LLM Mart Basic

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.

Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data

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.

Treat an AI agent skill as both an instruction package and a software dependency: inspect what it says, what it runs, what it can access, and how it updates.

Periodic multi-reviewer sweep of the whole codebase — surfaces a triaged checkpoint report.

Sanctioned lane for non-behavioral work — docs-only edits, dependency bumps, reverts. Type-scaled gates; no TDD demanded of prose.

Finish an already-merged branch — classify the leftover artifacts, return to a fast-forwarded default checkout, and delete the merged local branch. Every discard confirmed per item; containment proven, never assumed.

Show the codeArbiter command catalog — the public command list and what each routes to.

Run the full commit gate — the only sanctioned path to a git commit.

Stop everything and surface a rule conflict — persona vs. docs vs. code. Present both sides and the conflict-hierarchy level; the user resolves. No silent reconciliation.

Optional manual drift audit — report stale provenance-tracked docs, then per stale doc offer re-scout, re-baseline, or defer. Not the daily loop; commit-gate auto-heal owns routine maintenance.

Brownfield back-fill — scout an existing codebase and populate .codearbiter/, then lock it initialized.

Investigate-then-decide root-cause analysis for a defect whose cause is unknown. No code changes — exits to {{CMD:fix}}, {{CMD:adr}}, or a no-action close.

Greenfield decomposition interview — a layered interview that populates .codearbiter/ and locks it initialized.

Verify the active host install, package, command ownership, enforcement{{IF:pi}}, wrapper self-test, and active-dispatch coverage gap{{ELSE}}, and harmless live-fire probe{{END}}. Read-only.

Start a feature: brainstorm a spec, get it approved, then drive it test-first through the pipeline. The one entry to implementation.

Fix a confirmed bug: a failing regression test first, then a minimal fix, then the rest of the tdd gates.

Opt this repo into codeArbiter — scaffold the root-level .codearbiter/ state store.

Read-only 3-metric governance glance — override rate, small-lane rate, sprint low-confidence ratio — each with a trend arrow vs. the prior 20-commit window.

Author a new codeArbiter skill: prove the gap is real, get the spec approved, then write it.

Sanctioned, logged bypass of a gate or hard rule — one audit line, then proceed.

Open a pull request the only sanctioned way — clear every BLOCK-level review finding, then stage the PR. Never a direct write to the default branch.

Zero-onboarding, read-only dry-run of the reviewer fleet against the current uncommitted diff. Predicts reviewers, runs the state-free secret scan, writes nothing.

Trim transcript clutter to extend session lifetime — analyze, prune a copy, or toggle the after-each-turn service. Dry-run by default; gains land at resume/compaction, not the current turn.

Conduit — native SwiftUI iOS client for Hermes Agent

一个现代化的可视化规则引擎平台，用于编排复杂的 AI 工作流。在无限画布上设计、测试和部署 AI 流程——无需编写代码。结合 flowgram.ai 的能力与 Java 服务端，提供生产级工作流管理。在此之上提供AI Agent / Copilot的助手编排能力。

Job application tracker and AI-powered job search assistant. Helps job seekers manage their search journey with AI resume review, job matching, task logging, an…

📝 Markdown and HTML renderer for Svelte 5 — built for streaming AI agent output from Claude Code, ChatGPT, and agentic workflows. XSS-safe defaults, token cach…

ServiceNow MCP server: 500+ tools and 26 AI capabilities for any AI (Claude, ChatGPT, Gemini, Cursor, Copilot). Multi-transport (stdio, SSE, HTTP), A2A, dynamic…

Free crypto news API - real-time aggregator for Bitcoin, Ethereum, DeFi, Solana & altcoins. No API key required. RSS/Atom feeds, JSON REST API, historical archi…

Build production-ready AI agents in both Python and Typescript.

From agent user to agent builder: build a Claude Code-style coding agent from scratch in Python: 8 articles, 4 videos, one codebase

🪁 A lightweight, modern Kubernetes dashboard that unifies multi-cluster and resource management, enterprise-grade user governance (OAuth, RBAC, and audit logs)…

Stateful runtime management for LLM agents—inject, manipulate, and retrieve Python objects across turns.

AgentCall lets AI Agents join meetings with voice, video & screen-share to build together. Supports Google Meet, Teams, Zoom (Beta)

Kition brings Markdown, DataTable, WhiteBoard, a tool-using AI agent, browser research, and visual workflows into one desktop workspace.

IntentKit is an open-source, self-hosted cloud agent cluster that manages a collaborative team of AI agents for you.

A powerful Model Context Protocol (MCP) server providing comprehensive Google Maps API integration with LLM processing capabilities.

Turn your Claude Pro/Max subscription into an OpenAI-compatible API for your IDEs and devices — LAN auth, per-key quotas, response cache, disciplined cli.js ali…

Paw Work - selection-first web agent for Chrome: select on the live page, describe the outcome, take away an editable office file. BYOK, sandboxed, no server.

基于 AI Agent + MCP 工具链 + 渗透 Skill 编排， 配合大语言模型， 自然语言输入 → 自动完成「信息收集 → 漏洞发现 → 漏洞利用 → 报告生成」全流程。

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

First AI Journey for DevOps - with comprehensive learning paths, practical tips, and enterprise guidelines

AI coding agent with one Python core and three front-ends — headless CLI, Textual TUI, and an Electron desktop. Works with any OpenAI-compatible API, with risk-…