LLM Mart Basic

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.

Choose simple, maintainable software designs by removing speculative complexity, comparing alternatives, and making explicit tradeoffs. Use for architecture, API, data-model, dependency, and scope decisions.

Implement software through small, repeatable, integrated vertical slices with clear exit criteria and honest verification. Use when a design is understood and code needs to be built or changed.

Review software with careful attention to correctness, maintainability, security, operations, and meaningful detail. Use for diffs, branches, pull requests, architecture decisions, or final quality checks.

Author a greenfield build blueprint in four gated stages — business logic, tech stack, logic-to-stack mapping, and a phase plan — each requiring explicit user approval before the next. Use when building a new project or a substantial new subsystem from scratch.

Step 0 of consequential software work under Monozukuri. Classify the task, assess its risk tier, choose execute or sensei mode, and compose the sequence of Monozukuri skills and the Definition of Done for it. Skip for trivial one-line edits, pure questions, and throwaway scripts.

Clarify software goals, constraints, stakeholders, and risks before consequential design or implementation work. Use for greenfield ideas, ambiguous requirements, architecture decisions, or changes where misunderstanding would be costly.

Prevent software mistakes through strong boundaries, safe defaults, meaningful tests, and mechanically enforced invariants. Use for TDD, validation, schemas, authorization, edge cases, regression coverage, or reliability-sensitive behavior.

Prepare software for responsible release, migration, deployment, rollback, and handoff with evidence about compatibility, health, ownership, and recovery.

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.

Log derived files and trace provenance back to ENCODE source data

Store, check, or clear ENCODE API credentials for restricted data

Assess ENCODE experiment quality using audit counts and replicate counts

Search ENCODE experiments by assay, organ, biosample, or target

Track ENCODE experiments locally with publications and provenance

List, search, and inspect ENCODE files by format, type, and assembly

Generate ENCODE citations for publications, grants, and presentations

Check if two ENCODE experiments are compatible for combined analysis

Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv

Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification

Log derived files and trace provenance back to ENCODE source data

Store, check, or clear ENCODE API credentials for restricted data

Assess ENCODE experiment quality using audit counts and replicate counts

Search ENCODE experiments by assay, organ, biosample, or target

Track ENCODE experiments locally with publications and provenance

Record the present state by mode — decision (ADR, RFC, rule), code (spec, doc, guide, scenario), or research (a ready report or one external material); a gate picks the document type.

First-time Archcore setup — wire host configs, measure the authored context, compose the full first-day seed in one preview, and create it on one confirm; import converts CLAUDE.md, AGENTS.md, rule files, ADRs, and docs into native documents; refresh adds new facts or drills into one domain.

Plan a feature or initiative through a computed route — a small fix exits with no documents, one capability gets a spec and a plan, a large initiative gets an umbrella PRD with one spec per capability; start with sdd, sources (market research), iso (regulated work), or research (technical investigation) to run that path directly.

Review branch changes against Archcore docs, or report project health; drift runs staleness detection, deep a full documentation audit, closeout closes a finished feature, experience captures a repeated pattern.

Verify that citations actually exist and that the claims they support are faithful to the cited source. Runs deterministic existence checks (Crossref / OpenAlex / Semantic Scholar / arXiv) plus a claim-faithfulness pass via the alterlab-citation-verifier skill.

MCP server for reusable prompt templates, multi-step workflow chains, and quality gates. Compose agentic workflows with an operator syntax; export as native ski…

中国股票数据基础设施，覆盖行情、研报、资金面、筹码、公告、龙虎榜、ETF/期权、舆情互动、基本面、行业板块、宏观与风险事件等核心数据。42+A股数据集，日更、自托管、MCP 原生，零注册、零 API Token

OKF (Open Knowledge Format): Durable, structured memory for AI agents. Author, validate, consume, and maintain portable knowledge bundles through an ecosystem o…

토스증권을 AI 에이전트와 터미널에서 다루는 도구. CLI 와 MCP 서버로 계좌·시세·주문은 물론 웹앱 전용 기능(수급·AI 시그널·스크리너·배당)까지, JSON·CSV 구조화 출력으로 AI 도구·자동화에 바로 연동.

Claude skills for LinkedIn. 11 Claude Code and Codex skills that write human-sounding LinkedIn posts, craft comments that get noticed, analyze your feed, and bu…

MCP server connecting AI agents to ITASCA engines (PFC, FLAC, 3DEC, MPoint, MassFlow) — run geotechnical & geomechanics simulations through natural conversation

A curated list of amazingly awesome articles, people, applications, software libraries and projects related to the knowledge management space

One local dashboard for every Claude Code, Codex, Cursor, Antigravity, and Kilo Code session on your Mac. Spawn in parallel, ship in parallel. Open source, MIT.

Building blocks for frontier OpenAI agents in Rust. Nanocodex empowers you with Codex-level performance anywhere.

The AI agent that lives in your framework/browser

Self-Programming AI Assistant. Capture, automate, and refine all your workflows.

Consider it done. The open-source AI agent that works out of the box · 想到，就能做到。开源、开箱即用的 AI Agent。

Make Any Website into CLI & Use your logged-in browser by AI agent.

ISO 24495 Plain Language skills and Claude Code plugin

Deterministic, fail-open tool routing for Hermes Agent with an optional local-model fallback.

1인 사업가 생산성 키트 — 직원 없이 49개를 자동화했고, 그중 바로 쓸 수 있는 AI 에이전트 스킬 26개(+실행 스크립트)를 공개합니다

AI Agents & MCPs & AI Workflow Automation • (~400 MCP servers for AI agents) • AI Automation / AI Agent with MCPs • AI Workflows & AI Agents • MCPs for AI Agent…

The open-source, self-hosted video conferencing software. Scalable, customizable, and with a powerful AI Meeting Agent.

Business operating system for Claude Code — 57 skills, 21 agents, smart daemon. Unified inbox (WhatsApp/Email/Slack/Telegram), autonomous PR merge, full-AWS mon…

A local-first, cross-platform Electron desktop workspace for Pi Coding Agent, with sessions, project files, browser tools, skills, plugins, and messaging integr…