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

Fourteen posts of being wrong in production, compressed to checkboxes

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.

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.

{{SKILL_ENTRY:post-merge-cleanup}}

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

{{SKILL_ENTRY:commit-gate}}

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.

{{SKILL_ENTRY:context-check}}

{{SKILL_ENTRY:context-creation}}

{{SKILL_ENTRY:debug}}

{{SKILL_ENTRY:decompose}}

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.

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

{{SKILL_ENTRY:finishing-a-development-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.

{{SKILL_ENTRY:decision-variance}}

Open-source, self-hosted AI media server. One server replaces your entire media stack, with a web app, native iPhone app, and an AI agent that gets things done.…

A curated list of tools built for Jev — TypeSafe AI's System One model for typed decisions.

🦦 Crayotter: A Multimodal AI-Agent for Video-Editing, Video-Composing, and Video Production. Powered by Multimodal LLMs for autonomous Text-to-Video agentic fr…

Webextension tool for Odoo

基于多模态视觉感知与 LLM Agent 的 macOS 微信自动化框架 | Visual RPA for WeChat

The operational superset of Pi Coding Agent — everything Pi, plus observability, governance, recovery, evaluation and multi-agent orchestration. Pi Coding Agent…

Metrik 可以集中查看本机多个 Agent 的配额余量和 Token 消耗，目前支持 ChatGPT、Claude、GLM、Kimi 等主流 AI 服务。

An AI agent with a real self — soul she wrote, desires that drive her, a heartbeat for autonomous action, dreams she processes when you're away. Capability supe…

Production-ready open source terminal coding agent with readable, layered code: permission rules, OS sandboxing, MCP, skills, sub-agents, and Anthropic, OpenAI-…

Answer me with HTML — an agent skill that answers hard questions with a one-page HTML you can actually read. 让 AI Agent 用一页 HTML 回答复杂问题。

Prompt packs that make any AI agent a LaTeX expert — fix errors, polish writing, format for venues, read papers, recover source

Claude Code plugin: universal radial-tree exploration engine. One tree skill + swappable presets (brainstorm / attack / design / code-audit) for divergent ideat…

Claude Code + OpenClaw + Codex + WorkBuddy 中文教程 | 50篇完整教程 + 1张速查卡 | 80万+内容量 | 1500+实操示例 | AI Coding / Agent 四线学习路径（编程+助手+Agent+办公）

SmartLabelBench 2026: LLM-Powered Auto Annotation and Dataset Builder for Everything

从零开始玩转OpenClaw：最全面的中文教程，涵盖安装、配置、实战案例和避坑指南（github版）

Native Android GUI for running AI coding agents locally on-device. No terminal or PC required.

基于 LangChain/LangGraph 的 ReAct Agent ，结合 RAG、工具调用与 Streamlit 界面，面向智能客服与报告生成场景。

An open-source, local-first AI learning workbench

Open-source coding agent for your terminal, built in Rust and on a journey of continuous community improvement. Issues and PRs welcome.

Matt Pocock 技能集的中文翻译版 — 地道中文，原汁原味的技术术语。基于 mattpocock/skills 复刻。每日中午12点钟同步