws-serverless-eda
AWS serverless and event-driven architecture expert based on Well-Architected Framework. Use when building serverless APIs, Lambda functions, REST APIs, microservices, or async workflows. Covers Lambda with TypeScript/Python, API Gateway (REST/HTTP), DynamoDB, Step Functions, EventBridge, SQS, SNS, and serverless patterns. Essential when user mentions serverless, Lambda, API Gateway, event-driven, async processing, queues, pub/sub, or wants to build scalable serverless applications with AWS best practices.
backend-dev-guidelines
Comprehensive backend development guide for Langfuse's Next.js 14/tRPC/Express/TypeScript monorepo. Use when creating tRPC routers, public API endpoints, BullMQ queue processors, services, or working with tRPC procedures, Next.js API routes, Prisma database access, ClickHouse analytics queries, Redis queues, OpenTelemetry instrumentation, Zod v4 validation, env.mjs configuration, tenant isolation patterns, or async patterns. Covers layered architecture (tRPC procedures → services, queue processors → services), dual database system (PostgreSQL + ClickHouse), projectId filtering for multi-tenant isolation, traceException error handling, observability patterns, and testing strategies (Jest for web, vitest for worker).
Backend Migration Standards
Create and manage database migrations with reversible changes, proper naming conventions, and zero-downtime deployment strategies. Use this skill when creating database migration files, modifying schema, adding or removing tables/columns, managing indexes, or handling data migrations. Apply when working with migration files (e.g., db/migrate/, migrations/, alembic/, sequelize migrations), schema changes, database versioning, rollback implementations, or when you need to ensure backwards compatibility during deployments. Use for any task involving database structure changes, index creation, constraint modifications, or data transformation scripts.
blockchain-developer
Expert blockchain developer specializing in smart contract development, DApp architecture, and DeFi protocols. Masters Solidity, Web3 integration, and blockchain security with focus on building secure, gas-efficient, and innovative decentralized applications.
Backend Models Standards
Define database models with clear naming, appropriate data types, constraints, relationships, and validation at multiple layers. Use this skill when creating or modifying database model files, ORM classes, schema definitions, or data model relationships. Apply when working with model files (e.g., models.py, models/, ActiveRecord classes, Prisma schema, Sequelize models), defining table structures, setting up foreign keys and relationships, configuring cascade behaviors, implementing model validations, adding timestamps, or working with database constraints (NOT NULL, UNIQUE, foreign keys). Use for any task involving data integrity enforcement, relationship definitions, or model-level data validation.
bap-identity
Manage BAP (Bitcoin Attestation Protocol) identity files using bap-cli. This skill should be used when users need to create, decrypt, list, or extract BAP identity backups, work with .bep encrypted files, or generate test fixtures for Playwright tests involving BAP identities.
bash-defensive-patterns
Master defensive Bash programming techniques for production-grade scripts. Use when writing robust shell scripts, CI/CD pipelines, or system utilities requiring fault tolerance and safety.
bats-testing-patterns
Master Bash Automated Testing System (Bats) for comprehensive shell script testing. Use when writing tests for shell scripts, CI/CD pipelines, or requiring test-driven development of shell utilities.
bd-issue-tracking
Track complex, multi-session work with dependency graphs using bd (beads) issue tracker. Use when work spans multiple sessions, has complex dependencies, or requires persistent context across compaction cycles. For simple single-session linear tasks, TodoWrite remains appropriate.
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