Scripting

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.

This skill should be used when the user asks to "run pentest commands", "scan with nmap", "use metasploit exploits", "crack passwords with hydra or john", "scan web vulnerabilities with nikto", "enumerate networks", or needs essential penetration testing command references.

This skill should be used when the user asks to "test for XSS vulnerabilities", "perform cross-site scripting attacks", "identify HTML injection flaws", "exploit client-side injection vulnerabilities", "steal cookies via XSS", or "bypass content security policies". It provides comprehensive techniques for detecting, exploiting, and understanding XSS and HTML injection attack vectors in web applications.

This skill should be used when working with DSPy.rb, a Ruby framework for building type-safe, composable LLM applications. Use this when implementing predictable AI features, creating LLM signatures and modules, configuring language model providers (OpenAI, Anthropic, Gemini, Ollama), building agent systems with tools, optimizing prompts, or testing LLM-powered functionality in Ruby applications.

This skill should be used when managing the file-based todo tracking system in the todos/ directory. It provides workflows for creating todos, managing status and dependencies, conducting triage, and integrating with slash commands and code review processes.

This skill should be used when the user asks to "demonstrate skills", "show skill format", "create a skill template", or discusses skill development patterns. Provides a reference template for creating Claude Code plugin skills.

AST-based code search and refactoring via ast-grep MCP

Choose optimal external AI models for code analysis, bug investigation, and architectural decisions. Use when consulting multiple LLMs via claudish, comparing model perspectives, or investigating complex Go/LSP/transpiler issues. Provides empirically validated model rankings (91/100 for MiniMax M2, 83/100 for Grok Code Fast) and proven consultation strategies based on real-world testing.

Implement authentication and authorization with Better Auth - a framework-agnostic TypeScript authentication framework. Features include email/password authentication with verification, OAuth providers (Google, GitHub, Discord, etc.), two-factor authentication (TOTP, SMS), passkeys/WebAuthn support, session management, role-based access control (RBAC), rate limiting, and database adapters. Use when adding authentication to applications, implementing OAuth flows, setting up 2FA/MFA, managing user sessions, configuring authorization rules, or building secure authentication systems for web applications.

Browser automation, debugging, and performance analysis using Puppeteer CLI scripts. Use for automating browsers, taking screenshots, analyzing performance, monitoring network traffic, web scraping, form automation, and JavaScript debugging.

Prompt engineering standards and context engineering principles for AI agents based on Anthropic best practices. Covers clarity, structure, progressive discovery, and optimization for signal-to-noise ratio.