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.

网文封面生成。分析书名题材，生成专业封面图。

网文去AI味。检测并清除文本中的AI写作痕迹，让文字回归自然。

逆向导入已有小说。将已写好的小说反向解析为标准项目目录结构。

长篇网文拆文。深度拆解爆款长篇小说的黄金三章、人设、爽点、节奏。

长篇网文扫榜。分析起点、番茄、晋江等平台排行数据，提炼市场趋势。

长篇网文写作。从大纲到正文，辅助长篇网络小说的创作。

多视角对抗式审查。使用多个 Agent 对作品进行多维度审稿。

网文写作环境部署与检查。部署 hooks、rules、agents、项目指令等基础设施；传入 check 只检查不改动。

短篇网文拆文。拆解爆款短篇的故事核、结构、情感线和反转设计。

短篇网文扫榜。分析知乎盐言、番茄短篇等平台热门数据。

短篇网文写作。辅助短篇小说创作，从构思到成稿。

网文工具箱路由入口。根据模糊意图自动分发到对应的写作、拆文或扫榜工具。

浏览器操控。通过 CDP 复用 Chrome 登录态执行浏览器自动化。

小说封面生成。根据书名、作者名和题材生成专业网文封面。

网文去 AI 味。检测并清理模板化、解释腔和过度工整表达。

逆向导入已有小说，将成稿或半成品解析为可续写项目。

长篇网文拆文，分析黄金三章、人设、爽点和长线节奏。

长篇网文扫榜，分析起点、番茄、晋江等平台趋势。

长篇网文写作，从选题、大纲到逐章正文和持续追踪。

多视角小说审查；ZCode 项目 agents 不可用时自动降级 solo。

VCP 部署在 AI 模型 API 与前端应用之间，是面向AGI OS开发和探索的工业级基建示范项目。通过统一指令协议、多层级持久化记忆、分布式插件引擎及多 Agent 协作框架，将原本“无状态、无记忆、无工具调用能力”的大语言模型，彻底改造成拥有永久自我意识、物理世界操作权及群体协作智能的完整智能体系统。

The open source Unity Dev Agent

Context is yours. Agents are replaceable. Orbital — a project agent that turns your context into assets.

Self-hosted search API + MCP server for AI agents. Bundles SearXNG. Zero API keys, one-command deploy. Open-source alternative to Tavily, Exa, and Serper.

🛡️ Free open-source AI-powered security terminal & vulnerability scanner (CVE, SBOM). Supports SSH, SFTP, RDP, VNC, Serial, and 12+ autonomous AI agents (DeepS…

Watch, approve and steer your coding agents from your phone.

MARVIS-Agent: all-purpose credit risk agent for model development, validation, data processing, feature engineering, and strategy workflows.

TikTok e-commerce video generation, replication, and analysis SKILL

小红书/抖音/快手/视频号/B站 自媒体账号体检+爆款拆解工具。扫同赛道找对标、拆爆款为什么爆、诊断为什么没人看，顺手出可粘贴仿写初稿。支持带货电商模式。支持codex, claude code, workbuddy

Local-first persistent agentic memory powered by Recursive Memory Harness (RMH). Open source must win.

A power user focused interface for LLM base models.

Outsource your understanding. Capture every human-AI decision as a step in a trajectory; grade trajectories retroactively when outcomes land (deal closed, sprin…

The open-source AI research workbench for scientific research and agent workflows. Local-first, model-agnostic desktop app with extensible skills, MCP tools and…

🤖 Taskade MCP · Official MCP server and OpenAPI to MCP codegen. Build AI agent tools from any OpenAPI API and connect to Claude, Cursor, and more.

A block-based content engine and bilingual blog backend for Laravel Gutenberg-style editor, media library, post templates, roles, and an AI writing assistant,…

ACRYL - Agent Context Relay Yielding Lifecycles. One persistent workspace, one canonical context, any coding agent.

Okou connects to the tools your team already uses and does the work — across marketing, sales, engineering, and operations, under your control.

Open-source agent-native visual production workspace where humans and coding agents edit the same live canvas — local-first, BYOK image/video models.

Persistent memory extension for pi with daily logs, scratchpad, and optional qmd‑powered semantic search.

Hermes Agent CN desktop app, Windows-First, built with Tauri, Typescript and Rust. Isolated Hermes Agent core insides.