AI & LLM Integration for Claude Code

Expert guide for designing and building high-quality skills from scratch through structured conversation. Use when someone wants to create a new skill, build a skill, design a skill, or asks for help making Agents do something consistently. Also use when someone says "turn this into a skill", "I want to automate this workflow", "how do I teach my Agent to do X", or mentions creating SKILL.md files. Covers standalone skills and MCP-enhanced workflows. Do NOT use for creating subagents (use subage

Guide for creating AI subagents with isolated context for complex multi-step workflows. Use when users want to create a subagent, specialized agent, verifier, debugger, or orchestrator that requires isolated context and deep specialization. Works with any agent that supports subagent delegation. Triggers on "create subagent", "new agent", "specialized assistant", "create verifier". Do NOT use for Cursor-specific subagents (use cursor-subagent-creator instead).

Generative Engine Optimization (GEO) specialist — the technical, on-page publishing work that makes a given page or site discoverable, understandable, trustworthy, quotable, and fresh for AI answer engines (Google AI Overviews, ChatGPT Search, Bing Copilot, Perplexity). Use when asked to 'optimize this page/site for GEO', 'optimize for AI search / answer engines', 'get my page cited by ChatGPT/Perplexity', 'improve AI visibility/citability', 'write an llms.txt', 'add citation-ready structure or

Configure MCP (Model Context Protocol) servers for Claude Code. Manage MCP servers at user or project scope with best practices to avoid context pollution.

Create new skills, modify and improve existing skills, and measure skill performance. Enhanced version with quick commands. Use when users want to create a skill from scratch, update or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy. Triggers on phrases like "make a skill", "create a new skill", "build a skill for", "improve this skill", "optimize my skill", "test my skill

Amazon Alexa for Shopping Q&A automation: submits questions to Amazon's Alexa/Rufus AI shopping assistant and collects response text; supports optional keyword search context (navigate to search results page before asking for category-specific answers). Use when user mentions Amazon Alexa, Rufus, Amazon shopping assistant, Amazon AI chat, ask Amazon, Amazon Q&A, automate Alexa questions, Rufus chatbot, Amazon assistant automation, collect Alexa responses, bulk question submission to Amazon, keyw

Deep-crawl any website from start URLs, return per-page LLM-ready text/markdown/HTML plus metadata (title, description, author, language, canonical URL, OG) and in-scope outbound links. Use when user mentions deep crawl website, recursive crawl, crawl a whole site, scrape entire website, scrape docs site, scrape documentation, scrape knowledge base, scrape blog, build RAG corpus, build vector database from website, knowledge base for chatbot, GPT knowledge files, llms.txt, sitemap crawl, BFS cra

X (Twitter) DM automated chat end-to-end Skill: scan DM inbox to identify pending-reply conversations, read message history, generate persona-based replies and send; also supports searching users and starting new conversations. Built-in E2E passcode unlock, DM permission filtering, and rate control. Use when user mentions X auto-reply DMs, Twitter DM automated chat, auto-handle unread DMs, reply to X private messages with persona, X DM outreach campaign, batch send DMs to Twitter users, auto-pro

Re-derive your knowledge system from first principles when structural drift accumulates. Analyzes dimension incoherence, vocabulary mismatch, boundary dissolution, and template divergence. Preserves all content while restructuring architecture.

> Create a new custom agent from scratch. Runs a 6-phase interview to understand purpose, capabilities, triggers, output format, and coordination rules, then generates the agent file. Triggers: EN: "create a new agent", "custom agent", "I need a new agent", "build an agent", "new crew member". IT: "crea un nuovo agente", "agente personalizzato", "nuovo membro del crew". FR: "créer un nouvel agent", "agent personnalisé". ES: "crear un nuevo agente", "agente personalizado". DE: "neuen Agenten erst

> Edit, update, or remove an existing custom agent. Shows current config and asks what to change. Also handles listing all custom agents. Triggers: EN: "edit my agent", "update agent", "remove agent", "delete agent", "list agents", "show my agents". IT: "modifica il mio agente", "aggiorna agente", "rimuovi agente", "lista agenti", "mostra i miei agenti". FR: "modifier mon agent", "supprimer agent", "lister les agents". ES: "editar mi agente", "eliminar agente", "listar agentes". DE: "Agenten bea

Look up any arxiv paper on alphaxiv.org to get a structured AI-generated overview. This is faster and more reliable than trying to read a raw PDF.

AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。

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Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel proteins, protein complexes, or when comparing predictions across multiple methods.

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> Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For ESM-based analysis, use esm.

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<!-- COPYRIGHT NOTICE This file is part of the "Universal Biomedical Skills" project. Copyright c 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu All Rights Reserved. This code is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. Provenance:

<!-- COPYRIGHT NOTICE This file is part of the "Universal Biomedical Skills" project. Copyright c 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu All Rights Reserved. This code is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. Provenance:

<!-- COPYRIGHT NOTICE This file is part of the "Universal Biomedical Skills" project. Copyright c 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu All Rights Reserved. This code is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. Provenance:

Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols. Implements suicide ideation detection, automated escalation, and crisis resource integration. Use for mental health apps, recovery platforms, support communities. Activate on "crisis detection", "suicide prevention", "mental health NLP", "intervention protocol". NOT for general sentiment analysis, medical diagnosis, or replacing professional help.

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Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

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Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance

Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.

<!-- COPYRIGHT NOTICE This file is part of the "Universal Biomedical Skills" project. Copyright c 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu All Rights Reserved. This code is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. Provenance:

Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.

Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.

An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literature reasoning.

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Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or running custom content transformations. Supports 16+

<!-- COPYRIGHT NOTICE This file is part of the "Universal Biomedical Skills" project. Copyright c 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu All Rights Reserved. This code is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. Provenance:

<!-- COPYRIGHT NOTICE This file is part of the "Universal Biomedical Skills" project. Copyright c 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu All Rights Reserved. This code is proprietary and confidential. Unauthorized copying of this file, via any medium is strictly prohibited. Provenance: