LLM Mart Basic

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

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE a

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene const

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

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.

Systematic workflow for fixing bugs including issue creation, branch management, and PR submission

Bulk import GitHub issues to Linear

Explore multiple business timeline scenarios with constraint validation and decision optimization.

Demo changelog automation features

Perform comprehensive analysis of $ARGUMENTS to identify code quality issues, security vulnerabilities, and optimization opportunities.

Run project checks and fix any errors without committing

Setup continuous integration pipeline

Clean up merged and stale git branches

Fix all linting and formatting issues across the codebase

Test multiple code variations through simulation before implementation with quality gates and performance prediction.

Perform comprehensive code quality review

Convert code analysis to Linear tasks

Perform comprehensive code analysis with quality metrics and recommendations

Automatically create and execute a git commit using the first suggested commit message

Create well-formatted git commits with conventional commit messages and emoji

Model world constraints with assumption validation, dependency mapping, and scenario boundary definition.

Containerize application for deployment

Load project context by reading README.md and exploring relevant project files

Generate comprehensive architecture documentation

Create a new command following existing patterns and organizational structure

AI agent orchestration kit for Windows, Linux/MacOS with Codex skills, hooks, routing rules and profiles for Claude, OpenCode, Cursor, Gemini and Windsurf.

Skills & reviewer agents for AI-first climate science — built and used by a PhD atmospheric scientist

出行路书工作流 skill：联网实查 + 多源交叉验证，产出可核验、能执行的旅行攻略。覆盖吃住行游拍避全维度，附美食情报卡、基准骨架与校验工具，支持一键部署在线版。

Self-hosted AI code reviewer with indexed PR reviews, walkthroughs, vulnerability scanning, dependency graphs, custom rules, and a learning loop.

🧬 Extend EvoScientist with Installable Skill & Knowledge Packs

Give the agent a machine. Just not yours. Each AI coding agent gets its own isolated machine with root, Docker, and systemd - active defense detects and stops t…

Automatic memory consolidation for OpenClaw agents — like sleep for your AI. Powered by MyClaw.ai

🗂 The essential checklist for modern web development, for humans and AI agents

Distribb CLI, Claude, Codex, Hermes, OpenClaw skill for AI-powered SEO. Write content with your own AI, publish through Distribb's backlink network.

Open-source AI browser agent — type plain-language commands and Bah operates the web for you. Works with cloud AI (DeepSeek, Mistral, NVIDIA) or local Ollama mo…

DeepSeek Harness Desktop (dsh-desktop). EAC: Embracing All Creation (揽尽万象). Bundled Node.js runtime with full dsh-CLI kernel, one-click startup, 10 built-in UI…

Use your ChatGPT / Codex subscription with DeepSeek Harness via OAuth, with model access, usage quotas, search, and image generation — no API key or Codex CLI r…

Local-first A-share research workbench for DeepSeek Harness: market dashboards, watchlists, valuation, four investor agents, versioned reports, and continuous p…

Open-source video pipeline (clipper, AI video & more) — scout trends, clip long videos, generate captioned shorts, design motion graphics. Local-first, BYOK. AG…

Desktop app for the pi coding agent: streaming timeline, Git review with hunk staging, session tree, native UI for pi extensions. Windows · macOS · Linux. pi 编程…

Zero-dependency browser video editor that AI agents can drive — JSON timeline, MCP + REST, live-reloading UI

Personal Context Manager for Claude Code. Your life in walnuts.

Fast way to switch between Claude Code configuration profiles

AutoClip｜一个链接，一键出片。开源 AI 视频剪辑桌面工具，将播客、访谈、课程等长视频自动剪成短视频，生成字幕、封面和发布文案，适配抖音、小红书、TikTok、Reels 与 YouTube Shorts。Open-source AI video clipping & content repurposing.