LLM Mart Basic

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.

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.

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.

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.

Run a systematic, reproducible literature review on a topic and return an APA 7.0 annotated bibliography with a documented search strategy. Invokes the alterlab-deep-research pipeline in lit-review mode.

Run a full multi-perspective peer review of a manuscript, simulating an Editor-in-Chief plus three peer reviewers and a Devil's Advocate, and produce a structured editorial decision and revision roadmap. Invokes the alterlab-paper-reviewer skill.

Orchestrate the end-to-end academic research-to-publication workflow (research, write, integrity check, review, revise, re-review, finalize) with mandatory integrity gates and two-stage peer review. Invokes the alterlab-research-pipeline orchestrator.

Infrastructure-first security audit — secrets, supply chain, CI/CD, LLM/skill security, OWASP, STRIDE. Complements /audit-solana (program-level)

Security audit for Solana programs (Anchor/native)

Benchmark CU usage and compare against baseline for regression detection

Build web client application (Next.js, React, Vite)

Build Solana program (Anchor or native)

Build Unity project (WebGL, Desktop, or PSG1)

Initialize forked template — setup CLAUDE.md and remove config repo scaffolding

Version the Solana AI Kit config in git (un-ignores .claude/, CLAUDE.md, .mcp.json, .gitmodules and commits them)

Reproduce and debug a user-reported failing transaction against forked cluster state, mapping the failure back to source code

Deploy Solana program (devnet first, then mainnet)

AI-powered diff review for Solana-specific issues and code quality

Health check for the dev environment and solana-ai-kit config — read-only, with one exact fix-it command per failure

AI coding platform for teams

AI Multi-Agent Framework in .NET

Production-ready code examples for Telnyx AI Communications Infrastructure — Voice AI, SMS, SIP, and IoT APIs

UltraGameStudio - AI coding agent for game development: engine workflows, gameplay code, and asset generation.

🦞 ResearchClawBench: Evaluating AI Agents for Automated Research from Re-Discovery to New-Discovery

The context-aware model router that learns & adapts to your long-horizon coding agent workflows. Lightweight & extensible, works with any harnesses, any models,…

Open-source sandboxes where coding agents build and deploy. Spin up isolated environments where Claude Code, Cursor, and other agents code and deploy software.

Native desktop UI for Claude Code with orchestration, streaming, background agents, and multi-provider support. Built with Tauri + React.

OpenCode mobile client via Telegram: run and monitor AI coding tasks from your phone while everything runs locally on your machine. Scheduled tasks support.

Terminal session manager for AI coding agents. One TUI for Claude, Gemini, OpenCode, Codex, and more.

Exposes internet search tools for use by LLM-backed Assist in Home Assistant

Templates and workflow for generating PRDs, Tech Designs, and MVP and more using LLMs for AI IDEs

Versus Incident is the self-hosted AI SRE agent. It learns what your system normally look like and escalates only what is new or unexpected issues — routing to…

Browser-native side panel for Hermes Agent — connect web context to your local Hermes runtime.

Agentic-friendly CLI generator for APIs: turn Swagger, OpenAPI, and google.api.http protos into single-binary CLIs with catalogs and generated Skills.

Open-source agent platform for Global × China enterprises — wire every system through one agent core. Self-hosted, any LLM.

Official python implementation of UTCP. UTCP is an open standard that lets AI agents call any API directly, without extra middleware.

An agent small enough to run anywhere. A minimal agentic runtime in C — ~380 lines, 54KB binary, ~2MB RAM. A skill file + an LLM + a shell loop, no framework.

AgentiLoop Agent! An Autonomous Agentic Agent for Mac, and exclusive Apple only harnesss. Suppprtd automation, scripting, coding, build anything and more. Power…

微信公众号 AI 运营助手 | 选题、写稿、审稿、排版、配图、发布全流程 Skill，支持 OpenClaw / Claude Code / Cursor / Codex