💻 Development

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.

Expert on Claude Code CLI, skills, commands, hooks, plugins, MCP, settings, and workflows. Triggers on claude code, cli, skill, command, hook, plugin, mcp, slash command, settings

Expert on Claude Code settings.json configuration, permissions, sandbox, environment variables, and settings hierarchy. Triggers when user mentions settings.json, permissions, allow rules, deny rules, sandbox, hooks configuration, or settings precedence.

CLI tool management for coding agents. This skill should be used when: - A command fails with "command not found" or similar errors - The user asks to install, update, or check CLI tools - A project needs environment setup or dependency checking - Tools are missing, outdated, or need reconciliation Provides auto-installation of 74+ tools via optimal package managers, project environment auditing, and batch update capabilities.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

FrankenPHP Documentation - Modern PHP application server built on Caddy

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

This skill orchestrates the creation of a complete documentation system by invoking 6 specialized documentation workers in sequence. Each worker handles one domain (root/reference/tasks/project/presentation/test) and validates its own output, eliminating Worker→Worker coupling. This skill should be ...

Performs manual testing of Story AC (API/UI) with curl/puppeteer, documents results in Linear (structured comment) and provides reusable scripts. Worker only.

Plans Story test task by Risk-Based Testing after manual testing. Calculates priorities, selects E2E/Integration/Unit, delegates to ln-311-task-creator. Invoked by ln-340-story-quality-gate.

Test authenticated routes in the your project using cookie-based authentication. Use this skill when testing API endpoints, validating route functionality, or debugging authentication issues. Includes patterns for using test-auth-route.js and mock authentication.

Comprehensive Supabase expert with access to 2,616 official documentation files covering PostgreSQL database, authentication, real-time subscriptions, storage, edge functions, vector embeddings, and all platform features. Invoke when user mentions Supabase, PostgreSQL, database, auth, real-time, storage, edge functions, backend-as-a-service, or pgvector.

Evaluate TYPO3 extensions for conformance to TYPO3 12/13 LTS standards, coding guidelines (PSR-12), and architecture patterns. Use when assessing extension quality, generating conformance reports, identifying technical debt, or planning modernization. Validates: extension architecture, composer.json, ext_emconf.php, ext_* files, v13 deprecations, backend module v13 compliance (ES6 modules, DocHeader, Modal/Notification APIs, Module.html layout, ARIA, extension key consistency, CSRF, icons), dependency injection, services, testing, Extbase patterns, Crowdin, GitHub workflows. Dual scoring (0-100 base + 0-22 excellence). Delegates to typo3-tests and typo3-docs skills for deep analysis. PHP 8.1-8.4 support.

Guide contributors through the complete TYPO3 Core contribution workflow from account setup to patch submission for both code and documentation contributions. Trigger when: working with TYPO3 Forge issues (forge.typo3.org/issues/*), preparing patches for TYPO3 Core, contributing to TYPO3 (code or documentation), submitting patches to Gerrit (review.typo3.org) or GitHub PRs (TYPO3-Documentation/*), fixing TYPO3 bugs, managing WIP state, or debugging CI failures. Covers: Account setup, environment configuration with DDEV, commit message formatting, Gerrit review workflow, GitHub PR workflow for documentation, WIP state management (command-line and web UI), CI/CD debugging (CGL, PHPStan, unit tests), troubleshooting (60+ scenarios), code quality enforcement, and systematic patch submission for both code and documentation repositories.

Automate DDEV environment setup for TYPO3 extension development. Use when setting up local development environment, configuring DDEV for TYPO3 extensions, or creating multi-version TYPO3 testing environments. Covers: DDEV configuration generation, TYPO3 11.5/12.4/13.4 LTS installation, custom DDEV commands, Apache vhost setup, Docker volume management, and .gitignore best practices (avoid double-ignore anti-pattern). Provides complete automation from metadata detection to ready-to-use TYPO3 backend access.

Create, configure, and manage TYPO3 extension tests (unit, functional, acceptance) following official TYPO3 testing framework patterns. Use when setting up tests, writing test cases, configuring PHPUnit, managing fixtures, or integrating CI/CD pipelines for TYPO3 extensions. Covers PHPUnit 11/12, TYPO3 v12/v13 LTS, modern dependency injection testing patterns, and comprehensive quality tooling (PHPStan level 10, Rector, php-cs-fixer).