LLM Mart Basic

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

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.

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.

This is the only sanctioned way a version tag gets created, and it holds no knowledge of any

A read-only review of the current change, dispatched by path against a reviewer-to-path matrix:

This is the outlet for "I need to write code to find out" rather than "I know what to build." The

This is codeArbiter's autonomy mode. It collapses the usual spec-plan-execute cycle into one

The daily hygiene checklist, made routine and gated: fetch and offer a fast-forward pull, list

A read-only snapshot of `.codearbiter/` state: the project's `stage:` maturity value, every

Wires codeArbiter's renderer into `~/.claude/settings.json`, or removes it. A plugin can't own a

The only blessed way to mutate `.codearbiter/open-tasks.md`. It runs a thin writer over pure

An opt-in, lightweight STRIDE pass over a design before it's built — invoked deliberately, never

codeArbiter's deepest, most expensive review, convened rarely and never as a required gate. Eleven

Watches a pull request's CI checks to completion without polling by hand. The wait is a real

A fixture command named debug, colliding with the debug skill/agent.

A fixture command named prune, used to regression-test forge badges.

Another command, description only, no argument hint.

A sample command for fixtures — single sanctioned path to a thing.

Convert an animated HTML file (like /fig output) to a perfectly looping high-quality small GIF using Playwright + ffmpeg

Find a free licensed image on the internet and add it to the project, optimized

Art-direction photo pass over the site: add photography only where it earns its place

Audit consolidate or forget stale sensitive or superseded Tree Ring Memory entries

Capture a concise validated lesson decision warning or preference in Tree Ring Memory

Atom Agent, Open-Source Governed AI Agent Platform for Self-Hosted Automation

The agent engineering intelligence harness, optimized tools, memory system, subagents and mixture of models packages ⚚

Sesori iOS/Android app and the Sesori Bridge CLI — drive Claude, Codex, OpenCode, Cursor, Pi, OMP, Hermes coding sessions from your phone

🧠 RepoBrain (formerly Antigravity) — Give your repo a brain. ChatGPT for your codebase: works in Claude Code, Cursor, Codex, Windsurf & more.

Use ChatGPT (Codex), Claude, and Grok (X Premium) subscriptions as DeepSeek Harness LLM providers — OAuth login in the web UI, no API keys

Latitude is the open-source AI monitoring platform.

Open-source AI browser agent for Chrome and Firefox (monorepo) 🧠

Official Model Studio CLI（阿里云百炼 CLI）built for AI Agent frameworks, exposing models, search, multimodal, and workflow capabilities as structured tool calls.

Curated DeepSeek Harness (DSH) plugins, extensions, tools, skills, clients, runtimes, integrations, and verified references — English and Chinese.

Turn papers, code, and docs into presentation-ready, natively editable PPTX in Codex / Claude Code. Native charts and equations, speaker notes, click-build anim…

Grix : Work with agents like talking to people.

Local First Ai Agent. Optimized for Local Ai models. Long context window. Proper tools callings. Runs privately on your device.

Model Context Protocol server that integrates AgentQL's data extraction capabilities.

AI that ships your tickets.

Metadata-driven CLI for AI Agent Bots — 48 operations across 7 domains, structured JSON envelope I/O, zero interactive prompts.

An open-source, extensible, self-hosted agent workspace with multi-runtime support for Codex, Claude Code, and more, plus reusable local apps for custom interfa…

Open-source Windows desktop client and GUI for DeepSeek Harness — zero-setup installer with Codex, plugins, skills, SSH, mobile remote access, and 11 skins.

The open-source AI workbench for scientific research

DeepSeek-native AI coding agent for your terminal. Engineered around prefix-cache stability — leave it running.

A Fully free agentic browser driver for AI , few tools, full control, real stealth, top-tier token efficiency.