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.

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.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Search for configuration items (assets) in ConnectWise PSA

Create a schedule entry/appointment in ConnectWise PSA

Search for tickets in ConnectWise PSA by various criteria

Update fields on an existing ConnectWise PSA ticket

Search recent Crewhu surveys, surfacing detractors and promoters

Run the reliability scorecard for one service, or every connected service if omitted - error-budget burn rate where an SLO is defined, trend reporting otherwise

Generate the current on-call handoff brief - what's paging, what's escalated without an owner, last-shift history, and known-flaky alerts to watch

Draft a blameless postmortem for a given incident (by ID or name), or the most recent significant incident within a time window

List all devices at a Domotz-monitored site

Find a Domotz device by name, IP address, or MAC address

Overview of a Domotz site's network health

Pull full detail for one Checkpoint Harmony Email detection and the message behind it

Restore quarantined mail to its recipients in Checkpoint Harmony Email, with task polling

Find messages in Checkpoint Harmony Email by sender, subject, attachment hash or quarantine state

Sweep security events in Checkpoint Harmony Email by type, state, severity and date range

Get summary of recent phishing and training campaigns from KnowBe4

Get security awareness metrics for a KnowBe4 group

View phishing campaign results and click rates from KnowBe4

Check training completion status for users or groups in KnowBe4

Get risk score and risk history for a KnowBe4 user

Open-source MCP servers for Latin American commerce — Pix, NF-e, banking, fiscal, logistics, and messaging across Brazil, Mexico, Argentina, Colombia, Chile, an…

pi coding agent in a technicolor web trenchcoat

Open-source AI Search Intelligence Platform — track, analyze, and improve AI visibility, citations, prompts, competitors, and content opportunities across ChatG…

Open-source toolkit for the QVeris capability routing network: CLI, MCP server, Python SDK, skills, and REST API docs for agents to discover, inspect, call, and…

⚡ The Complete X/Twitter Automation Toolkit — Scrapers, MCP server for AI agents (Claude/GPT), CLI, browser scripts. No API fees. Open source. Unfollow people w…

The AI agent that interacts with you in the real world.

Offline Codex Desktop migration for Windows and macOS.

LLM 驱动的多市场股票智能分析系统：多源行情、实时新闻、决策看板与自动推送，支持零成本定时运行。 LLM-powered multi-market stock analysis system with multi-source market data, real-time news, decision dashbo…

Your smart, reliable, and friendly personal AI assistant.

The LLM Anti-Framework

A general-purpose AIGC video engine: script to finished film in one pipeline — dramas, ads, product videos, otome games, and more. | 通用 AIGC 视频引擎 —— 从剧本到成片一条流水线…

GTM agent for technical founders. Pay-per-result. Signed receipts. Two surfaces: terminal CLI + local web dashboard.

Desktop automation MCP server — computer use for any AI agent: control screen, windows, mouse/keyboard, and Chrome via Model Context Protocol (stdio)

DeepSeek Harness (dsh) Windows desktop client - bundled Node.js + dsh CLI, one-click launch

Open-source, real-time collaborative AI canvas - notes, mini-apps, and agents on one infinite board.

MCPSafari: Native Safari MCP Server for AI Agents

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Po…

The AI agent with a wallet — spends USDC autonomously to get real work done. Apache-2.0, TypeScript.

The fastest browser for AI agents to run browser automation, built for sharing your logged-in browser state with your AI agents, like Codex or Claude Code, with…

Ouroboros — self-creating AI agent. Born Feb 16, 2026.