LLM Mart Basic

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

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.

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.

Author a numbered, dated, user-attributed Architecture Decision Record under .codearbiter/decisions/.

Assemble the governance record for a range — commits, overrides, ADRs, sprint auto-decisions, open questions, checkpoint findings — into one dated audit packet. Read-only.

Lightweight Q&A about the project — answer from context and return, no routing, no state change.

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 /ca:fix, /ca: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, and harmless live-fire probe. 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.

An open-source, privacy-first, self-hosted knowledge workspace where humans and AI agents work together 开源、隐私优先、自托管的知识工作空间，让人与智能体在此协作

Scale computer-use 2.0 with open-source drivers, cross-OS fleets, and benchmarks for training, evaluation, and data generation.

The go-to web for your AI coding agent — local-first search, fetch, crawl & research over MCP. No API keys, no cloud, $0/query. Public beta.

Transform and optimize your markdown documentation for Large Language Models (LLMs) and RAG systems. Generate llms.txt automatically.

合乎周礼：DeepSeek-powered Zhouli-style Chinese translator, web app, and distributable Skill package.

This is a fork of the https://dockbox.dev project I made

🏆 Curated, ranked list of AI agent harnesses (100+) — plus an MCP server, llms.txt & JSON so agents can recommend them too. Rescored weekly.

A Python framework for modular, self-contained skill management for machines.

ADHD — a skill for coding agents. Tree-of-thought with pruning, built on the Claude & Codex Agent SDK. Fans out parallel divergent thoughts under different cogn…

AI Agent 驱动的开源可自部署视频工作台：将小说与剧本转为角色、场景、道具资产、分镜、视频和剪映草稿，支持跨镜头一致性、多供应商与费用追踪 | Self-hosted AI video workspace for stories, storyboards and short-form video producti…

DeepSeek Harness Desktop App: a local AI desktop workspace for DSH Sessions, projects, files, web research, plugins, and Office artifacts.

Autonomous Offensive Security, Bug Bounty & Red Teaming Agent Framework powered by Hermes Agent, specialized reasoning skills, and multi-model LLM orchestration…

⌥ Coding agent with the IDE wired in

Supercharge AI Agents, Safely

X (Twitter) Scraper API and X API Alternative. You do not need an official X developer account. You do not need to connect or use an X account for supported scr…

My AI Stand. Realtime by day, rewriting itself by night. Summon my AI superpower.

Open-source coding agent for your terminal, built in Rust and on a journey of continuous community improvement. Issues and PRs welcome.

观澜 / Guanlan：AI Agent 的中文互联网研究、阅读与信源路由工具。

Mac Agent for macOS 26: the agentic AI harness for your Mac Desktop. Computer use, automation, scripting, coding, and more. Powered by 18+ providers across loca…

Semantic version control => entity-level diffs, blame, and impact analysis on top of git. 28 languages via tree-sitter. Built for coding agents.