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 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.

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.

Periodic multi-reviewer sweep of the whole codebase — surfaces a triaged checkpoint report.

Sanctioned lane for non-behavioral work — docs-only edits, dependency bumps, reverts. Type-scaled gates; no TDD demanded of prose.

Finish an already-merged branch — classify the leftover artifacts, return to a fast-forwarded default checkout, and delete the merged local branch. Every discard confirmed per item; containment proven, never assumed.

Show the codeArbiter command catalog — the public command list and what each routes to.

Run the full commit gate — the only sanctioned path to a git commit.

Stop everything and surface a rule conflict — persona vs. docs vs. code. Present both sides and the conflict-hierarchy level; the user resolves. No silent reconciliation.

Optional manual drift audit — report stale provenance-tracked docs, then per stale doc offer re-scout, re-baseline, or defer. Not the daily loop; commit-gate auto-heal owns routine maintenance.

Brownfield back-fill — scout an existing codebase and populate .codearbiter/, then lock it initialized.

Investigate-then-decide root-cause analysis for a defect whose cause is unknown. No code changes — exits to {{CMD:fix}}, {{CMD:adr}}, or a no-action close.

Greenfield decomposition interview — a layered interview that populates .codearbiter/ and locks it initialized.

Verify the active host install, package, command ownership, enforcement{{IF:pi}}, wrapper self-test, and active-dispatch coverage gap{{ELSE}}, and harmless live-fire probe{{END}}. Read-only.

Start a feature: brainstorm a spec, get it approved, then drive it test-first through the pipeline. The one entry to implementation.

Fix a confirmed bug: a failing regression test first, then a minimal fix, then the rest of the tdd gates.

Opt this repo into codeArbiter — scaffold the root-level .codearbiter/ state store.

Read-only 3-metric governance glance — override rate, small-lane rate, sprint low-confidence ratio — each with a trend arrow vs. the prior 20-commit window.

Author a new codeArbiter skill: prove the gap is real, get the spec approved, then write it.

Sanctioned, logged bypass of a gate or hard rule — one audit line, then proceed.

Open a pull request the only sanctioned way — clear every BLOCK-level review finding, then stage the PR. Never a direct write to the default branch.

Zero-onboarding, read-only dry-run of the reviewer fleet against the current uncommitted diff. Predicts reviewers, runs the state-free secret scan, writes nothing.

Trim transcript clutter to extend session lifetime — analyze, prune a copy, or toggle the after-each-turn service. Dry-run by default; gains land at resume/compaction, not the current turn.

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.