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.

Create a multi-page funding proposal with your organization's branding

Create a program report or annual report with your organization's branding

Create HTML presentation slides with your organization's branding

Check for updates and install the latest version

Sandboxed pre-install scan plus cooldown bypass for urgent npm/bun installs. Use when a package must ship despite the cooldown.

Generate a visual HTML diff review, before/after architecture comparison with code review analysis

Verify the factual accuracy of a document against the actual codebase, correct inaccuracies in place

Generate a stunning magazine-quality slide deck as a self-contained HTML page

Generate a visual HTML implementation plan, detailed feature specification with state machines, code snippets, and edge cases

Generate a beautiful standalone HTML diagram and open it in the browser

Generate a visual HTML plan review, current codebase state vs. proposed implementation plan

Generate a visual HTML project recap, rebuild mental model of a project's current state, recent decisions, and cognitive debt hotspots

Deploy a generated visual-explainer HTML page and return a live Vercel URL

View your cognitive methodology profile and reasoning patterns

Diagnostique l'environnement Cortex et guide la réparation (DB, extensions, modèles)

Resolve the ⟦rcpt:id⟧ injection markers in context into presence-in-context evidence (blame path)

Please summarize your current changes, generate a commit message in English, then add and commit.

Create an annotated git tag with an auto-generated summary of changes since the last tag.

Run OCR in delegation mode — OCR handles file selection and rules, the host agent performs the actual review.

Run OpenCodeReview (OCR) to review code changes and autonomously apply fixes.

A systematic AI Agent development tutorial covering LLM agents, RAG, tool use, memory systems, multi-agent systems, LangChain, LangGraph, MCP, and agentic RL.｜从…

Convert Files / Folders / GitHub Repos Into AI / LLM-ready Files

Open-source, local-first conversational AI video editor with a professional multi-track timeline, Agent Skills, MCP integration, and Remotion rendering.

Maintainer-governed agent for evidence-backed open-source contribution proposals

A Claude Code skill by Hao (駱君昊) that learns your Facebook voice and auto-posts to FB / IG / Threads / X with a 14-day content calendar. Mega-viral validated: 8…

Local-first AI agent workspace for coding, writing, design, research, and automation — one runtime for desktop GUI and TUI.

Open-source AI Agent platform for teams. Your agents don't just chat — they read files, run code, call APIs, and deliver results.

Give your AI agent eyes for PDFs — structured text, tables, OCR, visual evidence, and page-level citations via MCP. Native Rust, local-first.

Real-world AI penetration testing engineer for authorized assessments — built-in cloud module covering AWS/Azure/GCP + Aliyun/Tencent/Huawei clouds. Built on Cl…

OpenGUI is an Android GUI agent framework for phone-use AI that can see, plan, and operate real mobile apps through the GUI.

Tinybot is a lightweight personal AI Agent that is constantly evolving

Goink 桌面 AI 小说创作助手，对话式写作 + 自动状态追踪 + 本地语义搜索。跨平台开箱即用。AI Agent Novel Generator.

Pluggable DeepSeek-colored TUI for DeepSeek Harness

Entity-level git merge driver. Resolves false conflicts git invents when independent agents edit the same file. ~95% reduction vs. line-based merge.

Percho: Minimalist desktop GUI for the Pi coding agent — the same engine as the Pi CLI, in a clean visual interface. Multi-session chat, visual tool approvals,…

Run Claude Code, Codex & Gemini in parallel on Windows & macOS — git worktree fan-out with atomic hunk adoption, approval gates, reboot-surviving sessions

A hierarchical memory framework for personalized presentation agents. Try it at memslides.com.

Real-time multimodal desktop agent evolving toward a persistent AI OS interface (0.1 α).

clawdcursor compiles whatever's on screen into one UI map — accessibility tree and OCR fused into stable, addressable elements, with a screenshot only when need…

Repeatable agentic engineering. The workflow layer that turns AI coding agents into a disciplined factory: durable specs, fresh-context workers, adversarial cro…