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.

CoalWash self-update — check for a newer version and offer to apply it, or set how updates are handled.

Create an AI skill from any source (URL, repo, PDF, video, notebook, etc.)

One-command skill creation and packaging for a target platform

Sync a scraping config's URLs against the live documentation site

Generate and run validation queries for the current change

Generate and run validation queries for the current change

Check code-intelligence prerequisites (ripgrep + a language server) and print install hints

Create space-efficient paper and proposal figures (HTML mockups, TikZ, or skia-canvas) from tool selection through LaTeX insertion

Design concise overview, mechanism, or workflow figures as editable PowerPoint objects

Run the implement-review staged-change review loop

Detect the work type (papers, proposals, code, figures, admin) and dispatch to the right domain skill

Run prun: parallel delegation fan-out on Agy workers (the session coordinates)

Audit a GitHub README and rewrite it with modern patterns for a scannable ten-second skim

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

Create space-efficient paper and proposal figures (HTML mockups, TikZ, or skia-canvas) from tool selection through LaTeX insertion

Design concise overview, mechanism, or workflow figures as editable PowerPoint objects

Run the implement-review staged-change review loop

Detect the work type (papers, proposals, code, figures, admin) and dispatch to the right domain skill

Run prun: parallel delegation fan-out on Agy workers (the session coordinates)

Audit a GitHub README and rewrite it with modern patterns for a scannable ten-second skim

Your Personal AI Assistant; easy to install, deploy on your own machine or on the cloud; supports multiple chat apps with easily extensible capabilities.

Agent OS: the agent gets smarter on its own. We just hold the line: the grading command and expected result never make it into the success contract we hand it.…

Curated systems, benchmarks, and papers etc. on memory for LLMs/MLLMs --- long-term context, retrieval, and reasoning.

:memo: Vimlike Modal Text Editor in Rust

CI-native security testing for MCP servers. Attack simulation, schema drift detection, and health scoring before agents depend on them.

Hermes Agent memory plugin/provider for scope-aware recall, SQLite truth, LanceDB semantic search, and hybrid retrieval.

For You Agent——AI 时代的个人随身数字人格。把你的模型、AI 账号、技能、提示词和工作方式，带到每一个 AI 工具里。

A coding agent: give it a prompt and it reads, writes, runs commands, and searches code in a loop until the work is done, using native tool-calling across OpenA…

A secure persistent personal agent server in Rust. One binary, sandboxed execution, multi-provider LLMs, voice, memory, Telegram, WhatsApp, Discord, Teams, and…

Self-evolving agent: grows skill tree from 3.3K-line seed, achieving full system control with 6x less token consumption

DeepSeek Harness Desktop (dsh-desktop). EAC: Embracing All Creation (揽尽万象). Bundled Node.js runtime with full dsh-CLI kernel, one-click startup, 10 built-in UI…

See your agent think. Zero-config observability & governance for 26 AI agent runtimes: Claude Code, Cursor, OpenAI Codex, GitHub Copilot, Gemini CLI, Cline, Ope…

Save 94% on AI coding tokens. Index your codebase, agents search instead of reading files. Works with Claude Code, Codex, Copilot, Cursor, Gemini CLI. Local MCP…

Yet another coding agent harness, lightweight and written in go.

a coding Agent from pi. ∞ providers, sub-agents, hashline edits, and a permission gate

Omnigent is an open-source AI agent framework and meta-harness: orchestrate Claude Code, Codex, Cursor, Pi, and custom agents — swap harnesses without rewriting…

🧠 Leon is your open-source personal assistant.

The Station, an open-world multi-agent environment that models a miniature scientific ecosystem.

The Frontend Stack for Agents & Generative UI. React, Angular, Mobile, Slack, and more. Makers of the AG-UI Protocol

VelaTerm = iTerm2 + Codex, The Best Terminal for AI Coding