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

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

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.

Repoint Jira configuration and regenerate catalogs after explicit approval.

Generate or refresh the risk-ranked master test plan.

Synchronize AI-critical repository documents without modifying Engram memory.

Adapt KATA and repository tooling after an approved no-write analysis and plan.

Explain existing automated tests and assertions without editing code.

Generate or refresh the business-level API map.

Generate or refresh the business data and flow map.

Generate or refresh the business feature inventory.

Audit and repair one ticket's TMS traceability after explicit approval.

Plan and reconcile Jira Components after explicit approval.

Repoint Jira configuration and regenerate catalogs after explicit approval.

Generate or refresh the risk-ranked master test plan.

Synchronize AI-critical repository documents without modifying Engram memory.

View your cognitive methodology profile and reasoning patterns

Diagnostique l'environnement Cortex et guide la réparation (DB, extensions, modèles)

Resolve the ⟦rcpt:id⟧ injection markers in context into presence-in-context evidence (blame path)

Please summarize your current changes, generate a commit message in English, then add and commit.

Create an annotated git tag with an auto-generated summary of changes since the last tag.

Run OCR in delegation mode — OCR handles file selection and rules, the host agent performs the actual review.

Run OpenCodeReview (OCR) to review code changes and autonomously apply fixes.

AI skill for OpenClaw & Claude Code — recommend from 10000+ Nano Banana Pro (Gemini) image prompts. Smart search by use case, content remix, sample images.

嘉立创EDA专业版(EasyEDA Pro)自动化：给 AI harness 装上画板的「手」—— 一套 typed 原理图/PCB 动作，CLI / Agent Skill / stdio MCP 三形态融合接入。承接嘉立创「不以卖板赚钱，以培养中国工程师为己任」 | EasyEDA Pro automation:…

Claude Code session log viewer for JSONL files in ~/.claude/projects. Browse conversations, tool calls, tokens, and live tail sessions on desktop, web, and TUI.

Shared memory MCP server — persistent, searchable, cross-client Claude, Opencode

OpenAI Codex CLI session log viewer for JSONL files in ~/.codex/sessions. Browse conversations, tool calls, tokens, collaboration chains, and live sessions on d…

High-performance Google Drive CLI and Model Context Protocol (MCP) Server for LLM/AI agents. Natively execute Google Apps Script (GAS) under a secure whiteliste…

"Vibe-Trading: Your Personal Trading Agent"

Local-first chat history analyzer with AI. | 本地优先的 AI 聊天记录分析工具

Official Oxylabs MCP integration

Persistent memory for Claude Code & Codex CLI. Auto-extracted knowledge graph, multi-representation embeddings, 3D WebGL visualization. LongMemEval R@5=97.45%.…

One person, a team of agents. Multi-session CLI that collaborates across terminals; /goal keeps long tasks running; WeChat/WeCom/Feishu gateway lets you call th…

AI 基础知识 - GPU 架构、CUDA 编程、大模型基础及AI Agent 相关知识。

Self-hosted, open-source agent skill registry for enterprises. Publish & version skill packages, govern with RBAC and audit logs, deploy on-premise with Docke…

深度调研报告生成 Skill — 一条命令，十分钟出券商级深度调研报告 / Professional deep research report generation Skill · Supports 19 languages

The OKF toolkit for Claude Code — author, maintain, validate & visualize Open Knowledge Format bundles. Plugin, agent skills, and a GitHub Action.

Autonomous AI pentesting agents — real-time reconnaissance, vulnerability detection, and exploitation orchestration. Go + TypeScript.

Native macOS and iOS App for the Hermes AI agent — multi-window, multi-server (local + remote over SSH). Chat, dashboard, sessions, memory, cron, MCP, and more.

Multiplayer Claude Code and Codex. Self-hosted team workspace for Claude Code and Codex. Multi-user, browser-based, AI mates with memory.

Every past session, subagent, and workflow -- queryable by your agent, browsable by you

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