LLM Mart Basic

Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality, wants to filter for high-quality experiments, needs to interpret quality metrics (FRiP, NSC, RSC, NRF, IDR, TSS enrichment, fragment size), wants to understand EN

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

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.

Fourteen posts of being wrong in production, compressed to checkboxes

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

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.

Plural alias for task status, pause, prompts, recovery, and ignore

Verify that the autorun plugin command surface is loaded

Tmux session management - create, list, cleanup isolated sessions, short for /ar:tmux

Tmux session management - create, list, cleanup isolated sessions

CLI testing in isolated tmux sessions, short for /ar:ttest

CLI testing in isolated tmux sessions

Graceful stop - finish current task then stop (short for /ar:stop)

Set AutoFile policy to ALLOW — permit creation of new files without justification

Refresh git commit guidelines before staging changes

Set AutoFile policy to FIND — restrict edits to existing files only

Start an autorun task with three-stage verification (initial → critical review → final verification)

Refresh the universal system design philosophy before designing or reviewing code

Show the current AutoFile policy and any active autorun state

Extract text from PDF files or directories to markdown

Trigger: `/ship` or "ship it" or "deploy to production"

Suppress 5-question enforcement for rapid sessions

Check a Dutch address for KPN outages and report what connectivity is available there

Find the KPN business-mobile contract for a lost or stolen phone and block its SIM after confirmation

Atom Agent, Open-Source Governed AI Agent Platform for Self-Hosted Automation

The agent engineering intelligence harness, optimized tools, memory system, subagents and mixture of models packages ⚚

Sesori iOS/Android app and the Sesori Bridge CLI — drive Claude, Codex, OpenCode, Cursor, Pi, OMP, Hermes coding sessions from your phone

🧠 RepoBrain (formerly Antigravity) — Give your repo a brain. ChatGPT for your codebase: works in Claude Code, Cursor, Codex, Windsurf & more.

Use ChatGPT (Codex), Claude, and Grok (X Premium) subscriptions as DeepSeek Harness LLM providers — OAuth login in the web UI, no API keys

Latitude is the open-source AI monitoring platform.

Open-source AI browser agent for Chrome and Firefox (monorepo) 🧠

Official Model Studio CLI（阿里云百炼 CLI）built for AI Agent frameworks, exposing models, search, multimodal, and workflow capabilities as structured tool calls.

Curated DeepSeek Harness (DSH) plugins, extensions, tools, skills, clients, runtimes, integrations, and verified references — English and Chinese.

Turn papers, code, and docs into presentation-ready, natively editable PPTX in Codex / Claude Code. Native charts and equations, speaker notes, click-build anim…

Grix : Work with agents like talking to people.

Local First Ai Agent. Optimized for Local Ai models. Long context window. Proper tools callings. Runs privately on your device.

Model Context Protocol server that integrates AgentQL's data extraction capabilities.

AI that ships your tickets.

Metadata-driven CLI for AI Agent Bots — 48 operations across 7 domains, structured JSON envelope I/O, zero interactive prompts.

An open-source, extensible, self-hosted agent workspace with multi-runtime support for Codex, Claude Code, and more, plus reusable local apps for custom interfa…

Open-source Windows desktop client and GUI for DeepSeek Harness — zero-setup installer with Codex, plugins, skills, SSH, mobile remote access, and 11 skins.

The open-source AI workbench for scientific research

DeepSeek-native AI coding agent for your terminal. Engineered around prefix-cache stability — leave it running.

A Fully free agentic browser driver for AI , few tools, full control, real stealth, top-tier token efficiency.