LLM Mart Basic

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 datase

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstruct

Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inve

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially express

Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple

Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filt

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux q

Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functiona

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

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.

Explain how tasks in an issue were implemented with detailed breakdown

Search and locate tasks across all orchestrations using various criteria.

Apply the Five Whys root cause analysis technique to systematically investigate issues

Analyze and fix a GitHub issue with comprehensive testing and verification

Fix a specific issue or problem with the given identifier or description

Fetch unresolved comments for current branch's PR and fix them

Generate and analyze future scenarios with plausibility scoring, trend integration, and uncertainty quantification.

Auto-generate API reference documentation

You are tasked with generating a technical work log comment for a Linear issue based on recent git commits.

Generate comprehensive test cases automatically

Generate comprehensive test suite for $ARGUMENTS following project testing conventions and best practices.

Show detailed git repository status

Deploy critical hotfixes quickly

Verify repository is in working state by running CI checks and fixing issues

Design and implement caching solutions

Implement GraphQL API endpoints

Initialize new project with essential structure

Build reference documentation by creating markdown files and updating CLAUDE.md

Convert GitHub issues to Linear tasks

Triage and prioritize issues effectively

Conduit — native SwiftUI iOS client for Hermes Agent

一个现代化的可视化规则引擎平台，用于编排复杂的 AI 工作流。在无限画布上设计、测试和部署 AI 流程——无需编写代码。结合 flowgram.ai 的能力与 Java 服务端，提供生产级工作流管理。在此之上提供AI Agent / Copilot的助手编排能力。

Job application tracker and AI-powered job search assistant. Helps job seekers manage their search journey with AI resume review, job matching, task logging, an…

📝 Markdown and HTML renderer for Svelte 5 — built for streaming AI agent output from Claude Code, ChatGPT, and agentic workflows. XSS-safe defaults, token cach…

ServiceNow MCP server: 500+ tools and 26 AI capabilities for any AI (Claude, ChatGPT, Gemini, Cursor, Copilot). Multi-transport (stdio, SSE, HTTP), A2A, dynamic…

Free crypto news API - real-time aggregator for Bitcoin, Ethereum, DeFi, Solana & altcoins. No API key required. RSS/Atom feeds, JSON REST API, historical archi…

Build production-ready AI agents in both Python and Typescript.

From agent user to agent builder: build a Claude Code-style coding agent from scratch in Python: 8 articles, 4 videos, one codebase

🪁 A lightweight, modern Kubernetes dashboard that unifies multi-cluster and resource management, enterprise-grade user governance (OAuth, RBAC, and audit logs)…

Stateful runtime management for LLM agents—inject, manipulate, and retrieve Python objects across turns.

AgentCall lets AI Agents join meetings with voice, video & screen-share to build together. Supports Google Meet, Teams, Zoom (Beta)

Kition brings Markdown, DataTable, WhiteBoard, a tool-using AI agent, browser research, and visual workflows into one desktop workspace.

IntentKit is an open-source, self-hosted cloud agent cluster that manages a collaborative team of AI agents for you.

A powerful Model Context Protocol (MCP) server providing comprehensive Google Maps API integration with LLM processing capabilities.

Turn your Claude Pro/Max subscription into an OpenAI-compatible API for your IDEs and devices — LAN auth, per-key quotas, response cache, disciplined cli.js ali…

Paw Work - selection-first web agent for Chrome: select on the live page, describe the outcome, take away an editable office file. BYOK, sandboxed, no server.

基于 AI Agent + MCP 工具链 + 渗透 Skill 编排， 配合大语言模型， 自然语言输入 → 自动完成「信息收集 → 漏洞发现 → 漏洞利用 → 报告生成」全流程。

Lexora — Personal AI workspace built around Desktop / 以 Desktop 为核心的个人 AI 工作台

First AI Journey for DevOps - with comprehensive learning paths, practical tips, and enterprise guidelines

AI coding agent with one Python core and three front-ends — headless CLI, Textual TUI, and an Electron desktop. Works with any OpenAI-compatible API, with risk-…