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.

Improve an existing agent through performance baselines, prompt engineering, A/B testing, and staged rollout

Optimize multi-agent system performance through profiling, context window tuning, coordination efficiency, and cost and latency tradeoffs

Debug issues using competing hypotheses with parallel investigation by multiple agents

Task delegation dashboard for managing team workload, assignments, and rebalancing

Develop features in parallel with multiple agents using file ownership boundaries and dependency management

Launch a multi-reviewer parallel code review with specialized review dimensions

Gracefully shut down an agent team, collect final results, and clean up resources

Spawn an agent team using presets (review, debug, feature, fullstack, research, security, migration) or custom composition

Display team members, task status, and progress for an active agent team

Build realistic API mock servers with request stubbing, dynamic data, test scenarios, and contract testing

Orchestrate end-to-end application performance optimization from profiling to monitoring

Orchestrate end-to-end feature development from requirements to deployment

Set up PreToolUse hook to block --no-verify and other git bypass flags in Claude Code projects

Generate comprehensive C4 architecture documentation (Context, Container, Component, Code) for a codebase using bottom-up analysis and four coordinated C4 agents.

Automate CI/CD pipelines, releases, and development workflows with GitHub Actions, pre-commit hooks, and infrastructure automation

Explain complex code, algorithms, and design patterns with step-by-step breakdowns, visual diagrams, and interactive examples

Generate API, architecture, code, and user documentation from a codebase and automate keeping it current

Restore saved project context and decisions to resume a session

Refactor provided code for cleanliness, maintainability, and alignment with SOLID principles and modern best practices — no over-engineering.

Analyze and remediate technical debt — inventory debt items, score by impact, and produce a prioritized remediation plan with estimated effort.

MCP server for reusable prompt templates, multi-step workflow chains, and quality gates. Compose agentic workflows with an operator syntax; export as native ski…

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OKF (Open Knowledge Format): Durable, structured memory for AI agents. Author, validate, consume, and maintain portable knowledge bundles through an ecosystem o…

토스증권을 AI 에이전트와 터미널에서 다루는 도구. CLI 와 MCP 서버로 계좌·시세·주문은 물론 웹앱 전용 기능(수급·AI 시그널·스크리너·배당)까지, JSON·CSV 구조화 출력으로 AI 도구·자동화에 바로 연동.

Claude skills for LinkedIn. 11 Claude Code and Codex skills that write human-sounding LinkedIn posts, craft comments that get noticed, analyze your feed, and bu…

MCP server connecting AI agents to ITASCA engines (PFC, FLAC, 3DEC, MPoint, MassFlow) — run geotechnical & geomechanics simulations through natural conversation

A curated list of amazingly awesome articles, people, applications, software libraries and projects related to the knowledge management space

One local dashboard for every Claude Code, Codex, Cursor, Antigravity, and Kilo Code session on your Mac. Spawn in parallel, ship in parallel. Open source, MIT.

Building blocks for frontier OpenAI agents in Rust. Nanocodex empowers you with Codex-level performance anywhere.

The AI agent that lives in your framework/browser

Self-Programming AI Assistant. Capture, automate, and refine all your workflows.

Consider it done. The open-source AI agent that works out of the box · 想到，就能做到。开源、开箱即用的 AI Agent。

Make Any Website into CLI & Use your logged-in browser by AI agent.

ISO 24495 Plain Language skills and Claude Code plugin

Deterministic, fail-open tool routing for Hermes Agent with an optional local-model fallback.

1인 사업가 생산성 키트 — 직원 없이 49개를 자동화했고, 그중 바로 쓸 수 있는 AI 에이전트 스킬 26개(+실행 스크립트)를 공개합니다

AI Agents & MCPs & AI Workflow Automation • (~400 MCP servers for AI agents) • AI Automation / AI Agent with MCPs • AI Workflows & AI Agents • MCPs for AI Agent…

The open-source, self-hosted video conferencing software. Scalable, customizable, and with a powerful AI Meeting Agent.

Business operating system for Claude Code — 57 skills, 21 agents, smart daemon. Unified inbox (WhatsApp/Email/Slack/Telegram), autonomous PR merge, full-AWS mon…

A local-first, cross-platform Electron desktop workspace for Pi Coding Agent, with sessions, project files, browser tools, skills, plugins, and messaging integr…