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.

List recent Blackpoint Cyber detections for a tenant

Build a prioritized exposure report for a Blackpoint Cyber / CompassOne tenant

Sweep and prioritize the open Blackpoint Cyber / CompassOne detection queue across tenants

List all devices and agents across the organization with status and health information

Triage open Blumira findings by severity, presenting a prioritized list for review

Deep investigation of a specific Blumira finding with details, context, and comment history

MSP dashboard showing all managed accounts with open finding counts and severity breakdown

Resolve a Blumira finding with the appropriate resolution type and notes

Overall security posture review including open findings by severity, agent coverage, and trends

Run the complete CIPP M365 offboarding workflow for a departing user — capture audit state, revoke access, handle mailbox, reclaim licenses

Generate a portfolio-wide M365 security posture report — Secure Score equivalents, MFA enrollment, conditional access coverage, and domain authentication across all managed tenants

Find tenants that have drifted from the MSP's configured CIPP standards baseline — missing standards, standards in Report-only mode, recent compliance failures

Quick health snapshot for a single tenant — BPA failures, conditional access enforcement, MFA gaps, domain authentication, standards compliance

Log a time entry (billable activity) against a Clio matter

Consolidated view of one Clio matter — contacts, open tasks, recent activities, recent communications, and bills

Search Clio contacts by name, company, or email

Search or list Clio matters by name/client and status

Capacity forecast for cloud resources, scoped to a resource type or covering everything connected

Cloud cost anomaly and reclaimable-spend report for a given window

Full network health sweep across all connected network-monitoring tools — devices down, degraded links, and topology changes

Your efficient agentic AI coding CLI assistant

AI coding with Aegis governance built into execution: baseline-aware changes, evidence-backed delivery. Free desktop client, your choice of model. 将哲科思维融入 AI 开发…

Android in docker solution with noVNC supported, video recording, mcp server and AI-agent

Your AI assistant, built for the agentic era. Open source and local: talk to it, and it runs your agents, your coding CLIs, your browser and your apps. Windows,…

Verifiable program-level self-evolution for AI-for-Science agents: Skills and typed Operators grow from replay-verified executions.

Let Claude Code and other coding agents drive and debug Chrome from the shell. DOM, network, console and raw CDP as short commands, no screenshots and no MCP ne…

Unofficial, agent-friendly Mercadona shopping CLI (Go) — search products, read prices, build a cart and prepare checkout from the terminal. BYO credentials.

Local-first AI canvas for visual workflows, AI short drama, image/video generation, storyboarding and asset management. ComfyUI, AI agents, MCP & Blender. 本地优先…

Let any AI coding tool — Claude Code, Cursor, Codex — drive your real Chrome. One-prompt setup, muscle memory, local-first.

runs anywhere. uses anything

Open-source dots for the web: an AI agent with its own browser, one that does not get blocked.

Free MIT AI coding agent — no API key needed. Built-in free model, or bring Claude, GPT, Gemini, DeepSeek, Ollama +50 more. Swarm mode, 40+ tools, browser & des…

Open-source AI customer support system. AI-first support, human-ready operations.

A durable, multiplayer, mobile-first web app for Pi agents, built on Pi Durable

Embedded Cypher knowledge graph for Python and Rust. Bundled MCP server, describe() schema, and code-graph parser for LLM agents.

Turn PDFs, books and papers into interactive learning webpages｜将复杂材料转化为可追溯、可测验、可做笔记的学习网页

PhysicsOS 是一个面向初高中物理学习的公益可视化智能体，通过 AI 理解题目并结合物理引擎，将抽象物理过程转化为可交互、可观察、可计算、可验证的真实物理场景。

Open-source, self-hosted alternative to OpenAI Dots, Meta Muse, Grok Bot, Manus Cue and Claude Cowork. AI agents, each with a virtual machine on your PC with a…

Quant infrastructure for AI agents — a free, open-source desktop workspace for macOS and Windows where your Claude Code or Codex turns a trading idea into a bac…

Build stateful agent workflows with typed outputs, reusable tools, session forks, and ordinary TypeScript.