LLM Mart Basic

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

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

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.

Vet the staged change: run the implement-review review loop (short alias)

Extract a learning from the recent conversation and add it to the appropriate instruction file

Extract a learning from the recent conversation and add it to the appropriate instruction file

Create a new pipeline from a task description. Fans out agent, skill, and hook scaffolding in parallel, then integrates into the routing system.

Jev-first router: A/B variant of /do. One TypeSafe call replaces the manifest read; falls back to /do when unavailable or unconfident.

Smart router: classify requests and route to the correct agent + skill

Generate project-specific CLAUDE.md from repo analysis.

Triage GitHub notifications: fetch, classify, report actions needed.

`github-profile-rules` — extract programming rules and coding conventions from a GitHub user's public profile via API.

Run the complete 34-stage implementation workflow for a large, multi-system, multi-wave, or CPU-delegated 5 Star Booker GM program.

Plan, then apply, the VexJoy Agent install with the vexinstall engine

Comprehensive PR review using specialized agents, with automatic retro knowledge capture

Reddit moderation: fetch modqueue, classify content, take mod actions

Learning system interface: stats, search, graduate learnings. Backed by learning.db (SQLite + FTS5).

Systematic upgrade pipeline for adapting agents, skills, and hooks when Claude Code ships updates, user goals change, or retro learnings accumulate.

agentii.full-equity-research — the spec 046 kit command. Use the Skill tool to run agentii:full-equity-research on this workspace.

agentii.synthesize — the spec 046 kit command. Use the Skill tool to run agentii:synthesize on this workspace.

Audit agents spawned in the current/last run against the agent-selection taxonomy

Run the Agent Diversity Review gate and emit the result table

Meta-analyze the effectiveness of a /loop arc — per-iteration metrics, LOC delta trend, saturation detection, and a keep/lengthen/delete recommendation.

Implementation of Podlite markup language

Open-source AI video workbench. Bring any model or your local ComfyUI, and let Claude Code / Codex / Cursor direct it over MCP — storyboard, references, generat…

《深入理解 AI Agent：设计原理与工程实践》（李博杰 著）开源主仓库：全书正文、编译版 PDF 与按章配套代码

Distilly — Distill how they think into reusable Skills for any Agent or Bot. Formerly Colleague Skill（原同事 Skill）.

本地优先的类飞书 Markdown 编辑器,内置可审改的 AI 助手 | Local-first WYSIWYG Markdown editor with a reviewable AI agent

A lightweight all-in-one terminal with 20+ protocols — SSH, RDP, SFTP, databases, Kubernetes and more. With a built-in autonomous AI Agent that plans and runs m…

一款专注于桌宠方向的AIAgent。特点是一键安装、功能齐全、极低开销、完全暴露上下文、全功能插件化、AI自主插件开发、永久唯一会话、类游戏引擎交互策略。具有极高的扩展性和拟人程度上限，非常适合想长期培养和自定义需求高的用户。

Control Gmail, Google Calendar, Docs, Sheets, Slides, Chat, Forms, Tasks, Search & Drive with AI - Comprehensive Google Workspace MCP Server & CLI Tool

一个先接住情绪、再分析关系并给出可执行策略的 Codex 恋爱军师，内置心理、法律、社会、人文、哲学、婚姻家庭与性学知识库，支持多元关系。

AI-powered SRE platform — read-only infrastructure diagnostics with deep investigation, security governance, and team collaboration

An open-source AI desktop companion inspired by Cyrene, combining immersive Chat, personalized long-term memory, and an agentic Work mode.

A local-first AI agent with persistent memory, emotional intelligence, and a peer-to-peer skills economy.

The open-source, multi-agent alternative to Claude Tag. @ any agent, wherever work happens, your agents work alongside your team and each other, learning as the…

Simple LLM service identification - translate IP:Port to Ollama, vLLM, LiteLLM, or 60+ other AI services in seconds

🔥 Official Firecrawl MCP Server - Adds powerful web scraping and search to Cursor, Claude and any other LLM clients.

Claude in Chrome, reverse-engineered and open-source. No domain blocklist. Any Chromium browser. Same 18 MCP tools, same performance.

Agent-native flight & hotel search and booking — MCP server, CLI, and Python/JS SDKs. Hundreds of airlines plus the major booking sites, with per-flight reliabi…

Open-source desktop AI agent for tools, files, knowledge, workflows, and real deliverables.

Open-source AI job search: scan job portals, evaluate listings into a structured A-H report with a global 1-5 score, tailor your CV, track applications — runs l…

Privacy-first Codex skill for discovering, validating, completing, and tracking job applications