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.

Generate ranked improvement ideas by scanning the codebase, divergent ideation, adversarial critique, and impact ranking

Full autonomous engineering workflow (plan, build, review, ship)

Transform feature descriptions into well-structured project plans following conventions

Report a bug in the whetstone plugin

Reproduce a GitHub issue bug with visual evidence (browser screenshots, log analysis). Takes a GitHub issue number. For non-issue bug validation, use the bug-reproduction-validator agent.

Resolve PR review comments with cluster analysis and parallel agents. Use when bulk-fixing PR comments after triage.

Perform exhaustive code reviews using multi-agent analysis, ultra-thinking, and worktrees

Diagnose the whetstone environment and configure review agents. Checks CLI dependencies and plugin version, then runs the review-agent wizard that writes whetstone.local.md. Use when onboarding a project, troubleshooting missing tools, or configuring review agents.

Run browser tests on pages affected by current PR or branch

Run pre-PR verification chain: build, types, lint, tests, security scan, diff review

Execute work plans efficiently while maintaining quality and finishing features

Run a dry run first:

Run:

Run:

Create or update an OpenCode skill using the bundled skill-creator workflow

Rebuild the OpenCode skill registry for the current project and installed skills

Session-2 fix loop for Agentation — read structured annotations from the dev overlay and apply targeted UI fixes.

Consume the project's design contract — a .design file or DESIGN.md — and thread its tokens through UI code (CSS, Tailwind, or design-system components).

Fork pov.md for installer taste, or append a one-liner to gotchas.md after a real agent failure.

Audit animation timing, easing, springs, and transitions — decide first whether motion should exist, then apply the motion cluster.

Open-source MCP servers for Latin American commerce — Pix, NF-e, banking, fiscal, logistics, and messaging across Brazil, Mexico, Argentina, Colombia, Chile, an…

pi coding agent in a technicolor web trenchcoat

Open-source AI Search Intelligence Platform — track, analyze, and improve AI visibility, citations, prompts, competitors, and content opportunities across ChatG…

Open-source toolkit for the QVeris capability routing network: CLI, MCP server, Python SDK, skills, and REST API docs for agents to discover, inspect, call, and…

⚡ The Complete X/Twitter Automation Toolkit — Scrapers, MCP server for AI agents (Claude/GPT), CLI, browser scripts. No API fees. Open source. Unfollow people w…

The AI agent that interacts with you in the real world.

Offline Codex Desktop migration for Windows and macOS.

LLM 驱动的多市场股票智能分析系统：多源行情、实时新闻、决策看板与自动推送，支持零成本定时运行。 LLM-powered multi-market stock analysis system with multi-source market data, real-time news, decision dashbo…

Your smart, reliable, and friendly personal AI assistant.

The LLM Anti-Framework

A general-purpose AIGC video engine: script to finished film in one pipeline — dramas, ads, product videos, otome games, and more. | 通用 AIGC 视频引擎 —— 从剧本到成片一条流水线…

GTM agent for technical founders. Pay-per-result. Signed receipts. Two surfaces: terminal CLI + local web dashboard.

Desktop automation MCP server — computer use for any AI agent: control screen, windows, mouse/keyboard, and Chrome via Model Context Protocol (stdio)

DeepSeek Harness (dsh) Windows desktop client - bundled Node.js + dsh CLI, one-click launch

Open-source, real-time collaborative AI canvas - notes, mini-apps, and agents on one infinite board.

MCPSafari: Native Safari MCP Server for AI Agents

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Po…

The AI agent with a wallet — spends USDC autonomously to get real work done. Apache-2.0, TypeScript.

The fastest browser for AI agents to run browser automation, built for sharing your logged-in browser state with your AI agents, like Codex or Claude Code, with…

Ouroboros — self-creating AI agent. Born Feb 16, 2026.