LLM Mart Basic

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

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak s

Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, o

Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts,

Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger o

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinica

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs

Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCOD

Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models,

Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build over

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domai

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE a

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene const

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.

Add a note or comment to an existing Autotask ticket

View contract status, entitlements, and remaining hours for a company or specific contract

Check pricing details for an Autotask product or service from price lists

Create a new Autotask quote with line items for products, services, and service bundles

Create a new service ticket in Autotask PSA

Use this skill when working with Autotask expense reports - creating reports, adding expense items, searching by status or submitter, and tracking reimbursable and billable expenses

Search for Autotask configuration items/assets by name, serial number, or company

Search for Autotask companies by name, ID, or other attributes

Search for Autotask contacts by name, email, phone, or company

List tickets currently assigned to you with optional filtering

Reassign a ticket to a different resource or queue

Search the Autotask product catalog for products, services, or inventory items

Search for tickets in Autotask PSA by various criteria

Log time against tickets or projects in Autotask PSA

Update fields on an existing Autotask ticket (status, priority, queue, due date)

Find a device in Datto RMM by hostname, IP address, or MAC address

Resolve an open alert in Datto RMM

Run a quick job on a device in Datto RMM

List all devices at a site in Datto RMM

Read, edit, and restructure sections of an IT Glue document

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…