LLM Mart Basic

Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods,

Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq dat

Search and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what data is available for specific assays, organs, cell lines, or targets.

Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs

Track ENCODE experiments locally with publications, citations, and provenance. Use when the user wants to build a collection of experiments, manage citations, compare experiments, or track data provenance.

Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under

Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact o

Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots. Use when users need to create visualizations of ChIP-seq signal, peak landscapes, genome browser views, or any visual representation of E

Make software health, failure, degradation, and recovery visible through useful observability and diagnostics. Use when adding logs, metrics, traces, health checks, alerts, incident signals, or operational feedback.

Inspect the real repository, environment, dependencies, and runtime evidence before designing or changing software. Use for greenfield construction, unfamiliar codebases, uncertain behavior, or any task where assumptions could create rework.

Reflect on failures, incidents, reviews, and completed software work to turn evidence into durable tests, guardrails, documentation, and process improvements.

Debug software by making failures visible, reproducing them, finding contributing causes, and adding durable regression protection. Use for bugs, failing tests, incidents, regressions, flaky behavior, and unexplained production errors.

Improve software continuously through small, safe, behavior-preserving changes that reduce maintenance cost. Use for refactoring, cleanup, technical debt, naming, duplication, dead code, or post-change polish.

Choose simple, maintainable software designs by removing speculative complexity, comparing alternatives, and making explicit tradeoffs. Use for architecture, API, data-model, dependency, and scope decisions.

Implement software through small, repeatable, integrated vertical slices with clear exit criteria and honest verification. Use when a design is understood and code needs to be built or changed.

Review software with careful attention to correctness, maintainability, security, operations, and meaningful detail. Use for diffs, branches, pull requests, architecture decisions, or final quality checks.

Author a greenfield build blueprint in four gated stages — business logic, tech stack, logic-to-stack mapping, and a phase plan — each requiring explicit user approval before the next. Use when building a new project or a substantial new subsystem from scratch.

Step 0 of consequential software work under Monozukuri. Classify the task, assess its risk tier, choose execute or sensei mode, and compose the sequence of Monozukuri skills and the Definition of Done for it. Skip for trivial one-line edits, pure questions, and throwaway scripts.

Clarify software goals, constraints, stakeholders, and risks before consequential design or implementation work. Use for greenfield ideas, ambiguous requirements, architecture decisions, or changes where misunderstanding would be costly.

Fourteen posts of being wrong in production, compressed to checkboxes

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Scaffold a Python project (FastAPI, Django, library, or CLI) with uv, type hints, testing, and dev tooling

Open a review-action approval window by creating the ./.review-approved flag file. Takes an optional reason string that is recorded in the flag file and an unsigned approval log.

List the review actions that the review-governance policy blocked in this session. protect-mcp 0.7.4 writes no receipt for a denied call, so the list comes from the session, not from ./review-receipts/.

Review software compliance controls, regulatory requirements, and audit readiness

Scan dependencies for vulnerabilities and generate supply chain security evidence

Orchestrate comprehensive security hardening with defense-in-depth strategy across all application layers

Static Application Security Testing (SAST) for code vulnerability analysis across multiple languages and frameworks

Initialises the ShipMate pipeline in the current project. Creates the stories folder, sets up the pipeline state directory, and runs the initial codebase scan to generate project-doc.md and AGENTS.md.

Master pipeline entry point. Routes requirements from a story file through scan → orchestrate → architect → implement → review → QA → playwright stages. Use /ship stories/foo.md to start, /ship status to check progress, /ship resume to continue.

Generate comprehensive investor-ready business case document with market, solution, financials, and strategy

Create detailed 3-5 year financial model with revenue, costs, cash flow, and scenarios

Generate comprehensive market opportunity analysis with TAM/SAM/SOM calculations

Scaffold a Rust project (binary, library, workspace, or Axum web API) with Cargo, testing, and dev tooling

Execute a comprehensive TDD workflow with strict red-green-refactor discipline

Implement minimal code to make failing tests pass in TDD green phase

Write comprehensive failing tests following TDD red phase principles

Refactor code while keeping all tests green in TDD refactor phase

Resolve a GitHub issue from triage and root cause analysis through test-driven implementation and a pull request

Generate async standup notes from git commits, Jira tickets, and Obsidian notes

Audit UI code for WCAG compliance

Persistent session memory for AI coding agents — local-first, with on-device inference, associative recall, and drift detection. Works with Claude Code, Cursor,…

Run Hermes Agent and OpenClaw on the same WeChat account

An AI co-scientist running on your desktop. Claude Science but better.

Emotion Ball 是一套面向 AI 助手的表情引擎:32 种状态表情全部由纯 SVG 与原生 JavaScript 实时驱动,零框架、零图片资源。AI 侧只需输出一个 emotionId,小球即可切换到对应表情,可直接用作聊天机器人、桌面宠物、悬浮助手的情绪表达层。

Agent communication SDK. The open-source agent communication layer for AI agents — email, WhatsApp, Slack, Discord, Telegram, SMS. Python & TypeScript.

The micro-VM for AI agents — light enough to embed on your laptop, elastic enough to power an agentic cloud.

Give each AI agent its own isolated machine with root, Docker, and systemd. Active defense detects and stops threats automatically.

Webhook integration skills for AI coding agents (Claude Code, Cursor, Copilot). Step-by-step guidance for setting up webhook receivers, signature verification,…

Token burn reducer and focus keeper for Claude Code, Codex, Copilot, Gemini CLI, and more: surgical read hints, PDF/Office/CSV/markdown file interception, 160+…

RuvNet Brain — a downloadable, source-grounded brain for Claude Code over Reuven Cohen's (rUv's) RuvNet stack: RuVector/RVF, Ruflo, AgentDB, RuLake, SPARC + 21…

💼 One MCP server to search job boards and company career sites

C++ MCP SDK - build Model Context Protocol (MCP) servers and clients in C++ / CPP. Enterprise-grade security, observability, connectivity. Stdio, HTTP+SSE, Stre…

Open-Source AI Presentation Generator and API (Gamma, Canva, Beautiful AI, Decktopus, Presentations AI Alternative)

Secure, Fast, and Extensible Sandbox runtime for AI agents.

Give your AI agent eyes to see the entire internet. Read & search Twitter, Reddit, YouTube, GitHub, Bilibili, XiaoHongShu — one CLI, zero API fees.

Browser Harness | Self-healing harness that enables LLMs to complete any task.

The World's First Agentic IDE. Visual dashboard: live sessions, task management, code editor, terminal. Epic Swarm parallel workflows. Auto-proceed rules. Autom…

Agenta is a workspace where you and your team build agents and automations.

Terminal Director. One lightweight app, eight features, your whole dev workflow in a single window.

AI turns documents or topics into real, native PowerPoint decks—with native shapes, transitions and animations, data-backed charts and tables on demand, audio n…