LLM Mart Basic

Quantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2g

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data

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

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.

Validate application configuration with schemas, per-environment rules, runtime checks, and secure handling of sensitive values

Preflight a DGX Spark system for an ML training or inference workload and emit env-report.json

Set up debugging and tracing with remote debugging, distributed tracing, debug logging, profiling, and production diagnostics

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

Analyze and resolve errors across the full application lifecycle — from stack traces to distributed tracing — using systematic root-cause analysis and observability tools.

Set up error tracking and monitoring — implement structured logging, configure alerts, and integrate with error tracking services for real-time error detection.

Coordinate specialized review agents in parallel or in sequence and synthesize their findings into one code review

Analyze and resolve errors across the full application lifecycle — from stack traces to distributed tracing — using systematic root-cause analysis and observability tools.

Set up error tracking and monitoring — implement structured logging, configure alerts, and integrate with error tracking services for real-time error detection.

AI-assisted smart debugging — parse error messages, stack traces, and failure patterns to identify root causes and produce a fix with automated observability steps.

Generate comprehensive migration plans and scripts for transitioning codebases between frameworks, languages, versions, or platforms with minimal disruption.

Plan and execute safe, incremental dependency upgrades with minimal risk — including breaking-change migration paths and proper test verification.

Orchestrate legacy system modernization using the strangler fig pattern with gradual component replacement

Scaffold React and React Native components with TypeScript, tests, styles, and Storybook stories

Scan React, Vue, Angular, and vanilla JavaScript code for XSS vulnerabilities and report fixes with secure coding examples

Orchestrate end-to-end full-stack feature development across backend, frontend, database, and infrastructure layers

Orchestrate git workflow from code review through PR creation with quality gates

Create a role-specific onboarding plan for a new team member, from pre-arrival setup through the first 90 days

Enhance a pull request with a generated description, review checklist, risk assessment, and test coverage report

Orchestrate multi-agent incident response with modern SRE practices for rapid resolution and learning

Ultra-lightweight, open-source, self-hosted personal AI agent framework in Python with WebUI, tools, memory, MCP, multi-agent workflows, automation, and chat ap…

Governance framework for AI coding agents. It runs them through a five-step workflow (plan, build, review, test, ship) where no step counts as done without evid…

Ultimate Multi-Agent OS for Autonomous AI NPCs 2026

Personal AI Agent Hub 2026 — Build Your 24/7 Autonomous Assistant

Proven 2026 Multi-Agent AI Review System – Verdict-Driven Quality Control

Slash API Batch: Cut AI Costs by 50% in 2026

Web dashboard for Hermes Agent — multi-platform AI chat, session management, scheduled jobs, usage analytics

Agent Skills for Solopreneurs

AirLLM dramatically reduces inference memory usage, letting 70B large language models run on a single 4GB GPU card

Zero, your trustworthy AI teammate for real work.

一套 DSH runtime，Desktop、Web 与 TUI 三种开发体验。

Open-source operational advisor for ClickHouse — real-time monitoring plus AI-driven index/partition/materialized-view recommendations.

⚙️ TypeScript Style Guide and Agent Skill. A concise set of conventions and best practices for consistent, maintainable code.

Framework for AI agents to build and maintain a digital brain through Obsidian wiki

Apache Maka (Incubating) is a local-first AI agent workspace. Model messages, tool calls, tool results, permission decisions, and termination events are recorde…

Neo.mjs is a self-evolving software organism: a professional end-to-end AI engineering team whose cross-model swarm inhabits live apps via Neural Link, Active H…

Agentic development harness for Claude Code — SPEC-driven plan/run/sync, TRUST 5 quality gates, model+effort routing, and Claude×GLM multi-LLM cost control. Sin…

NocoBase is an open-source AI + no-code platform for building business systems fast. Instead of generating everything from scratch, AI works on top of productio…

An open-source AI coding agent that lives in your terminal.

PawWork — free, open-source desktop AI agent for macOS and Windows. Alternative to Codex App and Claude Cowork. BYOK with 75+ providers, ChatGPT OAuth, local mo…