LLM Mart Basic

Execute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing WGBS/bisulfite-seq data, calling methylation levels, generating bedMethyl f

Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks

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.

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.

Run an ad-hoc ordered chain of pm-skills with shared context (ephemeral; routes to the pm-workflow-orchestrator)

Run the Customer Discovery workflow (research -> JTBD -> opportunities -> problem)

Run the Design Sprint workflow (5-day prototype-and-test arc producing a Decider's build/iterate/pivot/stop call)

Run the Feature Kickoff workflow (problem -> hypothesis -> PRD -> stories)

Run the Foundation Sprint workflow (2-day strategic-alignment arc producing a Founding Hypothesis)

Run the end-to-end Foundation Sprint + Design Sprint workflow with narrative handoff

Run the Post-Launch Learning workflow (instrumentation -> dashboard -> results -> retro -> lessons)

Run the Product Strategy workflow (competitive analysis -> stakeholders -> opportunities -> solution -> ADR)

Run the Sprint Planning workflow (refinement -> stories -> edge cases)

Run the Stakeholder Alignment workflow (stakeholders -> problem -> solution -> launch)

Run the Technical Discovery workflow (spike -> ADR -> design rationale)

Placeholder command file for the WS-T9 dual-shell parity smoke. No count phrases.

Fast non-interactive briefing before any meeting — auto-detects your next calendar event, pulls relationship history, surfaces open commitments, and produces a one-page brief in under 30 seconds. Use this whenever the user says "brief me", "give me a quick brief", "what's coming up", "background on my next call", "who am I meeting next", "brief me on Sarah", "I have a call in 10 min", "quick rundown", or right before walking into a meeting. Different from /minutes-prep — brief is the fast hook-fireable version that doesn't ask questions and doesn't set goals. Use brief when speed matters; use prep when the user wants to think hard about goals first.

Manage old recordings — find large files, archive old meetings, delete processed originals. Use when the user says "clean up recordings", "how much space are meetings using", "delete old recordings", "archive meetings", "manage meeting storage", or asks about disk space from minutes.

Start and control Minutes Coach, the separate real-time copilot HUD, with an explicit meeting goal. Use only for explicit Coach or HUD lifecycle requests such as "start Minutes Coach", "open the Coach HUD", "pause Minutes Coach", "resume Minutes Coach", "Minutes Coach status", or "stop Minutes Coach". Do not use for requests that explicitly ask the current terminal agent to watch or strategize; those belong to minutes-live-sidekick. An ambiguous request such as "coach me live" requires one short surface clarification and must not automatically start Coach.

Post-meeting debrief — analyzes what happened, compares outcomes to your prep intentions, tracks decision evolution. Use when the user says "debrief", "what just happened in that meeting", "what did we decide", "debrief that call", "post-meeting", "what changed", or right after stopping a recording.

Policy-safe relationship rankings, commitments, aliases, person profiles, and topic research. Always use Minutes' bounded native CLI surfaces; never build or read a durable graph cache.

Surface recent voice memos and ideas captured from any device. Use when the user asks "what ideas did I have?", "what were my recent memos?", "what did I record while walking?", or wants to recall a captured thought.

Extract facts from meetings and update your knowledge base — person profiles, chronological log, and index. Use when the user asks "ingest my meetings", "update my knowledge base", "extract facts from meetings", "sync meetings to wiki", "backfill knowledge", or wants their PARA/Obsidian/wiki profiles updated from conversation data.

Health-check your meeting knowledge for contradictions, stale commitments, and decision conflicts. Use when the user asks "any conflicts in my meetings", "check for stale action items", "lint my meetings", "consistency check", "are there contradictions", or wants to audit their decision history.

Offline-first Python AI agent that runs a tiny research business: quotes each job against its own costs, collects via Stripe, fulfils with NVIDIA Nemotron, pays…

DSH 插件 · 注入式优化器 0.8（主线）：你照常说话，它在你发送后,AI接收前把"这一轮到底要什么"理清楚，再把这份理解交给工作 AI(上下文注入) —— 原话不改写，条条带逐字依据。含控制界面（档位/权限/模型/上下文/只读工具）、拦截浮层（思维层+产出层）与真实 token 用量。可明显提升大多数模型的发挥稳…

Reliable AI Skill + MCP toolkit for agent-driven desktop CAD automation.

Curated real-world use cases for Hermes Agent — the self-improving AI agent from Nous Research. Backed by primary sources.

AI Agent 教学仓库 | 系统化 LangChain、RAG、LangGraph、MCP 全栈实战代码 | 万字博客详解 | 开源可运行示例 | 从零构建智能体

从 0 复刻 WorkBuddy-style 桌面 AI 助手 Harness：24 章 Python 教程，覆盖 Agent Loop、工具调用、记忆系统、Sidecar、沙盒审计、DeepSeek/OpenAI 评测轨迹

MCP server and CLI tools for web search and crawling, built on SearXNG and Crawl4AI

Delta MCP is a free app that sits between your AI apps and their MCP servers: one program per task instead of one tool call per step, up to 24.1× fewer tokens i…

Ava turns any Android 5+ device into a voice-first Home Assistant kiosk. Native C++ under the hood, so a 10-year-old tablet still listens, talks, and runs the h…

Roblox Studio macOS Window Capture Fix 2026: Real Screenshot Tool Instead of Magenta Playtest Glitch

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