LLM Mart Basic

Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, or calling loops. Trigger on: Hi-C pipeline, chromatin co

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression

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.

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.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

An MCP server exposes tools, resources, or prompts through a standard protocol so an AI application can discover and use external capabilities.

Execute a script on an endpoint in ConnectWise Automate

Create a ConnectWise CPQ quote by copying a template or an existing quote

Get a ConnectWise CPQ quote with its tabs, line items, customers, and terms

List ConnectWise CPQ quote templates available to copy

Search ConnectWise CPQ quotes by account, status, or date range

Add an internal or external note to a ConnectWise PSA ticket

View agreement status and entitlements for a company in ConnectWise PSA

Close a ConnectWise PSA ticket with resolution notes

Create a new service ticket in ConnectWise PSA

Retrieve detailed ticket information from ConnectWise PSA

Log a time entry against a ConnectWise PSA ticket

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

The fastest way to put Volcengine Ark in your terminal and your AI agent — go from prompt to generated media, multimodal answer, or deployed endpoint in a sin…

本地私有、开源的自进化跨平台 AI 内容发现 Agent：先理解你，再主动从 B站、小红书、抖音、YouTube、X、知乎、Reddit、微博等平台与开放 Web 寻找内容。（支持 deepseek harness 插件） | Local-first open-source cross-platform AI cont…

Persistent memory for AI coding agents — one verified kb_search replaces the grep/find/ls orientation loop. Cross-repo, CPU-only, zero token spend.

AI 时代的伯克希尔：基于 Claude Code / Codex 的价值投资研究框架。巴菲特·芒格·段永平·李录四大师方法论 + 多Agent并行研究。| AI-era Berkshire: a value investing research framework built for Claude Code / Co…

The batteries-included, No-Code FinOps automation platform, with the AI you trust.

Open-source 3D AI agent framework — GLB/glTF avatars with LLM brains, memory, emotions, and autonomous payments. MCP server · x402 · Solana/EVM · Three.js. Embe…

XLSX parser for LLMs, RAG, LangChain, LangGraph, CrewAI, Claude, MCP — turns Excel (.xlsx) into citation-ready JSON with formulas, charts, dependency graphs, an…

Hermes-Relay — Your Hermes AI agent, in your pocket — chat, voice, and control.

A minimalist, terminal-native coding agent written in C.

AI-powered OSINT agent with interactive REPL, MCP server, and CLI. 19 tools. Works with Claude, GPT-4, or local models. For authorized security research only.

AI pair programming in your terminal — one static binary, sub-ms startup, any model

Where data access meets operational intelligence

Build your own security agents. Open-source framework for agents with live, read-only access to your infrastructure, with no path to widen it. Reasons across AW…

Multi-workspace terminal aggregator with Claude Code AI integration

Go implementation of AI coding agent

Harness engineering beginner tutorial, from 0 to 1

Generate images directly in DeepSeek Harness chats

A smarter, self-hosted AI assistant — multi-user, multi-agent.

Turn any research paper into a commercialization report — 6 AI agents, TRL/MRL scoring, patent landscape, market intelligence, verified citations. DeepSeek / Op…

Power BI CLI - semantic models (.NET TOM) and PBIR reports for token-efficient AI agent usage, built for Claude Code