IDE & Editors

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.

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

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.

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.

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.

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.

Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.

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

Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.

Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.

This skill should be used when the user asks to "perform vulnerability scanning", "scan networks for open ports", "assess web application security", "scan wireless networks", "detect malware", "check cloud security", or "evaluate system compliance". It provides comprehensive guidance on security scanning tools and methodologies.

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.

Comprehensive guide for writing modern Neo4j Cypher read queries. Essential for text2cypher MCP tools and LLMs generating Cypher queries. Covers removed/deprecated syntax, modern replacements, CALL subqueries for reads, COLLECT patterns, sorting best practices, and Quantified Path Patterns (QPP) for efficient graph traversal.

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.

Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with specialized knowledge, workflows, or tool integrations.

Build modern full-stack web applications with Next.js (App Router, Server Components, RSC, PPR, SSR, SSG, ISR), Turborepo (monorepo management, task pipelines, remote caching, parallel execution), and RemixIcon (3100+ SVG icons in outlined/filled styles). Use when creating React applications, implementing server-side rendering, setting up monorepos with multiple packages, optimizing build performance and caching strategies, adding icon libraries, managing shared dependencies, or working with TypeScript full-stack projects.