LLM Mart Basic

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differe

Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq, MultiVI for multiome)

Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighb

Store and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets that are too large for

Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel

Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use when running end-to-end

Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES, producing pose confidence scores for virtual screening and structure-based drug design. Use when docking ligands into a protein, generating binding poses, or scre

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or lib

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PA

Featurizes molecules for machine learning with molfeat — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, pharmacophore and shape descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, CheMeleon) exposed as scikit-learn transformers that convert S

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or

Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark datas

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization,

Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), wi

Builds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectures, task/dataset abstractions, molecular generation, retrosynthesis planning, and knowledge-graph reasoning. Use when a project specifically needs TorchDrug's dat

Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms, supporting GRADE evidence

Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a doc

Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when

Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images, anonymizing DICOM files, wo

Develops, tests, and validates clinical machine learning models with the PyHealth 2.x healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, length of stay, drug recommendation), medical coding systems (ICD

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.

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.

This is the lane for changes with no behavior to test-drive — prose edits, a version bump on an

Use this after a pull request has merged but your local checkout is still on the topic branch.

Prints the public command catalog straight from `COMMANDS.md` — the plugin's own single source

This is the single entry point for turning staged work into a commit — nothing in codeArbiter

The protocol for a rule conflict — not a skill route, an orchestrator-level halt. When two sources

An optional, on-demand drift audit for the bypass case: a merge, a direct push, or a manual edit

This is the populator for a project that already has code to read. Instead of interviewing you about

This is where an unexplained defect goes before anyone touches code. The investigation is

This is the populator for a project that has no code yet to read. Rather than guessing at

Proves the install is actually enforcing, rather than just present. codeArbiter's worst failure

This is the standard entry point for new work with a human in the loop at every step. A short

This is the entry point for a defect that already has a known cause, or one you can describe

This is how a repository opts into codeArbiter for the first time. It writes the root-level state

A bare-numbers governance glance — three metrics, each with a trend arrow against the prior

The sanctioned, logged escape hatch. A routine gate — a lint rule, a style check, a non-security

Explicit PR entry and a direct request to open a PR use the same branch-finishing owner.

A zero-onboarding, read-only dry-run of the reviewer fleet against whatever is currently

This is a Feature Forge preview command — the after-each-turn service ships **off** by default and

Compares architectural records with the scaffold and prior decisions using SMARTS.

This is the lane for moving or reshaping code without changing what it does — a rename, an extract,

Paper trading simulator for Polymarket — built for AI agents. MCP server, live order books, strategy backtesting. Install: npx clawhub install polymarket-paper-…

An SSH tool dedicated to addressing all pain points · (macOS/Windows/Linux/Android/iOS)

The first AI agent harness native to the browser. A browser extension that runs a full agent loop where you already work: it drives your tabs, spins up sandboxe…

SmartLabel AI 2026: Auto-Annotate Any Object via LLM-Powered Prompt Parsing

Local-first visual generation runtime and studio for people and coding agents, with reproducible image and video workflows across multiple providers.

Scholar All-In-One: A research infrastructure for AI agents

Give your AI agent a real browser — with a human in the loop. Open-source MCP-native browser agent.

同花顺免费开源AI插件FQGate-agent（原插件名 tonghuasun-agent）：为 Codex、Claude Code、DeepSeek 等 AI 工具提供本机 A 股实时行情、K 线、Level-2、资讯、账户查询与可选交易能力。

A non-linear AI agent workbench — session is a tree: branch anytime, and context follows the branch

Production-grade AutoCAD MCP server for AI agents — 122 tools, dual COM (live AutoCAD) + headless ezdxf engines, ISO GD&T and dimension-tolerance validation for…

A DeepSeek coding agent harness: persistent shell, Ultra subagents, auto approval, Chrome MCP and session telemetry

Waku Waku! Waku Agent is a local-first AI agent harness you actually own, including loop, memory, eval, all in code built to stay legible as it grows.

Remote control for Claude Code, Codex, Grok, and Cursor on Mac or PC. View sessions, send tasks, and drive them remotely from your phone, PIN, or Ring. OpenClaw…

Next-gen AI-native server ops panel with an in-workspace SRE agent. Crash self-healing, safe rollbacks, Docker/game servers, and local Ollama support.

Professional cloud architecture diagrams with official AWS, Azure and GCP icons, from Terraform code or a plain JSON graph. MCP server + agent skill.

A ready-to-use self-growing desktop AI assistant for long-running tasks, memory, agents, tool reviews, MCP, and high-concurrency workspace automation. / 开箱即用的自我…

Collection of templates using the Alchemyst AI Platform for your next big AI app.

Fast, exact LLM decoding on Apple Silicon (MLX) behind an OpenAI-compatible endpoint

The open source AI research agent.

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