LLM Mart Basic

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

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak s

Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, o

Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts,

Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger o

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinica

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs

Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCOD

Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models,

Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build over

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domai

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.

Update the Hivemind plugin to the latest version

credo - Disable credo for this directory (silence onboarding and the [credo] line here, reversible)

credo - Enable credo for this directory (opt in; overrides a previous decline)

credo - Explain something in depth (what/why/example/consequences)

credo - Migrate an existing repo into the .credo/ structure

credo - Pin the target repo for credo's project layer (hub-aware), or show the resolved target

credo - Interactive guide to available topics and workflows

credo - Clear this session's default role (back to no role; the agent does everything)

credo - Set this session's default role to plan/clarify (owns clarifying 1_clarify items, no commits/push)

credo - Set this session's default role to task/build (owns implementing GO items incl. commits/push per dogma)

credo - Promote an accepted sandbox artifact from .credo/sandbox-tmp/ to .credo/sandbox/

credo - Set the session mode to active (intensive live collaboration, no keep-alive)

credo - Set the session mode to autonomous (work approved GO items unattended, hook-enforced keep-alive ON)

credo - Initialize session with main agent workflow instructions

credo - Set the session mode to passive (user available for clarifications only, no keep-alive)

credo - Set up Claude Code with recommended workflows and plugins

dogma - Find and fix AI-typical patterns in code (reactive cleanup)

dogma - Sync documentation across README files and wiki articles

dogma - Interactively collect and apply CLAUDE rules to the project

dogma - Add ignore patterns to multiple locations at once

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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