IDE & Editors

Pairwise and multiple sequence alignment algorithms. Use when comparing biological sequences, finding conserved regions, or computing sequence similarity and identity scores using tools like MUSCLE, ClustalW, or pairwise alignment algorithms.

Efficient iterator combinatorics and operations for memory-efficient looping. Provides combinations, permutations, cartesian products, and chainable iterators. Use when generating all possible currency pairs, exploring trading paths, creating sequences without loading into memory, grouping sorted data, computing running accumulations, or working with infinite sequences. Ideal for combinatorial analysis and lazy iteration.

Molecular dynamics simulation tools for atomistic modeling. Use for simulating ion transport, diffusion coefficients, and electrolyte molecular behavior at the atomic level.

Solve vehicle routing problems using Google OR-Tools. Use this skill for VRP, CVRP, VRPTW, and multi-vehicle routing optimization. Provides routing model setup, constraint handling, and solution extraction for delivery and logistics problems.

BLAST (Basic Local Alignment Search Tool) for sequence similarity searches. Use when searching for homologous sequences in databases, identifying protein or nucleotide sequence matches, or performing local BLAST queries.

Create and manipulate 3D models using Blender's Python API (bpy). Use for mesh modeling, animation, rendering, and batch processing. Requires Blender installation; scripts run inside Blender or via command line.

Virtual screening tools for drug discovery. Use for high-throughput compound screening, similarity searching, and identifying drug candidates from large compound libraries.

Quantitative Structure-Activity Relationship modeling for drug discovery. Use for predicting drug activity from molecular descriptors, building predictive models, and identifying important molecular features.

Molecular dynamics simulation tools for atomistic modeling. Use for simulating ion transport, calculating diffusion coefficients, viscosity, and electrolyte molecular behavior.

Guide for using the ct (CommonTools) binary to interact with charms, recipes, and the Common Fabric. Use this skill when deploying recipes, managing charms, linking data between charms, or debugging recipe execution. Triggers include requests to "deploy this recipe", "call a handler", "link these charms", "get data from charm", or "test this recipe locally".

IDE-grade project scaffolding wizard for creating new projects with comprehensive configuration. Supports 70+ project types: HTML/CSS websites, React, Next.js, Vue, Astro, Remix, React Native, Flutter, Expo, FastAPI, Django, Express, NestJS, Go/Gin, Rust/Axum, Spring Boot, Hono, Elysia, Chrome Extensions, VS Code Extensions, Tauri desktop apps, serverless functions, and more. Provides WebStorm/PyCharm-level project creation with interactive SDK selection, framework configuration, database setup, and DevOps tooling. Use when: creating a new project, setting up a framework application, initializing a codebase, scaffolding boilerplate, building extensions, creating mobile/desktop/web apps, setting up monorepos, or making static websites/landing pages.

Guide for developing CommonTools patterns (TypeScript modules that define reactive data transformations with UI). Use this skill when creating patterns, modifying existing patterns, linking patches (instantiated patterns), debugging pattern errors, or working with the pattern framework. Triggers include requests like "build a pattern", "fix this pattern error", "deploy this charm/patch", "link these charms", or questions about handlers, cells, and reactive patterns.

Guide for developing Lit web components in the Common UI v2 system (@commontools/ui/v2). Use when creating or modifying ct- prefixed components, implementing theme integration, working with Cell abstractions, or building reactive UI components that integrate with the Common Tools runtime.

Expert knowledge of IDE/LSP tools for code navigation, diagnostics, and refactoring. Use when working with TypeScript errors, linting issues, code navigation, or IDE operations.

Comprehensive guide for creating REST API endpoints in Bruno. Use when working with Bruno collections, creating .bru files, configuring API endpoints, setting up authentication, writing pre/post-request scripts, organizing Bruno collections, or testing REST APIs with Bruno.

Creates requirements documents through structured 3-phase discovery process. Guides through requirements discovery, practical scoping, and generates consolidated requirements document with clear, practical language. Use when user wants to create a requirements document, needs to define what the system must do and quality constraints, or is documenting business capabilities, user workflows, and system requirements. Follows established feature development process with single consolidated document covering user stories, business data, rules, quality attributes, and success criteria.

Revision and editing assistant for Crucible-drafted novels. Use when author has completed a first draft and wants to revise, edit, or polish their manuscript. Handles developmental editing, line editing, copy editing, and final polish. Triggers on "edit my novel," "revise chapter X," "polish my manuscript," "help me edit," or when user has completed draft chapters and wants to improve them.

Count the total number of MCP tools in the Umbraco MCP Server project and provide a breakdown by collection. Use when the user asks about tool counts, tool statistics, or how many tools exist.

Download YouTube video transcripts when user provides a YouTube URL or asks to download/get/fetch a transcript from YouTube. Also use when user wants to transcribe or get captions/subtitles from a YouTube video.

Verification before completion claims. Use when about to say "done", "fixed", or "complete". Runs checklist by workflow type with evidence requirements.