LLM Mart Basic

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

Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a gene is expressed in a tissue, correlate regulatory elements with expression, or validate ENCODE findings against GTEx. Trigger on: GTEx, tissue expression, gene e

Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, gen

Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolut

Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal cor

Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif datab

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

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.

Find an organization in IT Glue by name

Retrieve a password from IT Glue (with security logging)

Find a configuration item (asset) in IT Glue by name, hostname, serial number, or IP address

Search IT Glue documentation by keyword or phrase

Get a security posture summary for a RocketCyber customer account

Search RocketCyber security incidents by account, status, severity, verdict, and date range

Locate a Keeper record by description and return its UID and metadata without revealing any credential

Report exactly what the connected Keeper KSM application can reach - folders, record counts, and record types - reading no credential values

Generate a detailed summary of a Liongard environment

Check Liongard connectivity and return system health summary

Audit MFA enrollment across all M365 users, highlighting accounts with no MFA

Look up a Microsoft 365 user by name or email, showing account status, licenses, MFA, and last sign-in

Show Microsoft 365 license inventory - available SKUs, consumed seats, and optimization opportunities

Run the complete M365 offboarding workflow for a departing user - revoke access, handle mailbox, transfer data

Create a Mailprotector block rule for a sender address or domain at a chosen scope

Review the Mailprotector quarantine at any scope and summarize held messages

Onboard a new customer onto Mailprotector - customer, domain, user group, services, users

Release one or more quarantined Mailprotector messages to their recipients

Locate a Meraki device by serial, name, or MAC across an organization's networks

Pull and summarize a Meraki network's L3 firewall rules and flag overly-permissive (any/any allow) rules

AI assistant in Telegram that remembers everything and helps you run your life. Self-hosted in one command.

知更 — 本地 AI 的上下文与记忆层。Mac 上用语音输入、情境代回并调度 Codex / Claude Code；iOS 正在成为随身记忆终端和本地 Agent 遥控器。Local-first · BYOK.

Agent skill that turns Claude Code / Codex into a motion-design studio for voiceover-driven explainer videos — word-level voiceover sync, 78 motion recipe cards…

CoCo Super Intelligence is the orchestration layer that turns Claude Code, Cursor, or Codex into an engineering department: a routed advisory board, 185 skills,…

Deploy AI agent teams at scale without compromise

大师.skill — 输入行业，自动调研 6 轨[行业大佬 / 工具地图 / 工作流 / 知识正典 / 信息源 / 术语标准] → 提炼为可运行的行业 Master OS skill；装到任意 Claude Code / OpenClaw / Codex / Hermes agent 即让其进入「这一行的资深人」模式。…

Notion MCP server for Claude, Cursor, ChatGPT & Claude Desktop. Connect AI agents to Notion via Model Context Protocol — pages, databases, blocks, comments, fil…

Hook-based token compressor for 5 AI CLI hosts (Claude Code, Copilot CLI, OpenCode, Gemini CLI, Codex CLI). Up to 95% bash compression, signature-mode for code…

Model-neutral agent desktop/runtime for private, enterprise, and OpenAI-compatible / Anthropic-compatible model API. Tested on DeepSeek, Qwen, Kimi, GLM models.…

AI agent skill for end-to-end hotel search and booking—compare live rates across leading OTAs and hotel suppliers, verify availability, book stays, and manage r…

More than just Karpathy’s LLM Wiki, 100% local with Ollama. Drop Markdown notes → AI extracts concepts → your Obsidian wiki auto-links and grows. Zero sharing.…

Claude Code Guide - Setup, Commands, workflows, agents, skills & tips-n-tricks from beginner to power user!

A magical tool that changes how you use Agents. Install once — every Agent automatically discovers and uses all your MCP tools, and saves your tokens along the…

Open-source 24/7 Cowork app for OpenClaw, Hermes, Claude Code, Codex, OpenCode and 20+ more CLI Agent | Customize your assistants | Team them up｜Star if you lik…

AgenticX is a unified, production-ready multi-agent platform — Python SDK + CLI (agx) + Studio server + Machi desktop app. Features Meta-Agent orchestration, 15…

Query, provision and operate Cloud, SaaS, API and Model Context Protocol (MCP) resources through a unified SQL-based framework for humans and AI agents.

Open-source AI job search: scan job portals, evaluate listings into a structured A-H report with a global 1-5 score, tailor your CV, track applications — runs l…

A self-healing scraper for hostile sites: broken selectors repair themselves, browser rendering kicks in when needed, and a coherent identity layer (Chrome TLS…

Lightweight AI-native workflow builder for individuals and small teams — describe your idea in natural language, get a runnable workflow on a visual canvas, pub…

Minimal AI coding agent (~1,000 lines of Python) inspired by Claude Code. Works with any LLM. Think NanoGPT for coding agents. Formerly NanoCoder.