LLM Mart Basic

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux q

Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functiona

Quantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2g

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretraine

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

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.

Treat an AI agent skill as both an instruction package and a software dependency: inspect what it says, what it runs, what it can access, and how it updates.

Add remote HTTP or local stdio MCP servers to Claude Code, choose the right scope, protect credentials, verify the connection, and test with least privilege.

`crabbox attach` follows the recorded events of an active coordinator run and

`crabbox azure` groups Azure provider setup commands. It currently has a single

`crabbox bench` records and reports local benchmark timing observations. It is a

`crabbox cache` inspects, purges, or warms package and build caches on a

`crabbox capsule` captures, replays, and tracks lightweight failure capsules.

Save the state of a lease, then restore it onto another box or fork it into a

`crabbox claims list` prints the lease claims stored on the current machine. It

`crabbox cleanup` sweeps direct-provider machines and local provider state that

`crabbox code` bridges a Linux lease's `code-server` workspace into the

`crabbox config` inspects and updates user configuration. It has three

`crabbox connect` resolves a lease and opens an interactive SSH session to it.

`crabbox cp` copies files or directories between the host and a Crabbox-owned

`crabbox desktop` drives a visible desktop session on a lease that was warmed

`crabbox doctor` runs a preflight before you commit to a long workflow. It is

`crabbox egress` gives a lease mediated outbound network: a lease-local browser

`crabbox events` prints the broker's event log for a recorded run.

`crabbox heartbeat` refreshes the idle deadline for one owned lease and prints

`crabbox history` lists recorded remote command runs from the broker. Each run is

`crabbox image` holds the trusted-operator controls for provider base images:

`crabbox init` onboards the current repository: it writes the minimal config

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…