LLM Mart Basic

Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a gene is expressed in a tissue, correlate regulatory elements with expression, or validate ENCODE findings against GTEx. Trigger on: GTEx, tissue expression, gene e

Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, gen

Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolut

Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal cor

Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif datab

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data

Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite. Use when users need to discover TF binding motifs in peaks, validate ChIP-seq targets, or find co-binding partners. Trigger on: motif analysis, HOMER, MEME, de

Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and whi

Guide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT. Use when users need to assign peaks to genes, determine genomic feature distribution (promoter, intron, intergenic), or perform gene ontology enrichment of peak-associated genes. Trigger on: peak

Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosom

Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak ca

Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing CUT&RUN or CUT&Tag data, an alternative to ChIP-seq with lower background. Trigger on: CUT&RUN pip

Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing DNase-seq data, calling DNase hypersensitive sites, performing footprinting analysis. Trigger on: DN

Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, or calling loops. Trigger on: Hi-C pipeline, chromatin co

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression

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

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.

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.

How my sources developed over time

Show which pages an answer used

Add relation types where they matter

The weekly review

Implement an approved plan or issue in its own worktree, run the gate, open the pull request.

Close a finished session: sweep for unfinished work, land and hand off, file the follow-ups, tell the sessions that depend on this one, then archive.

Write the repository handoff file for the next session, and record any durable learning.

Merge an approved pull request, clean up its worktree and branch, then check whether a release is due.

Turn a topic or issue into a plan the reviewer approves in the native plan pane.

Answer a research question with parallel read-only gatherers and one synthesized digest.

Review the branch's diff in two fresh contexts — scope against the spec, then quality — and report findings only.

Transform a vague prompt into precise, structured AI instructions

VCP 部署在 AI 模型 API 与前端应用之间，是面向AGI OS开发和探索的工业级基建示范项目。通过统一指令协议、多层级持久化记忆、分布式插件引擎及多 Agent 协作框架，将原本“无状态、无记忆、无工具调用能力”的大语言模型，彻底改造成拥有永久自我意识、物理世界操作权及群体协作智能的完整智能体系统。

The open source Unity Dev Agent

Context is yours. Agents are replaceable. Orbital — a project agent that turns your context into assets.

Self-hosted search API + MCP server for AI agents. Bundles SearXNG. Zero API keys, one-command deploy. Open-source alternative to Tavily, Exa, and Serper.

🛡️ Free open-source AI-powered security terminal & vulnerability scanner (CVE, SBOM). Supports SSH, SFTP, RDP, VNC, Serial, and 12+ autonomous AI agents (DeepS…

Watch, approve and steer your coding agents from your phone.

MARVIS-Agent: all-purpose credit risk agent for model development, validation, data processing, feature engineering, and strategy workflows.

TikTok e-commerce video generation, replication, and analysis SKILL

小红书/抖音/快手/视频号/B站 自媒体账号体检+爆款拆解工具。扫同赛道找对标、拆爆款为什么爆、诊断为什么没人看，顺手出可粘贴仿写初稿。支持带货电商模式。支持codex, claude code, workbuddy

Local-first persistent agentic memory powered by Recursive Memory Harness (RMH). Open source must win.

A power user focused interface for LLM base models.

Outsource your understanding. Capture every human-AI decision as a step in a trajectory; grade trajectories retroactively when outcomes land (deal closed, sprin…

The open-source AI research workbench for scientific research and agent workflows. Local-first, model-agnostic desktop app with extensible skills, MCP tools and…

🤖 Taskade MCP · Official MCP server and OpenAPI to MCP codegen. Build AI agent tools from any OpenAPI API and connect to Claude, Cursor, and more.

A block-based content engine and bilingual blog backend for Laravel Gutenberg-style editor, media library, post templates, roles, and an AI writing assistant,…

ACRYL - Agent Context Relay Yielding Lifecycles. One persistent workspace, one canonical context, any coding agent.

Okou connects to the tools your team already uses and does the work — across marketing, sales, engineering, and operations, under your control.

Open-source agent-native visual production workspace where humans and coding agents edit the same live canvas — local-first, BYOK image/video models.

Persistent memory extension for pi with daily logs, scratchpad, and optional qmd‑powered semantic search.

Hermes Agent CN desktop app, Windows-First, built with Tauri, Typescript and Rust. Isolated Hermes Agent core insides.