LLM Mart Basic

Execute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing WGBS/bisulfite-seq data, calling methylation levels, generating bedMethyl f

Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks

Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality, wants to filter for high-quality experiments, needs to interpret quality metrics (FRiP, NSC, RSC, NRF, IDR, TSS enrichment, fragment size), wants to understand EN

Discover and characterize regulatory elements (enhancers, promoters, silencers, insulators, super-enhancers) using ENCODE data and the cCRE catalog. Use when the user wants to find candidate regulatory elements, identify active enhancers in a tissue, map promoter states, classify

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.

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

Open‑WebUI Tools is a modular toolkit designed to extend and enrich your Open WebUI instance, turning it into a powerful AI workstation. With a suite of over 15…

The token-efficient agentic coding workbench. Built for a future where every token counts — it optimizes token usage at the agent-loop level, saving 70%+ on lon…

MCP server for controlling a real iPhone via macOS iPhone Mirroring...and any MacOs app. Screenshot, tap, swipe, type — from any MCP client.

One desktop for all your AI coding Agent — Claude Code, Codex CLI & Gemini CLI. Auto-detect, one-click install, unified chat, file explorer, terminal & editor.…

Pi — A cross-platform AI coding agent, bringing the Claude Code experience to your desktop. No environment setup, no terminal commands. Download and start codin…

DeepSeek Harness Desktop (dsh-desktop). EAC: Embracing All Creation (揽尽万象). Bundled Node.js runtime with full dsh-CLI kernel, one-click startup, 10 built-in UI…

A telegram bot for searching and auto-saving.

金蝶云星空 K3Cloud MCP Server，让 AI 助手（Claude Desktop、Claude Code、Cursor、Cline、Cherry Studio、Openclaw 等任意支持 MCP 协议的客户端）通过自然语言查询和操作金蝶 ERP 系统。

Rewrite frontier research using allegorical structural mapping.

Free4Chat is a temporary collaboration fabric for Humans and Agents.

Give any AI agent a full desktop — it sees the screen, clicks, types, and runs apps like a human. Automate anything with a UI: browsers, legacy software, intern…

A personal AI agent that can work safely on your machine, remember useful context, and keep its data under your control.

A framework for AI-driven economic activity. Declarative, composable, observable, deterministic.

Open-source, self-hosted customer support desk in a single binary. A lightweight alternative to Intercom, Zendesk, Chatwoot.

54 rigorous skills for Codex, OpenCode, and Pi: code review, security audit, feature development, frontend design, MCP tools, Hugging Face ML/training, and more…

A wonderful list of Game Development resources.

Open Science Desktop — local-first, model-agnostic AI research workbench for macOS, Windows & Linux. Open-source Claude Science desktop alternative built on Tau…

Lexora — Personal AI workspace built around Desktop / 以 Desktop 为核心的个人 AI 工作台

Open-source, AI-native Evernote alternative with native MCP. Zero-cost on Cloudflare or self-hosted with Docker.

Full job-hunt Claude skill bundle — Job Description decoder + Resume builder (11 templates) + Behavioral Interview / story bank. Three self-contained sub-skills…