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.

`crabbox inspect` prints the full record for a single lease: state, provider,

Run named, repo-local jobs defined in your Crabbox config.

`crabbox list` shows the current Crabbox machines (leases) for a provider. It is

`crabbox login` authenticates the CLI against a coordinator, stores the

`crabbox logout` clears the stored broker token from your user config so the CLI

`crabbox logs` prints the retained command output for a recorded run.

`crabbox marketplace` previews the Crabbox credits gateway: one Crabbox billing

`crabbox media` turns a recorded desktop video into lightweight review

`crabbox open` prepares an existing SSH-capable lease for an external editor.

`crabbox pause` pauses a single lease, freeing the remote compute while

`crabbox pond` is the cross-provider peer-discovery and lifecycle surface for a

`crabbox pool` contains machine-pool helpers. `pool list` keeps the older

`crabbox ports` bridges provider-native port publishing for an existing Crabbox

`crabbox prewarm` leases a reusable box and prepares it for test runs. For

`crabbox providers` prints the provider capability matrix that the CLI compiles

`crabbox receipt <run-id>` retrieves a brokered run's committed terminal

`crabbox results` prints the structured test summary attached to a recorded

`crabbox resume` resumes a lease previously paused with [`pause`](pause.md),

`crabbox run` syncs the current dirty checkout to a box, runs a command there,

`crabbox screenshot` captures a single PNG from a desktop lease without opening a

Your Personal AI Assistant; easy to install, deploy on your own machine or on the cloud; supports multiple chat apps with easily extensible capabilities.

Agent OS: the agent gets smarter on its own. We just hold the line: the grading command and expected result never make it into the success contract we hand it.…

Curated systems, benchmarks, and papers etc. on memory for LLMs/MLLMs --- long-term context, retrieval, and reasoning.

:memo: Vimlike Modal Text Editor in Rust

CI-native security testing for MCP servers. Attack simulation, schema drift detection, and health scoring before agents depend on them.

Hermes Agent memory plugin/provider for scope-aware recall, SQLite truth, LanceDB semantic search, and hybrid retrieval.

For You Agent——AI 时代的个人随身数字人格。把你的模型、AI 账号、技能、提示词和工作方式，带到每一个 AI 工具里。

A coding agent: give it a prompt and it reads, writes, runs commands, and searches code in a loop until the work is done, using native tool-calling across OpenA…

A secure persistent personal agent server in Rust. One binary, sandboxed execution, multi-provider LLMs, voice, memory, Telegram, WhatsApp, Discord, Teams, and…

Self-evolving agent: grows skill tree from 3.3K-line seed, achieving full system control with 6x less token consumption

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…

See your agent think. Zero-config observability & governance for 26 AI agent runtimes: Claude Code, Cursor, OpenAI Codex, GitHub Copilot, Gemini CLI, Cline, Ope…

Save 94% on AI coding tokens. Index your codebase, agents search instead of reading files. Works with Claude Code, Codex, Copilot, Cursor, Gemini CLI. Local MCP…

Yet another coding agent harness, lightweight and written in go.

a coding Agent from pi. ∞ providers, sub-agents, hashline edits, and a permission gate

Omnigent is an open-source AI agent framework and meta-harness: orchestrate Claude Code, Codex, Cursor, Pi, and custom agents — swap harnesses without rewriting…

🧠 Leon is your open-source personal assistant.

The Station, an open-world multi-agent environment that models a miniature scientific ecosystem.

The Frontend Stack for Agents & Generative UI. React, Angular, Mobile, Slack, and more. Makers of the AG-UI Protocol

VelaTerm = iTerm2 + Codex, The Best Terminal for AI Coding