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.

Review and triage abuse mailbox cases in Abnormal Security

Search for specific threat patterns in Abnormal Security by sender, recipient, attack type, or keywords

Triage recent email threats detected by Abnormal Security by severity and attack type

List open and overdue Alternative Payments invoices and optionally generate hosted payment links for them

Reconcile an Alternative Payments payout by listing its transactions and matching them against invoices and customers

EOL/EOS risk report — devices, OS versions, and firmware approaching or past end-of-life/end-of-support, prioritized by criticality

Forward-looking hardware refresh calendar for the given window — replace-now / plan-this-year / monitor tiers

Warranty status snapshot — expired, expiring-soon, and unknown-coverage devices for one client or the whole portfolio

Create a threshold-based monitor for an Atera agent

Create a new service ticket in Atera

Search the Atera knowledge base for articles

List active RMM alerts from Atera

Log work hours on an Atera ticket

Resolve an RMM alert in Atera

Execute a PowerShell script on an Atera agent

Search for RMM agents in Atera by customer or machine name

Search for Atera customers by name or criteria

Update fields on an existing Atera ticket

Triage open Auvik alerts, rank by severity, and recommend dismissals for known noise

Scan Auvik interface statistics for saturated links and recurring congestion

Build AI Agents like playing LEGOs. Everything is a Plugin.

The coding agent that answers to you, your model, your machine, your rules.

CI-native agent CLI tool for deterministic pipeline gating.

Local-first cross-platform desktop workspace for Claude Code / agents: multi-agent, Git worktrees, code diffs, skill marketplace, multi-model, Computer Use, tas…

Local-first visual generation runtime and studio for people and coding agents, with reproducible image and video workflows across multiple providers.

A token-efficient MCP server for safe, line-oriented text file editing with partial reads, hash-based conflict detection, and atomic multi-file operations.

Open-source, evidence-driven MCP server for RTL simulation debugging: correlate VCS/Xcelium logs, VCD/FSDB waveforms, SystemVerilog/UVM source, hierarchy, and c…

runs anywhere. uses anything

One macOS app for Claude Code, Codex, and every agent runtime you use — scheduled runs, global hotkey launcher, per-run git worktrees, one review board.

Soul-driven AI agent with permission-hardened tools, token budgets, and multi-channel access. Runs 24/7 from CLI or Telegram.

Email, SMS & phone-call infrastructure for AI agents — send and receive real email and text messages, and place agent-driven outbound voice calls, all programma…

55 MCP tools to drive the Unity Editor from any MCP-compatible AI agent — scenes, GameObjects, prefabs, assets, tests, and builds. OpenClaw gateway included for…

Google Ads MCP + Meta Ads MCP + GA4 in one server for Claude, ChatGPT, Cursor & n8n — 250+ tools, hosted remote MCP, OAuth login, no API keys. By Ryze AI.

Claude Code & Codex 本地 token 追踪 — 状态栏（Codex 业界首创伪 statusline）、GitHub 风格热力图、多模型成本分析。 | Local token tracker for Claude Code & Codex — status line (industry-first…

Empower the Shell to think. Evolve Operations.

🤖 A full-stack Agent Chat Runtime for pre-production validation, built with act, TypeScript, and LangGraph JS combining streaming, multimodal, HITL, and tools…

Cerul — video memory infrastructure for AI products. SDKs, CLI, MCP, and developer integrations.

Stealth headless browser for AI agents — bypass Cloudflare, bot detection, and anti-scraping. Drop-in Puppeteer/Playwright replacement.

Web research for your agents with smart and safe tooling + knowledge store

FuXi is a fast, self-contained AI coding agent that lives in your terminal — edit code, run commands, and drive tools, with cost-aware routing across LLM provid…