Tools

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.

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.

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

Comprehensive QA and testing skill for quality assurance, test automation, and testing strategies for ReactJS, NextJS, NodeJS applications. Includes test suite generation, coverage analysis, E2E testing setup, and quality metrics. Use when designing test strategies, writing test cases, implementing test automation, performing manual testing, or analyzing test coverage.

Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows.

Comprehensive code review skill for TypeScript, JavaScript, Python, Swift, Kotlin, Go. Includes automated code analysis, best practice checking, security scanning, and review checklist generation. Use when reviewing pull requests, providing code feedback, identifying issues, or ensuring code quality standards.

Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.

Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.

Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry. Enables building and training quantum circuits with automatic differentiation, seamless integration with PyTorch/JAX/TensorFlow, and device-independent execution across simulators and quantum hardware (IBM, Amazon Braket, Google, Rigetti, IonQ, etc.). Use when working with quantum circuits, variational quantum algorithms (VQE, QAOA), quantum neural networks, hybrid quantum-classical models, molecular simulations, quantum chemistry calculations, or any quantum computing tasks requiring gradient-based optimization, hardware-agnostic programming, or quantum machine learning workflows.

Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory selection and safety verification

Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions

Build MCP (Model Context Protocol) servers that give Claude new capabilities. Use when user wants to create an MCP server, add tools to Claude, or integrate external services.

Process PDF files - extract text, create PDFs, merge documents. Use when user asks to read PDF, create PDF, or work with PDF files.

Design and build AI agents for any domain. Use when users: (1) ask to "create an agent", "build an assistant", or "design an AI system" (2) want to understand agent architecture, agentic patterns, or autonomous AI (3) need help with capabilities, subagents, planning, or skill mechanisms (4) ask about Claude Code, Cursor, or similar agent internals (5) want to build agents for business, research, creative, or operational tasks Keywords: agent, assistant, autonomous, workflow, tool use, multi-step, orchestration

Manage semantic version updates for claude-mem project. Handles patch, minor, and major version increments following semantic versioning. Updates package.json, marketplace.json, and plugin.json. Creates git tags and GitHub releases. Auto-generates CHANGELOG.md from releases.

Run tests, linting, and quality checks for WooCommerce development. Use when running tests, fixing code style, or following the development workflow.

Keeps IdeaVim documentation in sync with code changes. Use this skill when you need to verify documentation accuracy after code changes, or when checking if documentation (in doc/, README.md, CONTRIBUTING.md) matches the current codebase. The skill can work bidirectionally - from docs to code verification, or from code changes to documentation updates.

Comprehensive GitHub code review with AI-powered swarm coordination